BACKGROUND
mirnas are an abundant class of small  noncoding rnas expressed by a variety of eukaryotic organisms and viruses  <cit> , which represent at least 1% of predicted genes within the genomes of individual species  <cit> .
a mammalian genome may contain > <dig> genes encoding mirnas  <cit> .
accumulating evidence shows that mirnas function in a broad range of biological processes, including development, cellular differentiation, proliferation, metabolism and apoptosis  <cit> .
organisms devoid of mirnas undergo arrest during development  <cit> .
recent studies additionally implicate mirnas in the pathogenesis of human diseases, including cancer and metabolic disorders  <cit> .
moreover, mirnas are required for normal steroid hormone signaling  <cit> .
interestingly, dicer and mirnas are not prerequisites for the development of zebrafish germline stem cells  <cit> , despite being essential for zebrafish development  <cit> .
however, in drosophila, mirna pathways appear essential for stem cell division and for bypassing the g1/s checkpoint of the cell cycle  <cit> .
this dissimilarity may reflect diverse mechanisms in the proliferation and differentiation of pluripotent stem cells  <cit> .
computational predictions of mirna targets indicate that these noncoding rnas regulate hundreds of different mrnas at the posttranscriptional level, and over 30% of animal genes  <cit> .
however, to date, the roles of only a handful of known mirnas have been experimentally determined.
the current repression models of the mechanisms of mirna-mediated gene silencing are still the subject of considerable debate  <cit> , and many potential targets may actually be pseudotargets, thus preventing mirnas from binding to their authentic targets via sequestration  <cit> .
b. mori, the characteristic representative of lepidoptera, undergoes four distinctive main developmental stages, defined as embryo, larva, pupa, and adult moth.
silkworms have no characteristic feeding behavior at the adult stage, but display prominent traits, such as silk production, monophagy, and voltinism  <cit> .
therefore, b. mori is considered an important model organism to investigate various biological phenomena, including development, gene regulation, and morphological innovation  <cit> .
increasing numbers of mirnas have been experimentally identified in the silkworm  <cit> .
several of these are temporally regulated or stage-specifically expressed, as observed by microarray analysis at four time-points  <cit> .
however, the lifespan of the silkworm is over  <dig> days, with each of the four main metamorphosis stages lasting for several to more than  <dig> days.
therefore, examination of a few time-points is unlikely to reflect the accurate expression patterns of mirnas over the entire life cycle of this animal  <cit> .
several heterochronic genes function in a regulatory pathway to influence the timing of cellular development, thereby ensuring a coordinated schedule of developmental events  <cit> .
correlation between mirna expression and normal behavior is suggested in drosophila adults  <cit> .
in the present study, particular attention was focused on the detailed temporal profiling of mirnas responding to developmental stage transitions of silkworms.
the microarray data discussed in this publication have been deposited in ncbi's gene expression omnibus  <cit>  under accession number gse <dig> .
the data revealed wide diversity in mirna expression, ranging from stage-specific to constitutive patterns.
our study provides a broad overview of mirna expression in the developing silkworm, and is thus an important initial step in elucidating the functions of mirnas in this animal.
RESULTS
general profile of mirna expression over the whole life cycle of bombyx mori
to determine the expression profiles of mirnas in the developing silkworm, we performed microarray hybridization with  <dig> cdna probes complementary to  <dig> mirnas .
additional file  <dig> contains the main information, including mature and putative precursor sequences, foldback arms, 9× genome location data , mirbase designation where available, and folding energy.
all probes for mirnas as well as negative and positive controls were printed in triplicate on the microarray slides .
half of the  <dig> mirnas passed the filtering expression threshold,  <dig> were also confirmed by northern blotting, and  <dig>  were robustly expressed from the embryo to adult stages .
the use of alternative probes for some mirnas generally resulted in similar expression profiles , strongly confirming probe authenticity.
expression peaks for all established mirnas were distributed over nine time-points.
we observed up-regulation of  <dig> mirnas and down-regulation of  <dig> mirnas over the whole life cycle of the silkworm .
one new silkworm mirna, mir- <dig>  presented the highest signal on microarray at the early 1st instar larva stage, which was confirmed by northern blotting .
four mirnas  were not detected until the silkworm hatched , and were subsequently expressed at high levels until the birth of the adult moth, in microarray analysis .
mir- <dig> was typically down-regulated during silkworm development from day  <dig> embryo to adult moth, and undetectable after the 3rd instar larva stage .
in contrast, both microarray and northern blotting analyses confirmed that let- <dig> and mir- <dig> were coordinately up-regulated, gradually accumulating from late 1st molt until the 3rd molt stage .
these oscillations were coincident with the traditional watershed in sericulture management between the early larval and late larval stages.
mir-29b displayed the highest expression at the embryo stage, and rapidly decreased in level after the 1st molt larval stage, but rose significantly once more in fresh female moths carrying eggs in the abdomen , raising the possibility of an involvement in oogenesis and embryogenesis.
interestingly, in other organisms, such as the mouse, mir-29b was almost undetectable in the embryo, but extensively expressed in the adult during brain development  <cit> .
the expression patterns of mir-34b and mir- <dig> fluctuated in a complementary manner .
specifically, mir-34b expression was restricted to instar larvae and adults, and was absent in the embryo, molt larvae, and pupae .
ecdysone and broad-complex are responsible for the down-regulation of mir- <dig> in the development of drosophila  <cit> .
in fact, mir- <dig> is highly conserved, and its homologs have been widely identified in several other species across phyla.
recent studies show that members of this family, mirna-34a-c, are direct transcriptional targets of p <dig>  and participate in the suppression of cell proliferation  <cit> .
in contrast to mir-34b, a faint expression signal from mir- <dig> was initially detected at early 3rd molt, followed by slight up-regulation in early 4th instar, early 4th molt, and early 5th instar larvae.
this mirna was highly expressed in early spinning larva and up-regulated to peak levels in the new pupa, but was remarkably absent in new female adults .
the expression profile derived from microarray data was supported by northern blotting results .
microarray analyses revealed that mir- <dig> was exclusively expressed at day  <dig> embryo, late 2nd molt, and early pupal stages , but strong expression was confirmed in day  <dig> embryos only by northern blotting .
the mirna profiles obtained with the general whole-life array provide an insight into the stage-specific mirna transcriptome, and may thus facilitate the identification of sequential classes of mirnas and their primary targets associated with distinct developmental stages.
expression profile of mirnas in silkworm embryos
in the course of embryogenesis, large gene regulatory networks generate refined spatial and temporal patterns of expression  <cit> .
silkworm embryogenesis is initiated by formation of the zygote nucleus  within about  <dig> hours after egg deposition, and develops through diverse phases for about  <dig> days before hatching  <cit> .
only one time-point  was examined using the whole-life array, and this did not provide sufficient information on expression profiles in developing embryos of silkworm.
we further assessed  <dig> and  <dig> time-points using microarray and northern blotting, respectively, leading to significant extension of the range of temporal profiles of mirna expression.
in all,  <dig> unique mirnas satisfied the expression standard for microarray analysis during embryogenesis .
the whole process was divided into two main sections in terms of hierarchical clustering of mirna expression, with one clear boundary between day  <dig> and day  <dig> embryos and the remaining time-points.
small and large mirna transcripts were detected in pre-laid eggs and embryos, and were identified as mir- <dig>  mir- <dig> and let- <dig> .
accumulating large fragments of these mirnas suggest that maturation of functional small molecules involves sequential cleavage from larger transcripts  <cit> .
seven "early" mirnas were detected in freshly deposited eggs , which continued to be expressed until the formation of the synkaryon  .
whole-life analysis revealed that mir- <dig> expression was restricted to three time-points during the course of development from embryo to moth, and peaked at the day  <dig> embryo stage .
a more precise examination disclosed a significantly extended existence during embryogenesis and a virtual expression peak in the day  <dig> embryo .
after fertilization, the synkaryon undergoes synchronous mitosis, resulting in the formation of blastoderm and the subsequent germband.
numerous cleavage nuclei begin to penetrate the periplasm about  <dig> h after oviposition.
however, microarray and northern blotting confirmed that few mirnas were expressed at this time  , possibly because of the impending diapause stage  <cit> .
after a further  <dig> h ,  <dig> mirnas were detected soon after egg release from diapause, including the  <dig> "early" mirnas and others observed for the first time .
expression of these mirnas continued for  <dig> h , with slight fluctuations during the time of cell differentiation, to successively form the germband, amnion, gastrulation apparatus, and even the appendages of the abdomen and telson.
one day later , expression of another group of mirnas was initiated during the blastokinesis period after formation of the neural groove and abdominal appendages.
in view of the finding that morphogenetic processes are severely affected in mirna-devoid embryos  <cit> , we propose that these mirnas act concertedly to regulate the morphogenesis oforgans.
after blastokinesis, the embryo resumes growth by successively forming dorsal integument, the alimentary canal, setae, the epidermis, and the trachea, possibly involving several genes expressed during formation of larval organs  <cit> .
this occurs around the head pigmentation stage in day  <dig> embryos.
at this time-point,  <dig> mirnas were initially expressed .
once the larval organs form, the serosa is digested and pigmentation of the head and body progresses, but no other important morphological changes occur in the embryo  <cit> .
however, a higher number of mirnas were initially present in day  <dig> embryos  at the body pigmentation stage, including mir-281-5p, mir-281-3p, mir- <dig>  mir- <dig>  mir- <dig>  mir- <dig>  and mir- <dig>  during the subsequent  <dig> h, the young larvae inside the eggshells eat and break the chorion around the micropylar region and emerge  <cit> .
no distinct differences in mirna expression existed between newly hatched silkworms and day  <dig> embryos.
mirna expression in silkworm larvae correlates with stage transitions
to further investigate the correlation between mirna expression and stage transition, we sampled throughout the larval stages from newly hatched silkworm to late 3rd molt larva , and early 4th instar larva to late 5th instar larva .
day  <dig> and day  <dig> embryos served as controls to ensure comparable results.
twenty unique mirnas were highly expressed, as shown by microarray experiments, during the early larval stages, including  <dig> strongly detected mirnas identified in the whole-life array .
late 2nd instar larvae expressed the largest number of mirnas, among which  <dig> displayed peak levels at this time-point .
the whole-life array revealed exclusive mir- <dig> expression at the early 1st instar and late 1st molt larval stages.
in fact, mir- <dig> was additionally expressed in late 1st instar, late 2nd instar, and late 3rd molt larvae.
mir- <dig> was absent from the early 1st, 2nd, and 3rd instar larval stages, but highly expressed in late 1st, 2nd, and 3rd instar larvae and late 1st, 2nd, and 3rd molt larvae.
the mir- <dig> level at the late 1st instar larval stage was two-fold higher than that during the early 1st instar larval stage.
mir- <dig> was sharply up-regulated to peak levels from the time of its initial expression in the day  <dig> embryo, followed by down-regulation, despite waning in early 2nd and early 3rd instar larvae and early 3rd molt larvae, and waxing in late 2nd and late 3rd instar larvae and late 3rd molt larvae.
in contrast, mir- <dig> and let- <dig> were initially expressed in late 2nd instar larvae, and accumulated to high levels in late 3rd molt larvae, with obvious fluctuations during the early larval stages.
mir-34b and mir- <dig> exhibited complementary changes in patterns in whole-life profiling, but displayed sympathetic vibrations, particularly from the early 2nd instar to late 3rd molt stages, upon more detailed examination .
the presence of mirnas during the early larval stages was further confirmed by northern blotting .
in total,  <dig> of the  <dig> mirnas expressed throughout the early larval stages were maintained at high levels during late larval stages .
the two remaining mirnas, mir- <dig> and mir- <dig>  showed low levels of expression during the whole 4th molt stage .
mir- <dig> and let- <dig> were up-regulated from 1st instar to 3rd molt, maintained over the 4th and 5th larval stages , and highly expressed from early to late 4th instar larvae and fifth-instar day  <dig> and day  <dig> larvae .
mir- <dig> displayed no expression signal during early larval stages, was initially detected in 5th instar day  <dig> larvae, and was subsequently up-regulated to peak levels in day  <dig> larvae.
mir-29b was detected at the late embryo and 1st instar larval stages , but was not expressed from early 4th to 5th instar day  <dig> larval stages .
mir- <dig> and mir- <dig> shared similar patterns with high expression at three time-points, specifically, late 4th larval instar, and day  <dig> and day  <dig> 5th instar larvae, but was absent from 4th molt larvae.
the expression profiles of mir- <dig> and mir-34b were regulated in a complementary manner throughout the penultimate and final larval stages .
the changing expression profile of mir- <dig> by microarray was supported by northern blotting results .
some mirnas displayed significant gender-specificity at the day  <dig> and day  <dig> fifth larval instar stages , whereby signal values in females were at least two-fold higher than those in males.
the majority of expressed mirnas oscillated with a clear-cut pattern corresponding to transitions between instar and molt stages, specifically, being higher at the late 1st, 2nd, and 3rd instars and the late 3rd molt, and lower at the early 1st, 2nd, and 3rd instars and the early 3rd molt .
as with expression patterns at the early larval stages, most mirnas exhibited a defined expression pattern during the 4th and 5th larval stages, specifically, up-regulation at the 4th instar, down-regulation at the 4th molt, up-regulation at the day  <dig> to day  <dig> fifth instar, down-regulation for  <dig> days, followed by a sharp increase again at day  <dig> .
interestingly, these coordinate expression changes were generally in keeping with ecdysone pulsing  <cit> .
expression profiles of mirnas in spinning larvae, pupae and moths
to determine the expression profiles of mirnas at the spinning larva , pupa , and adult  stages, the whole-life test  was applied from the development of the spinning larva to adult moth at  <dig> and  <dig> specific time-points for females and males, respectively.
based on hierarchical clustering, samples from the larval, pupal, and adult stages were clearly separated .
the proximal stages displayed similar mirna expression profiles.
therefore, mirna expression patterns may be applied as a developmental marker of silkworm individuals, as suggested for the developing mammalian brain  <cit> .
in total,  <dig> mirnas were highly expressed throughout pupal and adult stages by microarray, among which  <dig> were common to both sexes and  <dig> were robustly expressed over the whole life cycle  .
a number of mirnas were also confirmed in females by northern blotting  .
moreover, northern blotting revealed the presence of mir-263b throughout the metamorphosis process, although high expression was only evident in day  <dig> and day  <dig> pupae in microarray experiments.
in females, the  <dig> expressed mirnas peaked at eight time-points  whereas in males, the  <dig> expressed mirnas displayed the highest signals at nine time-points .
however, specific mirnas shared the same expression profile in both genders as larva-pupa-adult metamorphosis advanced, and expression of the majority of mirnas abruptly fell at the day  <dig> pupa time-point .
these results raise the issue of whether females and males share the same mechanism in coordinating mirnas for the larval-pupa-adult transition.
illustratively, five mirnas were compared between females and males .
in the whole-life test, mir-29b was not present in early female pupae, but was strongly expressed in the early female moth .
a more detailed examination revealed its initial expression in both genders at the day  <dig> pupal stage, and subsequent up-regulation.
whereas expression in both sexes fluctuated in a generally similar manner, mir-29b was far more highly expressed in females.
the whole-life array revealed that, in contrast to mir-29b, mir- <dig> expression peaked in early female pupae, but not in the early female moth .
a precise test further revealed strongest expression in the prepupa and day  <dig> pupa in both females and males .
moreover, both northern blotting and microarray tests revealed down-regulation of mir- <dig> in both sexes during this process .
unexpectedly, mir- <dig> was not expressed in the early female moth with eggs.
however, when the eggs were manually removed from the maternal abdomen, mir- <dig> expression was significantly increased, further confirming its absence in pre-laid eggs and early embryo stages.
although the whole-life array did not confirm the existence of mir- <dig> in silkworms, the presence of this mirna was verified in the fifth instar larva from days  <dig> to  <dig> .
interestingly, the detailed investigation revealed high expression in the spinning larvae of both genders, but no expression in pupae of either sex , strongly implying an important function for this mirna in the spinning activity of silkworms.
mir-29b and mir- <dig> appeared to share similar patterns by whole-life profiling, but the detailed assay revealed evident differences between their expression profiles.
mir-29b expression peaked in egg-removed moths, whereas mir- <dig> expression was maximal in the new pupae of both sexes.
mir-34b was robustly expressed in females at the early cocoon spinning and new adult moth stages, but was expressed at only low levels in early pupae in the whole-life test .
its expression in pupae and adults was further established by precise sampling .
mir-34b was not expressed, or was expressed at very low levels, in female pupae during the first  <dig> days, but was significantly up-regulated in day  <dig> pupa, and highly expressed in female adult moths with or without eggs.
however, this mirna was also nearly undetectable in the male prepupa and male pupae from  <dig> h to day  <dig>  but displayed a sharp increase at day  <dig> and attained its highest expression in the fresh male adult moth, followed by an evident decrease  <dig> days later.
the silkworm moth lives for only several days, and dies soon after mating or laying eggs.
in keeping with the development of the silkworm body, the expression levels of all mirnas in adults of both sexes decreased significantly within  <dig> days .
discussion
to the best of our knowledge, this is the first comprehensive investigation of mirna expression profiles over the whole life-cycle of bombyx mori.
although previous studies have examined four time-points representing the main developmental stages of the silkworm, to clarify the temporal expression profile of mirnas  <cit> , it is impossible to establish detailed expression patterns at stage transitions over the fifty-day life cycle with limited time measurements.
the whole-life test used in the present study provided a general expression profile of mirnas during silkworm development, and subsequent precise stage-by-stage examinations further confirmed the presence or absence of mirnas at multiple time-points.
the mirnas exhibiting significant expression changes over the whole life cycle and specific developmental stages are summarized in additional file  <dig>  for example, the mir-10b-5p/3p pair was down-regulated in whole-life profiling, but stage-by-stage examination revealed up-regulation of these mirnas during embryogenesis, followed by down-regulation during the early and late larval stages.
several mirnas, such as mir-34b and mir- <dig>  were up- or down-regulated in whole-life profiling, but in fact, displayed diverse or even opposite regulation patterns at some developmental stages.
despite stable culture conditions of a  <dig> h light: <dig> h dark cycle, the temporal niche varies dramatically within the life-cycle of the silkworm, consequently exerting vital pressure on the capacity for temporal adjustment  <cit> .
the dazao silkworm is a bivoltine strain in which the nature of the diapause is dependent on incubation temperature.
specifically, incubation at 25°c produces only diapause eggs and incubation at 15°c produces exclusively non-diapause eggs  <cit> .
therefore, the temporal expression profiles of silkworm mirnas may be under dual control of the developmental program and environmental stimuli, such as the polyprotein precursor mrna, which is common to diapause hormone  and pheromone biosynthesis activating neuropeptide   <cit> .
in zebrafish, few mirnas are expressed within  <dig> h post-fertilization.
an increasing number of mirnas are detected  <dig> to  <dig> days after fertilization and show strong expression when organogenesis is virtually complete  <cit> .
in the early embryo of drosophila, several mirnas initiate expression at the onset of zygotic transcription  <cit> .
their dynamic expression patterns are mediated by tissue-specific enhancers  <cit> .
in the silkworm, a small set of mirnas weakly accumulated at fertilization  or the early embryo stages .
the maternal dicer enables zygotic dicer mutants of zebrafish to live for almost  <dig> weeks  <cit> .
emergence of these mirnas in pre-laid or newly deposited eggs may also be attributed to maternal information, similar to the embryonic diapause induced by the diapause hormone , which is secreted by the maternal subesophageal ganglion during pupal-adult development  <cit> .
mirnas are absent in the zygotes of zebrafish, and are primarily detected during the blastula period  <cit> .
the majority of zebrafish mirnas are expressed in a tissue-specific manner during the late stage of embryonic development  <cit> , and present widely divergent expression profiles throughout the  <dig> dpf and  <dig> dpf embryonic brain  <cit> .
in frog , an increasing number of mirnas are expressed at specific stages as embryonic development proceeds, and are continuously expressed until the tadpole stage  <cit> .
few mirnas are detected during the formation of primary germ layers of the chick, but rapid accumulation occurs during organogenesis  <cit> .
several mirnas cannot be detected until the late specific stages of mouse  embryonic development, but their transcription levels are markedly increased thereafter  <cit> .
overall, these data leave the intriguing question open as to whether and how these mirnas are implicated in controlling the fate of protein-encoding genes during embryogenesis, consequently contributing to tissue differentiation and organogenesis.
during the prepupal and pupal stages of holometabolous insects, imaginal tissues and organs are newly formed from primordial cells and imaginal discs, whereas larval tissues degenerate in the pupa, and pupal tissues are fully lost in the adult  <cit> .
larval cuticles break down during the last day before pupal molt  <cit> .
oogenesis and ovarian development of b. mori are triggered by 20-hydroxyecdysone   <cit> , and then pass through various stages for approximately  <dig> days from the fifth instar larvae to the pharate adult  <cit> .
hundreds of genes are required for the dramatic morphological changes in wing disc development during metamorphosis, although their intrinsic roles are yet to be established  <cit> .
this in vitro progression is possibly controlled by unidentified non-coding rnas  <cit> .
four mirnas  were significantly up-regulated from the spinning larvae to adult stages, and nine  were significantly down-regulated during this time-course .
these opposite but coordinate expression changes during the non-feeding stages of females and males should pave the way for further analysis of the mechanisms underlying the metamorphosis of insects.
the normal formation of a mature insect egg is processed under concerted regulation of the steroid hormone ecdysone and its receptors  <cit> .
simultaneous expression of mir- <dig> and let- <dig> during drosophila development is synchronized with the high- titer ecdysone pulses that initiate metamorphosis  <cit> .
the ecdysone titer in silkworm fluctuates in response to stage transitions during embryogenesis  <cit> , instar larval stages  <cit> , and larval-pupal-adult development  <cit> .
the majority of mirnas are significantly up-regulated as the ecdysone synthesis rate rises at the end of each larval instar.
similarly, mirnas are clearly down-regulated when ecdysone synthesis falls during the period from molt to instar larval stage.
during pupal metamorphosis, several mirnas were down-regulated in day  <dig> pupae of both sexes, consistent with a significant decrease in the ecdysone level.
thus, over the whole life cycle of silkworm, expression rhythms of several mirnas may be coordinated by ecdysone.
however, the mirna expression profiles did not always fluctuate in accordance with the ecdysone titer.
for example, mir- <dig> and mir- <dig> expression was typically stage-specific and unrelated to ecdysone pulsing.
furthermore, several mirnas were upregulated at the end of the 3rd and 4th molt stages, presenting abnormal patterns in relation to ecdysone levels.
most mirnas displayed two expression peaks at the 5th instar larval stage , whereas the ecdysone peaks on the last day of the 4th instar larva rapidly declined at the early 4th molt, and ecdysone was maintained at a low level until the onset of the wandering stage  <cit> .
it is possible that additional factors, including hormones other than ecdysone, regulate mirnas, as the expression rhythms were sometimes out of step with the ecdysone pulse.
CONCLUSIONS
here, we obtained initial temporal measurements of the levels of abundant mirnas throughout the entire life-cycle of bombyx mori.
the diverse expression patterns of silkworm mirnas strongly supports the idea that the mirnas function at different levels to regulate silkworm development.
refined expression patterns corresponding to stage transitions may provide a strong molecular basis for further functional analysis of mirnas in this animal model.

 mirnas are an abundant class of small noncoding rnas expressed by a variety of eukaryotic organisms and viruses, which represent at least 1% of predicted genes within the genomes of individual species. a mammalian genome may contain > genes encoding mirnas. accumulating evidence shows that mirnas function in a broad range of biological processes, including development, cellular differentiation, proliferation, metabolism and apoptosis. organisms devoid of mirnas undergo arrest during development. recent studies additionally implicate mirnas in the pathogenesis of human diseases, including cancer and metabolic disorders. moreover, mirnas are required for normal steroid hormone signaling. interestingly, dicer and mirnas are not prerequisites for the development of zebrafish germline stem cells, despite being essential for zebrafish development. however, in drosophila, mirna pathways appear essential for stem cell division and for bypassing the g1/s checkpoint of the cell cycle. this dissimilarity may reflect diverse mechanisms in the proliferation and differentiation of pluripotent stem cells. computational predictions of mirna targets indicate that these noncoding rnas regulate hundreds of different mrnas at the posttranscriptional level, and over 30% of animal genes. however, to date, the roles of only a handful of known mirnas have been experimentally determined. the current repression models of the mechanisms of mirna-mediated gene silencing are still the subject of considerable debate, and many potential targets may actually be pseudotargets, thus preventing mirnas from binding to their authentic targets via sequestration. b. mori, the characteristic representative of lepidoptera, undergoes four distinctive main developmental stages, defined as embryo, larva, pupa, and adult moth. silkworms have no characteristic feeding behavior at the adult stage, but display prominent traits, such as silk production, monophagy, and voltinism. therefore, b. mori is considered an important model organism to investigate various biological phenomena, including development, gene regulation, and morphological innovation. increasing numbers of mirnas have been experimentally identified in the silkworm. several of these are temporally regulated or stage-specifically expressed, as observed by microarray analysis at four time-points. however, the lifespan of the silkworm is over days, with each of the four main metamorphosis stages lasting for several to more than days. therefore, examination of a few time-points is unlikely to reflect the accurate expression patterns of mirnas over the entire life cycle of this animal. several heterochronic genes function in a regulatory pathway to influence the timing of cellular development, thereby ensuring a coordinated schedule of developmental events. correlation between mirna expression and normal behavior is suggested in drosophila adults. in the present study, particular attention was focused on the detailed temporal profiling of mirnas responding to developmental stage transitions of silkworms. the microarray data discussed in this publication have been deposited in ncbi's gene expression omnibus under accession number gse. the data revealed wide diversity in mirna expression, ranging from stage-specific to constitutive patterns. our study provides a broad overview of mirna expression in the developing silkworm, and is thus an important initial step in elucidating the functions of mirnas in this animal.  general profile of mirna expression over the whole life cycle of bombyx mori to determine the expression profiles of mirnas in the developing silkworm, we performed microarray hybridization with cdna probes complementary to mirnas. additional file contains the main information, including mature and putative precursor sequences, foldback arms, 9× genome location data, mirbase designation where available, and folding energy. all probes for mirnas as well as negative and positive controls were printed in triplicate on the microarray slides. half of the mirnas passed the filtering expression threshold, were also confirmed by northern blotting, and were robustly expressed from the embryo to adult stages. the use of alternative probes for some mirnas generally resulted in similar expression profiles, strongly confirming probe authenticity. expression peaks for all established mirnas were distributed over nine time-points. we observed up-regulation of mirnas and down-regulation of mirnas over the whole life cycle of the silkworm. one new silkworm mirna, mir- presented the highest signal on microarray at the early 1st instar larva stage, which was confirmed by northern blotting. four mirnas were not detected until the silkworm hatched, and were subsequently expressed at high levels until the birth of the adult moth, in microarray analysis. mir- was typically down-regulated during silkworm development from day embryo to adult moth, and undetectable after the 3rd instar larva stage. in contrast, both microarray and northern blotting analyses confirmed that let- and mir- were coordinately up-regulated, gradually accumulating from late 1st molt until the 3rd molt stage. these oscillations were coincident with the traditional watershed in sericulture management between the early larval and late larval stages. mir-29b displayed the highest expression at the embryo stage, and rapidly decreased in level after the 1st molt larval stage, but rose significantly once more in fresh female moths carrying eggs in the abdomen, raising the possibility of an involvement in oogenesis and embryogenesis. interestingly, in other organisms, such as the mouse, mir-29b was almost undetectable in the embryo, but extensively expressed in the adult during brain development. the expression patterns of mir-34b and mir- fluctuated in a complementary manner. specifically, mir-34b expression was restricted to instar larvae and adults, and was absent in the embryo, molt larvae, and pupae. ecdysone and broad-complex are responsible for the down-regulation of mir- in the development of drosophila. in fact, mir- is highly conserved, and its homologs have been widely identified in several other species across phyla. recent studies show that members of this family, mirna-34a-c, are direct transcriptional targets of p and participate in the suppression of cell proliferation. in contrast to mir-34b, a faint expression signal from mir- was initially detected at early 3rd molt, followed by slight up-regulation in early 4th instar, early 4th molt, and early 5th instar larvae. this mirna was highly expressed in early spinning larva and up-regulated to peak levels in the new pupa, but was remarkably absent in new female adults. the expression profile derived from microarray data was supported by northern blotting results. microarray analyses revealed that mir- was exclusively expressed at day embryo, late 2nd molt, and early pupal stages, but strong expression was confirmed in day embryos only by northern blotting. the mirna profiles obtained with the general whole-life array provide an insight into the stage-specific mirna transcriptome, and may thus facilitate the identification of sequential classes of mirnas and their primary targets associated with distinct developmental stages. expression profile of mirnas in silkworm embryos in the course of embryogenesis, large gene regulatory networks generate refined spatial and temporal patterns of expression. silkworm embryogenesis is initiated by formation of the zygote nucleus within about hours after egg deposition, and develops through diverse phases for about days before hatching. only one time-point was examined using the whole-life array, and this did not provide sufficient information on expression profiles in developing embryos of silkworm. we further assessed and time-points using microarray and northern blotting, respectively, leading to significant extension of the range of temporal profiles of mirna expression. in all, unique mirnas satisfied the expression standard for microarray analysis during embryogenesis. the whole process was divided into two main sections in terms of hierarchical clustering of mirna expression, with one clear boundary between day and day embryos and the remaining time-points. small and large mirna transcripts were detected in pre-laid eggs and embryos, and were identified as mir- mir- and let-. accumulating large fragments of these mirnas suggest that maturation of functional small molecules involves sequential cleavage from larger transcripts. seven "early" mirnas were detected in freshly deposited eggs, which continued to be expressed until the formation of the synkaryon. whole-life analysis revealed that mir- expression was restricted to three time-points during the course of development from embryo to moth, and peaked at the day embryo stage. a more precise examination disclosed a significantly extended existence during embryogenesis and a virtual expression peak in the day embryo. after fertilization, the synkaryon undergoes synchronous mitosis, resulting in the formation of blastoderm and the subsequent germband. numerous cleavage nuclei begin to penetrate the periplasm about h after oviposition. however, microarray and northern blotting confirmed that few mirnas were expressed at this time, possibly because of the impending diapause stage. after a further h, mirnas were detected soon after egg release from diapause, including the "early" mirnas and others observed for the first time. expression of these mirnas continued for h, with slight fluctuations during the time of cell differentiation, to successively form the germband, amnion, gastrulation apparatus, and even the appendages of the abdomen and telson. one day later, expression of another group of mirnas was initiated during the blastokinesis period after formation of the neural groove and abdominal appendages. in view of the finding that morphogenetic processes are severely affected in mirna-devoid embryos, we propose that these mirnas act concertedly to regulate the morphogenesis oforgans. after blastokinesis, the embryo resumes growth by successively forming dorsal integument, the alimentary canal, setae, the epidermis, and the trachea, possibly involving several genes expressed during formation of larval organs. this occurs around the head pigmentation stage in day embryos. at this time-point, mirnas were initially expressed. once the larval organs form, the serosa is digested and pigmentation of the head and body progresses, but no other important morphological changes occur in the embryo. however, a higher number of mirnas were initially present in day embryos at the body pigmentation stage, including mir-281-5p, mir-281-3p, mir- mir- mir- mir- and mir- during the subsequent h, the young larvae inside the eggshells eat and break the chorion around the micropylar region and emerge. no distinct differences in mirna expression existed between newly hatched silkworms and day embryos. mirna expression in silkworm larvae correlates with stage transitions to further investigate the correlation between mirna expression and stage transition, we sampled throughout the larval stages from newly hatched silkworm to late 3rd molt larva, and early 4th instar larva to late 5th instar larva. day and day embryos served as controls to ensure comparable results. twenty unique mirnas were highly expressed, as shown by microarray experiments, during the early larval stages, including strongly detected mirnas identified in the whole-life array. late 2nd instar larvae expressed the largest number of mirnas, among which displayed peak levels at this time-point. the whole-life array revealed exclusive mir- expression at the early 1st instar and late 1st molt larval stages. in fact, mir- was additionally expressed in late 1st instar, late 2nd instar, and late 3rd molt larvae. mir- was absent from the early 1st, 2nd, and 3rd instar larval stages, but highly expressed in late 1st, 2nd, and 3rd instar larvae and late 1st, 2nd, and 3rd molt larvae. the mir- level at the late 1st instar larval stage was two-fold higher than that during the early 1st instar larval stage. mir- was sharply up-regulated to peak levels from the time of its initial expression in the day embryo, followed by down-regulation, despite waning in early 2nd and early 3rd instar larvae and early 3rd molt larvae, and waxing in late 2nd and late 3rd instar larvae and late 3rd molt larvae. in contrast, mir- and let- were initially expressed in late 2nd instar larvae, and accumulated to high levels in late 3rd molt larvae, with obvious fluctuations during the early larval stages. mir-34b and mir- exhibited complementary changes in patterns in whole-life profiling, but displayed sympathetic vibrations, particularly from the early 2nd instar to late 3rd molt stages, upon more detailed examination. the presence of mirnas during the early larval stages was further confirmed by northern blotting. in total, of the mirnas expressed throughout the early larval stages were maintained at high levels during late larval stages. the two remaining mirnas, mir- and mir- showed low levels of expression during the whole 4th molt stage. mir- and let- were up-regulated from 1st instar to 3rd molt, maintained over the 4th and 5th larval stages, and highly expressed from early to late 4th instar larvae and fifth-instar day and day larvae. mir- displayed no expression signal during early larval stages, was initially detected in 5th instar day larvae, and was subsequently up-regulated to peak levels in day larvae. mir-29b was detected at the late embryo and 1st instar larval stages, but was not expressed from early 4th to 5th instar day larval stages. mir- and mir- shared similar patterns with high expression at three time-points, specifically, late 4th larval instar, and day and day 5th instar larvae, but was absent from 4th molt larvae. the expression profiles of mir- and mir-34b were regulated in a complementary manner throughout the penultimate and final larval stages. the changing expression profile of mir- by microarray was supported by northern blotting results. some mirnas displayed significant gender-specificity at the day and day fifth larval instar stages, whereby signal values in females were at least two-fold higher than those in males. the majority of expressed mirnas oscillated with a clear-cut pattern corresponding to transitions between instar and molt stages, specifically, being higher at the late 1st, 2nd, and 3rd instars and the late 3rd molt, and lower at the early 1st, 2nd, and 3rd instars and the early 3rd molt. as with expression patterns at the early larval stages, most mirnas exhibited a defined expression pattern during the 4th and 5th larval stages, specifically, up-regulation at the 4th instar, down-regulation at the 4th molt, up-regulation at the day to day fifth instar, down-regulation for days, followed by a sharp increase again at day. interestingly, these coordinate expression changes were generally in keeping with ecdysone pulsing. expression profiles of mirnas in spinning larvae, pupae and moths to determine the expression profiles of mirnas at the spinning larva, pupa, and adult stages, the whole-life test was applied from the development of the spinning larva to adult moth at and specific time-points for females and males, respectively. based on hierarchical clustering, samples from the larval, pupal, and adult stages were clearly separated. the proximal stages displayed similar mirna expression profiles. therefore, mirna expression patterns may be applied as a developmental marker of silkworm individuals, as suggested for the developing mammalian brain. in total, mirnas were highly expressed throughout pupal and adult stages by microarray, among which were common to both sexes and were robustly expressed over the whole life cycle. a number of mirnas were also confirmed in females by northern blotting. moreover, northern blotting revealed the presence of mir-263b throughout the metamorphosis process, although high expression was only evident in day and day pupae in microarray experiments. in females, the expressed mirnas peaked at eight time-points whereas in males, the expressed mirnas displayed the highest signals at nine time-points. however, specific mirnas shared the same expression profile in both genders as larva-pupa-adult metamorphosis advanced, and expression of the majority of mirnas abruptly fell at the day pupa time-point. these results raise the issue of whether females and males share the same mechanism in coordinating mirnas for the larval-pupa-adult transition. illustratively, five mirnas were compared between females and males. in the whole-life test, mir-29b was not present in early female pupae, but was strongly expressed in the early female moth. a more detailed examination revealed its initial expression in both genders at the day pupal stage, and subsequent up-regulation. whereas expression in both sexes fluctuated in a generally similar manner, mir-29b was far more highly expressed in females. the whole-life array revealed that, in contrast to mir-29b, mir- expression peaked in early female pupae, but not in the early female moth. a precise test further revealed strongest expression in the prepupa and day pupa in both females and males. moreover, both northern blotting and microarray tests revealed down-regulation of mir- in both sexes during this process. unexpectedly, mir- was not expressed in the early female moth with eggs. however, when the eggs were manually removed from the maternal abdomen, mir- expression was significantly increased, further confirming its absence in pre-laid eggs and early embryo stages. although the whole-life array did not confirm the existence of mir- in silkworms, the presence of this mirna was verified in the fifth instar larva from days to. interestingly, the detailed investigation revealed high expression in the spinning larvae of both genders, but no expression in pupae of either sex, strongly implying an important function for this mirna in the spinning activity of silkworms. mir-29b and mir- appeared to share similar patterns by whole-life profiling, but the detailed assay revealed evident differences between their expression profiles. mir-29b expression peaked in egg-removed moths, whereas mir- expression was maximal in the new pupae of both sexes. mir-34b was robustly expressed in females at the early cocoon spinning and new adult moth stages, but was expressed at only low levels in early pupae in the whole-life test. its expression in pupae and adults was further established by precise sampling. mir-34b was not expressed, or was expressed at very low levels, in female pupae during the first days, but was significantly up-regulated in day pupa, and highly expressed in female adult moths with or without eggs. however, this mirna was also nearly undetectable in the male prepupa and male pupae from h to day but displayed a sharp increase at day and attained its highest expression in the fresh male adult moth, followed by an evident decrease days later. the silkworm moth lives for only several days, and dies soon after mating or laying eggs. in keeping with the development of the silkworm body, the expression levels of all mirnas in adults of both sexes decreased significantly within days. discussion to the best of our knowledge, this is the first comprehensive investigation of mirna expression profiles over the whole life-cycle of bombyx mori. although previous studies have examined four time-points representing the main developmental stages of the silkworm, to clarify the temporal expression profile of mirnas, it is impossible to establish detailed expression patterns at stage transitions over the fifty-day life cycle with limited time measurements. the whole-life test used in the present study provided a general expression profile of mirnas during silkworm development, and subsequent precise stage-by-stage examinations further confirmed the presence or absence of mirnas at multiple time-points. the mirnas exhibiting significant expression changes over the whole life cycle and specific developmental stages are summarized in additional file for example, the mir-10b-5p/3p pair was down-regulated in whole-life profiling, but stage-by-stage examination revealed up-regulation of these mirnas during embryogenesis, followed by down-regulation during the early and late larval stages. several mirnas, such as mir-34b and mir- were up- or down-regulated in whole-life profiling, but in fact, displayed diverse or even opposite regulation patterns at some developmental stages. despite stable culture conditions of a h light: h dark cycle, the temporal niche varies dramatically within the life-cycle of the silkworm, consequently exerting vital pressure on the capacity for temporal adjustment. the dazao silkworm is a bivoltine strain in which the nature of the diapause is dependent on incubation temperature. specifically, incubation at 25°c produces only diapause eggs and incubation at 15°c produces exclusively non-diapause eggs. therefore, the temporal expression profiles of silkworm mirnas may be under dual control of the developmental program and environmental stimuli, such as the polyprotein precursor mrna, which is common to diapause hormone and pheromone biosynthesis activating neuropeptide. in zebrafish, few mirnas are expressed within h post-fertilization. an increasing number of mirnas are detected to days after fertilization and show strong expression when organogenesis is virtually complete. in the early embryo of drosophila, several mirnas initiate expression at the onset of zygotic transcription. their dynamic expression patterns are mediated by tissue-specific enhancers. in the silkworm, a small set of mirnas weakly accumulated at fertilization or the early embryo stages. the maternal dicer enables zygotic dicer mutants of zebrafish to live for almost weeks. emergence of these mirnas in pre-laid or newly deposited eggs may also be attributed to maternal information, similar to the embryonic diapause induced by the diapause hormone, which is secreted by the maternal subesophageal ganglion during pupal-adult development. mirnas are absent in the zygotes of zebrafish, and are primarily detected during the blastula period. the majority of zebrafish mirnas are expressed in a tissue-specific manner during the late stage of embryonic development, and present widely divergent expression profiles throughout the dpf and dpf embryonic brain. in frog, an increasing number of mirnas are expressed at specific stages as embryonic development proceeds, and are continuously expressed until the tadpole stage. few mirnas are detected during the formation of primary germ layers of the chick, but rapid accumulation occurs during organogenesis. several mirnas cannot be detected until the late specific stages of mouse embryonic development, but their transcription levels are markedly increased thereafter. overall, these data leave the intriguing question open as to whether and how these mirnas are implicated in controlling the fate of protein-encoding genes during embryogenesis, consequently contributing to tissue differentiation and organogenesis. during the prepupal and pupal stages of holometabolous insects, imaginal tissues and organs are newly formed from primordial cells and imaginal discs, whereas larval tissues degenerate in the pupa, and pupal tissues are fully lost in the adult. larval cuticles break down during the last day before pupal molt. oogenesis and ovarian development of b. mori are triggered by 20-hydroxyecdysone, and then pass through various stages for approximately days from the fifth instar larvae to the pharate adult. hundreds of genes are required for the dramatic morphological changes in wing disc development during metamorphosis, although their intrinsic roles are yet to be established. this in vitro progression is possibly controlled by unidentified non-coding rnas. four mirnas were significantly up-regulated from the spinning larvae to adult stages, and nine were significantly down-regulated during this time-course. these opposite but coordinate expression changes during the non-feeding stages of females and males should pave the way for further analysis of the mechanisms underlying the metamorphosis of insects. the normal formation of a mature insect egg is processed under concerted regulation of the steroid hormone ecdysone and its receptors. simultaneous expression of mir- and let- during drosophila development is synchronized with the high- titer ecdysone pulses that initiate metamorphosis. the ecdysone titer in silkworm fluctuates in response to stage transitions during embryogenesis, instar larval stages, and larval-pupal-adult development. the majority of mirnas are significantly up-regulated as the ecdysone synthesis rate rises at the end of each larval instar. similarly, mirnas are clearly down-regulated when ecdysone synthesis falls during the period from molt to instar larval stage. during pupal metamorphosis, several mirnas were down-regulated in day pupae of both sexes, consistent with a significant decrease in the ecdysone level. thus, over the whole life cycle of silkworm, expression rhythms of several mirnas may be coordinated by ecdysone. however, the mirna expression profiles did not always fluctuate in accordance with the ecdysone titer. for example, mir- and mir- expression was typically stage-specific and unrelated to ecdysone pulsing. furthermore, several mirnas were upregulated at the end of the 3rd and 4th molt stages, presenting abnormal patterns in relation to ecdysone levels. most mirnas displayed two expression peaks at the 5th instar larval stage, whereas the ecdysone peaks on the last day of the 4th instar larva rapidly declined at the early 4th molt, and ecdysone was maintained at a low level until the onset of the wandering stage. it is possible that additional factors, including hormones other than ecdysone, regulate mirnas, as the expression rhythms were sometimes out of step with the ecdysone pulse.  here, we obtained initial temporal measurements of the levels of abundant mirnas throughout the entire life-cycle of bombyx mori. the diverse expression patterns of silkworm mirnas strongly supports the idea that the mirnas function at different levels to regulate silkworm development. refined expression patterns corresponding to stage transitions may provide a strong molecular basis for further functional analysis of mirnas in this animal model. 
our results show that mirnas display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult, up-regulation over the entire life cycle, down-regulation over the entire life cycle, expression associated with embryogenesis, up-regulation from early 3rd instar to pupa, and complementary pulses in expression between mir-34b and mir- stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of mirna groups in late embryos, expression associated with stage transition between instar and molt larval stages, expression associated with silk gland growth and spinning activity, continuous high expression from the spinning larval to pupal and adult stages, a coordinate expression trough in day pupae of both sexes, up-regulation in pupal metamorphosis of both sexes, and down-regulation in pupal metamorphosis of both sexes. to obtain a comprehensive overview of the correlation between mirna expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred mirnas in the silkworm. numerous mirnas have been identified in bombyx mori, but the temporal expression profiles of mirnas corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. we present the full-scale expression profiles of mirnas throughout the life cycle of bombyx mori. micrornas are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. our data provide an important resource for more detailed functional analysis of mirnas in this animal.
 micrornas are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. numerous mirnas have been identified in bombyx mori, but the temporal expression profiles of mirnas corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. to obtain a comprehensive overview of the correlation between mirna expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred mirnas in the silkworm.  our results show that mirnas display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult, up-regulation over the entire life cycle, down-regulation over the entire life cycle, expression associated with embryogenesis, up-regulation from early 3rd instar to pupa, and complementary pulses in expression between mir-34b and mir- stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of mirna groups in late embryos, expression associated with stage transition between instar and molt larval stages, expression associated with silk gland growth and spinning activity, continuous high expression from the spinning larval to pupal and adult stages, a coordinate expression trough in day pupae of both sexes, up-regulation in pupal metamorphosis of both sexes, and down-regulation in pupal metamorphosis of both sexes.  we present the full-scale expression profiles of mirnas throughout the life cycle of bombyx mori. the whole-life expression profile was further investigated via stage-by-stage analysis. our data provide an important resource for more detailed functional analysis of mirnas in this animal. 