bluuebunny/crossref_metadata_2025 huggingface dataset:
The Notch locus and the genetic circuitry involved in early Drosophila neurogenesis.
Authors: Xu T , Rebay I , Fleming R J , Scottgale T N , Artavanis-Tsakonas S
Published: June 2007

The genetic and molecular analysis of the Notch locus, which codes for a transmembrane protein sharing homology with the mammalian epidermal growth factor, suggests that the Notch protein is involved in a cell interaction mechanism essential for the differentiation of the embryonic nervous system of Drosophila. Taking advantage of the negative complementation between two Notch mutations that affect the extracellular domain of the protein, we have tried to dissect the genetic circuitry in which Notch is integrated by searching for genes whose products may interact with the Notch protein. This genetic screen has led to the identification of a surprisingly restricted set of interacting loci, including Delta and mastermind. Like Notch, both of these genes belong to a group of loci, the neurogenic loci, which have been previously identified by virtue of their similar mutant phenotype affecting early neurogenesis. We extend these studies by systematically exploring interactions between specific mutations in the Notch molecule and the other neurogenic genes. Furthermore, we show that the molecular lesions of two Notch alleles (nd and nd2), which interact dramatically with mastermind mutations, as well as with a mutation affecting the transducin homologous product of the neurogenic locus Enhancer of split, involve changes in the intracellular domain of the protein.
The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene.
Authors: Kunkel B , Losick R , Stragier P
Published: June 2007

The structural gene (sigK) for the mother-cell RNA polymerase sigma-factor sigma K in Bacillus subtilis is a composite of two truncated genes, named spoIVCB and spoIIIC, which are brought together by site-specific recombination during sporulation. We now show that the recombination event is compartmentalized in that the mother cell, but not the forespore chromosome, undergoes rearrangement. We also show that spoIIIC (encoding the carboxy-terminal portion of sigma K) lies approximately 42 kb downstream of spoIVCB (encoding the amino-terminal portion) and that the joining of the truncated coding sequences is a reciprocal recombination event in which intervening DNA is deleted from the chromosome as a circle. The rearrangement is governed by the product of a gene named spoIVCA located in the excised DNA, as demonstrated by the observations (1) that the product of spoIVCA, but not the product of any other stage-IV sporulation gene tested, is required for the rearrangement, and (2) that the presence of a cloned copy of the rearranged sigK gene in the chromosome bypasses the requirement for the spoIVCA gene product in sporulation. Because cells engineered to contain an intact copy of sigK sporulate normally, we conclude that the sigK rearrangement is not essential for the control of gene expression during sporulation, and we infer the existence of an additional mechanism for restricting sigma K-directed transcription to the mother-cell chamber of the sporangium. Finally, the construction of a strain deleted for the entire sigK intervening sequence shows that the 42-kb element contains no genes essential for viability.
Templated insertions in the rearranged chicken IgL V gene segment arise by intrachromosomal gene conversion.
Authors: Carlson L M , McCormack W T , Postema C E , Humphries E H , Thompson C B
Published: June 2007

Chickens create a repertoire for their immunoglobulin light-chain gene by a novel process of sequence substitution within a unique rearranged V gene segment (VL1) during B-cell development in the bursa of Fabricius. Sequence analysis has shown that these nucleotide substitutions are not random. Potential donors for observed sequence substitutions are present within the 25 psi VL segments located 5' of the VL1 gene. In this report, we demonstrate that VL1 sequence substitutions: (1) are derived from the psi VL donor segment templates in cis, (2) do not result in reciprocal transfer of VL1 gene sequences to the psi VL segments, and (3) lead to the rapid disappearance of cells with nondiversified rearranged VL1 genes during B-cell development in the bursa of Fabricius. Together, these data provide evidence that VL1 sequence diversity arises as a result of intrachromosomal gene conversion.
A retrotransposon 412 insertion within an exon of the Drosophila melanogaster vermilion gene is spliced from the precursor RNA.
Authors: Fridell R A , Pret A M , Searles L L
Published: June 2007

Three alleles of the Drosophila melanogaster vermilion (v) gene are suppressed by recessive mutations at the suppressor of sable [su(s)], gene. Previous work has established that these alleles have identical insertions of the 412 retrotransposon in the 5'-untranslated region of the gene. Despite the transposon insertion in an exon, v mutants accumulate trace amounts of apparently wild-type-sized transcripts in a su(s)+ background, and the level of v transcript accumulation is increased by su(s) mutations. Here, we have characterized transcripts from a suppressible v mutant in both su(s)+ and su(s)- backgrounds by S1 nuclease protection experiments and sequence analysis of polymerase chain reaction (PCR) generated cDNA clones. We find that transposon sequences are imprecisely eliminated from v mutant transcripts by splicing at donor and acceptor sites located near the ends of the 412 retrotransposon. Four different 5' donor sites are alternatively spliced to a single 3' acceptor site. The implications of this finding are discussed in relation to possible functions of the su(s)+ gene product.
Localized expression of a myogenic regulatory gene, qmf1, in the somite dermatome of avian embryos.
Authors: de la Brousse F C , Emerson C P
Published: June 2007

qmf1 is a quail myogenic regulatory gene that is transcribed in skeletal myoblasts and differentiated muscle and shows sequence homology to MyoD1 and Myf5. We used the qmf1 transcript as an in situ hybridization marker for determined myogenic cells to study myogenic lineages in developing embryos. We present evidence for the temporal and spatial regulation of qmf1 mRNA expression and slow cardiac troponin C (TnC), fast skeletal troponin T (TnT), and alpha-cardiac actin contractile protein mRNA expression in the somite myotome and limb buds. Our results show that qmf1 is a marker for myogenic lineages during both somite formation and limb development and that qmf1 mRNAs, but not contractile protein mRNAs, localize in dorsal medial lip (DML) cells of the somite dermatome. We propose that the DML is a site of myogenic lineage determination.
Myogenin resides in the nucleus and acquires high affinity for a conserved enhancer element on heterodimerization.
Authors: Brennan T J , Olson E N
Published: June 2007

Myogenin is a member of a family of muscle-specific factors that can activate the muscle differentiation program in nonmyogenin cells. Using antibodies directed against unique domains of myogenin, we show in the present study that myogenin resides in the nucleus of differentiated muscle cells. Myogenin translated in vitro does not exhibit detectable DNA binding activity; however, when dimerized with the ubiquitous enhancer-binding factor E12, it acquires high affinity for an element in the core of the muscle creatine kinase (MCK) enhancer that is conserved among many muscle-specific genes. Antibody disruption experiments show that myogenin, synthesized during differentiation of the BC3H1 and C2 muscle cell lines, is part of a complex that binds to the same site in the MCK enhancer as myogenin-E12 translated in vitro. Mutagenesis of the myogenin-E12-binding site in the MCK enhancer abolishes binding of the heterodimer and prevents trans-activation of the enhancer by myogenin. The properties of myogenin suggest that its functions as a sequence-specific DNA-binding factor that interacts directly with muscle-specific genes during myogenesis. The dependence of myogenin on E12 for high-affinity DNA binding activity also suggests that the susceptibility of various cell types to the actions of myogenin may be influenced by the cellular factors with which it may interact.
A spatial gradient of expression of a cAMP-regulated prespore cell-type-specific gene in Dictyostelium.
Authors: Haberstroh L , Firtel R A
Published: June 2007

Previously, we identified a class of genes in Dictyostelium that are prespore cell-type specific in their expression in the multicellular aggregate and are inducible by cAMP acting through cell-surface cAMP receptors. In this paper, we report the cloning and analysis of the regulatory regions controlling the expression of one such gene that encodes a spore coat protein, SP60. By use of a fusion of the firefly luciferase gene and Escherichia coli lacZ [expresses beta-galactosidase (beta-gal)], we have identified cis-acting regions required for proper spatial and temporal expression in multicellular aggregates and for cAMP induction in shaking cell culture. Deletion analysis suggests that a CA-rich element (CAE) and surrounding sequences present three times within the 5'-flanking sequence are required for proper regulation. SP60-lacZ fusions that include all three of these regions express lacZ only in the posterior approximately 85% of migrating slugs (prespore zone). Studies show that SP60 is expressed during mid to late aggregation, and SP60-lacZ-positive cells are spatially localized as a doughnut-shaped ring within the forming aggregate. Cells within the skirt that surrounds the aggregate and that are still migrating into the aggregate do not stain. Sequential 5' deletions of CAEs and surrounding regions affect the expression level of SP60-luciferase in response to developmental signals and cAMP, as well as the spatial pattern of SP60-lacZ. Deletion of the first (most 5') of these regions restricts the spatial expression of SP60-lacZ fusions to the anterior of the prespore zone. When both the first and second regions are removed, the expression level drops, and the staining is restricted to the prespore/prestalk boundary. Furthermore, the staining pattern that is seen with these two deletions is present as a gradient from anterior to posterior within the prespore zone. Deletion of all three regions results in a loss of both cAMP and developmentally induced expression. These results suggest the presence of a gradient within the prespore zone that differentially affects the activity of promoters containing different numbers of response elements.
Sarkosyl defines three intermediate steps in transcription initiation by RNA polymerase III: application to stimulation of transcription by E1A.
Authors: Kovelman R , Roeder R G
Published: June 2007

We used Sarkosyl to analyze steps along the pathway of transcription initiation by RNA polymerase III. Sarkosyl (0.015%) inhibited transcription when present prior to incubation of RNA polymerase III, TFIIIB, and TFIIIC with the VAI gene, whereas it had no detectable effect on initiation or reinitiation of transcription when added subsequently. The formation of the corresponding 0.015% Sarkosyl-resistant complex required the presence of TFIIIC, TFIIIB, and RNA polymerase III but not nucleoside triphosphates. The addition of 0.05% Sarkosyl after this early step selectively inhibited a later step in the preinitiation pathway, allowing a single round of transcription after nucleoside triphosphate addition but blocking subsequent rounds of initiation. This step occurred prior to initiation because nucleoside triphosphates were not required for the formation of the corresponding 0.05% Sarkosyl-resistant complex. These observations provided a means to distinguish effects of regulatory factors on different steps in promoter activation and function. Using 0.05% Sarkosyl to limit reinitiation, we determined that the E1A-mediated stimulation of transcription by RNA polymerase III resulted from an increase in the number of active transcription complexes.
Expression of the trk proto-oncogene is restricted to the sensory cranial and spinal ganglia of neural crest origin in mouse development.
Authors: Martin-Zanca D , Barbacid M , Parada L F
Published: June 2007

We have cloned and characterized the mouse homolog of the human trk proto-oncogene, a member of the protein tyrosine kinase (TK) receptor gene family. Here, we present the first report of a trk-encoded mRNA species in vivo. In situ hybridization analysis in the mouse embryo reveals a striking temporal and spatial regulation of trk transcription, with expression confined to the sensory cranial (trigeminal, superior, jugular) and dorsal root ganglia (DRG) of neural crest origin. Recent reports have shown that TK receptors can play regulatory roles in embryonic development. Thus, the developmental mutations W in mouse and torso and sevenless in Drosophila represent genes that code for defective TK receptors. Our data show that trk, a gene associated with malignancy in humans, is a specific marker for a set of neural crest-derived sensory neurons, and are consistent with the hypothesis that this proto-oncogene may have an important role in the development or phenotype of the neurons where it is expressed.
The Drosophila Fos-related AP-1 protein is a developmentally regulated transcription factor.
Authors: Perkins K K , Admon A , Patel N , Tjian R
Published: June 2007

Drosophila AP-1 consists of two proteins (dFRA and dJRA) that have functional and structural properties in common with mammalian Fos and Jun proto-oncogene products. Here, we report the isolation and characterization of cDNAs encoding the full-length dFRA and dJRA proteins. The predicted amino acid sequences reveal that both proteins contain a bipartite DNA-binding domain consisting of a leucine repeat and an adjacent basic region, which are characteristic of members of the AP-1 family. By using protein translated in vitro or expressed in Escherichia coli, we demonstrate that dFRA, in contrast to the mammalian cFos proteins, recognizes the AP-1 site on its own and activates transcription in vitro in the absence of dJRA or Jun. Heteromeric complexes formed between dFRA and dJRA bind the AP-1 site better than either protein alone, and the two proteins activate transcription synergistically in vitro. In the developing embryo, dFRA mRNA is first expressed in a limited set of cells in the head and is later restricted to a subset of peripheral neurons, several epidermal cells near the muscle attachment sites, and a portion of the gut. In contrast, dJRA appears to be uniformly expressed at a low level in all cell types. These results indicate that dFRA is a developmentally regulated transcription factor and suggest that its potential interplay with dJRA plays an important role in cell-type-specific transcription during Drosophila embryonic development.
Cloning and characterization of the segment polarity gene cubitus interruptus Dominant of Drosophila.
Authors: Orenic T V , Slusarski D C , Kroll K L , Holmgren R A
Published: June 2007

The segment polarity mutation, cubitus interruptus Dominant (ciD), of Drosophila melanogaster causes defects in the posterior half of every embryonic segment. We cloned sequences from the ciD region on the proximal fourth chromosome by "tagging" the gene with the transposable element P. Genetic and molecular evidence indicates that the P-element insertions, which all occurred within the same restriction fragment, are in 5'-regulatory regions of the ciD gene within 3 kb of the first exon of its transcript. The putative ciD transcript was identified on the basis of its absence in homozygous ciD embryos. Its spatial pattern of expression during development is unusual in that, unlike most other segmentation genes, it exhibits uniform expression throughout cellular blastoderm and gastrulation and does not resolve into a periodic pattern until the end of the fast phase of germ-band elongation when it is present in 15 broad segmentally repeating stripes along the anterior-posterior axis of the embryo. Registration of the ciD stripes of expression relative to the stripes of other segment polarity genes shows that ciD is expressed in the anterior three-quarters of every segment. This registration does not correlate with the pattern defects observed in ciD mutants. Sequence analysis indicates that the protein encoded by the ciD transcript contains a domain of five tandem amino acid repeats that have sequence similarity to the zinc-finger repeats of the Xenopus transcription factor TFIIIA and that share the highest degree of identity with the human zinc-finger protein GLI, which has been found to be amplified in several human glioblastomas.
The serendipity alpha gene encodes a membrane-associated protein required for the cellularization of the Drosophila embryo.
Authors: Schweisguth F , Lepesant J A , Vincent A
Published: June 2007

The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei. This pattern of transcription and a zygotic cellularization defect observed in embryos homozygous for Df(3R)X3F, a deficiency covering the sry locus, suggest that sry alpha plays a role in the cellularization of the syncytial blastoderm embryo. P-element rescue experiments show that one copy of the sry alpha gene rescues the defective cellularization phenotype associated with Df(3R)X3F. Lack of sry alpha activity results in erratic disruptions of the cytoskeleton at the beginning of the interphase of mitotic cycle 14. Multinucleate cells form during plasma membrane invagination. Immunodetection of the sry alpha protein using anti-sry alpha polyclonal antibodies indicates that the 58-kD sry alpha protein accumulates transiently at the blastoderm stage. The sry alpha protein is associated with the invaginating plasma membrane and colocalizes with F-actin. We propose that sry alpha is involved in the localization of membrane furrows within the syncytial blastoderm.
Identification of a retinoic acid-sensitive period during primary axis formation in Xenopus laevis.
Authors: Sive H L , Draper B W , Harland R M , Weintraub H
Published: June 2007

Retinoic acid (RA) is able to profoundly alter patterning of the primary body axis in embryos of the frog Xenopus laevis. The response to RA is dose-dependent, and leads to progressive truncation of the anteroposterior axis, with anterior structures most sensitive. Both mesodermal and ectodermal tissues are affected, and in vitro assays demonstrate that induced dorsal ectoderm is one direct target of RA. RA represses expression of anterior-specific genes and concomitantly induces expression of at least one posterior-specific gene. Resistance to RA is acquired gradually, during gastrula and early neurula stages, with posterior structures becoming resistant before anterior structures. These data demarcate in the embryo an anterior "domain," which may define the head rudiment and which transcends germ layers. RA can alter the axial pattern after its initial induction; thus, RA sensitivity defines a labile intermediate that occurs during axial patterning. These data suggest a possible role for RA in normal axis formation.
A novel enhancer in the immunoglobulin lambda locus is duplicated and functionally independent of NF kappa B.
Authors: Hagman J , Rudin C M , Haasch D , Chaplin D , Storb U
Published: June 2007

As a first step toward defining the elements necessary for lambda immunoglobulin gene regulation, DNase I hypersensitive sites were mapped in the mouse lambda locus. A hypersensitive site found 15.5 kb downstream of C lambda 4 was present in all the B-cell but not in the T-cell lines tested. This site coincided with a strong B-cell-specific transcriptional enhancer (E lambda 2-4). This novel enhancer is active in myeloma cells, regardless of the status of endogenous lambda genes, but is inactive in a T-cell line and in fibroblasts. The enhancer E lambda 2-4 functions in the absence of the transcription factor NF kappa B, which is necessary for kappa enhancer function. No evidence could be found for NF kappa B binding by this element. Rearrangement of V lambda 2 to JC lambda 3 or JC lambda genes deletes E lambda 2-4; however, a second strong enhancer was found 35 kb downstream of C lambda 1, which cannot be eliminated by lambda gene rearrangements. The second lambda enhancer (E lambda 3-1) is 90% homologous to the E lambda 2-4 sequence in the region determined to comprise the active enhancer and likewise lacks the consensus binding site for NF kappa B. The data support a model for the independent activation of kappa and lambda gene expression based on locus-specific regulation at the enhancer level.
RNA pseudoknot domain of tobacco mosaic virus can functionally substitute for a poly(A) tail in plant and animal cells.
Authors: Gallie D R , Walbot V
Published: June 2007

The genomes of many RNA viruses terminate in a tertiary structure similar to the L-conformation of tRNAs and this structure is recognized by many tRNA-specific enzymes such as aminoacyl-tRNA synthetase. Virtually the entire 3'-untranslated region (UTR) of tobacco mosaic virus (TMV) RNA is involved in an extended tertiary structure containing, in addition to a tRNA-like structure, a pseudoknot domain that lies immediately upstream. Although the functions of these structures are not well understood, they are essential to the virus. We demonstrate that the addition of the 204-base TMV 3'-untranslated region to foreign mRNA constructs can increase gene expression up to 100-fold compared to nonadenylated mRNA. The 3'-UTR of TMV was equal to or greater than a polyadenylated tail in enhancing gene expression in electroporated dicot and monocot protoplasts. The TMV 3'-UTR is functionally similar to a polyadenylated tail in that it increases mRNA stability and translation and must be positioned at the 3' terminus to function efficiently. Similar effects on expression were observed in Chinese hamster ovary cells, demonstrating that the sequence functions in a wide range of eukaryotes. When the extended tertiary structure was dissected, the upstream pseudoknot domain was found to be largely responsible for increasing expression. The inclusion of the tRNA-like structure, however, was important for full regulation.
Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells.
Authors: Krainer A R , Conway G C , Kozak D
Published: June 2007

SF2, an activity necessary for 5' splice site cleavage and lariat formation during pre-mRNA splicing in vitro, has been purified to near homogeneity from HeLa cells. The purest fraction contains only two related polypeptides of 33 kD. This fraction is sufficient to complement an S100 fraction, which contains the remaining splicing factors, to splice several pre-mRNAs. The optimal amount of SF2 required for efficient splicing depends on the pre-mRNA substrate. SF2 is distinct from the hnRNP A1 and U1 snRNP a polypeptides, which are similar in size. Endogenous hnRNA copurifies with SF2, but this activity does not appear to have an essential RNA component. SF2 appear to be necessary for the assembly or stabilization of the earliest specific prespliceosome complex, although in the absence of other components, it can bind RNA in a nonspecific manner. SF2 copurifies with an activity that promotes the annealing of complementary RNAs. Thus, SF2 may promote specific RNA-RNA interactions between snRNAs and pre-mRNA, between complementary snRNA regions, and/or involving intramolecular pre-mRNA helices. Other purified proteins with RNA annealing activity cannot substitute for SF2 in the splicing reaction.
A Sequential splicing mechanism promotes selection of an optimal exon by repositioning a downstream 5' splice site in preprotachykinin pre-mRNA.
Authors: Nasim F H , Spears P A , Hoffmann H M , Kuo H C , Grabowski P J
Published: June 2007

To explore the structural basis of alternative splicing, we have analyzed the splicing of pre-mRNAs containing an optional exon, E4, from the preprotachykinin gene. This gene encodes substance P and related tachykinin peptides by alternative splicing of a common pre-mRNA. We have shown that alternative splicing of preprotachykinin pre-mRNA occurs by preferential skipping of optional E4. The competing mechanism that incorporates E4 into the final spliced RNA is constrained by an initial block to splicing of the immediate upstream intervening sequence (IVS), IVS3. This block is relieved by sequential splicing, in which the immediate downstream IVS4 is removed first. The structural change resulting from the first splicing event is directly responsible for activation of IVS3 splicing. This structural rearrangement replaces IVS4 sequences with E5 and its adjacent IVS5 sequences. To determine how this structural change promoted IVS3 splicing, we asked what structural change(s) would restore activity of IVS3 splicing-defective mutants. The most significant effect was observed by a 2-nucleotide substitution that converted the 5' splice site of E4 to an exact consensus match, GUAAGU. Exon 5 sequences alone were found not to promote splicing when present in one or multiple copies. However, when a 15-nucleotide segment of IVS5 containing GUAAGU was inserted into a splicing-defective mutant just downstream of the hybrid exon segment E4E5, splicing activity was recovered. Curiously, the 72-nucleotide L2 exon of adenovirus, without its associated 5' splice site, activates splicing when juxtaposed to E4. Models for the activation of splicing by an RNA structural change are discussed.
Domains of yeast U4 spliceosomal RNA required for PRP4 protein binding, snRNP-snRNP interactions, and pre-mRNA splicing in vivo.
Authors: Bordonné R , Banroques J , Abelson J , Guthrie C
Published: June 2007

U4 small nuclear RNA (snRNA) contains two intramolecular stem-loop structures, located near each end of the molecule. The 5' stem-loop is highly conserved in structure and separates two regions of U4 snRNA that base-pair with U6 snRNA in the U4/U6 small nuclear ribonucleoprotein particle (snRNP). The 3' stem-loop is highly divergent in structure among species and lies immediately upstream of the binding site for Sm proteins. To investigate the function of these two domains, mutants were constructed that delete the yeast U4 snRNA 5' stem-loop and that replace the yeast 3' stem-loop with that from trypanosome U4 snRNA. Both mutants fail to complement a null allele of the yeast U4 gene. The defects of the mutants have been examined in heterozygous strains by native gel electrophoresis, glycerol gradient centrifugation, and immunoprecipitation. The chimeric yeast-trypanosome RNA does not associate efficiently with U6 snRNA, suggesting that the 3' stem-loop of yeast U4 snRNA might be a binding site for a putative protein that facilitates assembly of the U4/U6 complex. In contrast, the 5' hairpin deletion mutant associates efficiently with U6 snRNA. However, it does not bind the U4/U6-specific protein PRP4 and does not assemble into a U4/U5/U6 snRNA. Thus, we propose that the role of the PRP4 protein is to promote interactions between the U4/U6 snRNP and the U5 snRNP.
Analysis of the ftz upstream element: germ layer-specific enhancers are independently autoregulated.
Authors: Pick L , Schier A , Affolter M , Schmidt-Glenewinkel T , Gehring W J
Published: June 2007

The Drosophila fushi tarazu (ftz) upstream element is an enhancer-like element that is required for the correct expression of ftz in developing embryos and that directs transcription from a minimal promoter in a ftz-like seven-striped pattern. Using a deletion analysis, we have identified several independent cis-regulatory elements in the upstream element. A distal enhancer directs fusion gene expression in seven stripes primarily in the mesoderm. A more complex proximal enhancer contains a mesodermally active element and a second element with which it interacts to generate seven stripes in the ectoderm. Striped expression directed by each enhancer is ftz-dependent, and each contains binding sites for purified ftz homeo domain. We suggest that ftz protein acts in combination with germ layer-restricted transcription factors directly and positively to regulate the transcription of its own gene.
A homeo domain protein reveals the metameric nature of the developing chick hindbrain.
Authors: Sundin O H , Eichele G
Published: June 2007

The segmented embryonic hindbrain of vertebrates develops by sequential constriction of the neural tube into eight metameric units known as rhombomeres. The cellular and molecular basis of this segmentation process is largely unknown. Using an antibody, we analyzed the expression pattern of the chick homeo domain-containing protein Ghox-lab in the developing chick hindbrain. At the neural plate stage, prior to the appearance of rhombomeres, Ghox-lab is expressed within a single domain that extends anteriorly up to the site where rhombomere 4 will later form. After rhombomere 4 has appeared and as hindbrain segmentation progresses, the level of Ghox-lab protein increases significantly within the fourth rhombomere. This intensification, accompanied by the elimination of Ghox-lab protein in rhombomeres 5 and 6, eventually results in the formation of a distinct island of expression in rhombomere 4. All cells in the newly formed rhombomere 4 express Ghox-lab, except for the cells of the floor plate. In addition, neural crest cells migrating from the fourth rhombomere are also Ghox-lab-positive. These data raise the possibility that Ghox-lab protein might be one of the factors involved in the specification of the metameric pattern of the vertebrate hindbrain.
Interaction of the human immunodeficiency virus type 1 Rev protein with a structured region in env mRNA is dependent on multimer formation mediated through a basic stretch of amino acids.
Authors: Olsen H S , Cochrane A W , Dillon P J , Nalin C M , Rosen C A
Published: June 2007

Interaction of the human immunodeficiency virus type 1 (HIV-1) Rev protein with a structured region within env mRNA (termed RRE) mediates the export of virus structural mRNAs from the nucleus to the cytoplasm. We show that the region encompassing the basic stretch of amino acids is essential for the ability of Rev to bind to RRE RNA and function in vivo. By use of a functional truncated Rev protein in conjunction with authentic Rev, effects on gel mobilities of the Rev-RRE RNA complex attributable to multimerization of Rev protein were observed. Rev proteins, unable to multimerize, failed to bind RRE RNA. Identification of Rev mutants capable of forming multimers, but unable to bind RRE RNA, suggests that the multimerization and RNA-binding domains can be distinguished and that multimerization is likely a prerequisite for formation of the RRE RNA-binding site. A mutant Rev protein, shown previously to function as a trans-dominant inhibitor of Rev function, bound to RRE RNA as a multimer to a similar extent as wild-type Rev. This observation is consistent with the hypothesis that regulation of HIV gene expression by Rev involves the interaction with cellular factors and that the trans-dominant Rev is probably defective in this function.
Trypanosome variable surface glycoproteins: composite genes and order of expression.
Authors: Thon G , Baltz T , Giroud C , Eisen H
Published: June 2007

Combinatorial processes increase the diversity of variable surface glycoproteins (VSGs) expressed by Trypanosoma equiperdum. We show here that a single telomeric pseudogene provides the 3' portion of three distinct T. equiperdum VSG genes by recombination with different 5' donor pseudogenes. Regions of sequence homology among the pseudogenes determine the sites of recombination in the formation of the expressed copies. This suggests that the recombination between any given basic copy (BC) and the expression-linked copy (ELC) depends on their sharing homology. We present evidence that this is the case and propose that such rules account for the order of expression of the VSGs. These results demonstrate how homologous recombination can generate an ordered sequence of gene expression.
Light is required for conidiation in Aspergillus nidulans.
Authors: Mooney J L , Yager L N
Published: June 2007

Light is necessary for asexual sporulation in Aspergillus nidulans but will elicit conidiation only if irradiation occurs during a critical period of development. We show that conidiation is induced by red light and suppressed by an immediate shift to far red light. Conidiation-specific gene functions switch from light-independent to light-dependent activities coincident with the expression of brlA, a regulator of conidiophore development. We also show that light dependence is abolished by a mutation in the velvet gene, which allows conidiation to occur in the absence of light. We propose that the initiation of late gene expression is regulated by velvet and controlled by a red light photoreceptor, whose properties are reminiscent of phytochrome-mediated responses observed in higher plants.
The orthodenticle gene encodes a novel homeo domain protein involved in the development of the Drosophila nervous system and ocellar visual structures.
Authors: Finkelstein R , Smouse D , Capaci T M , Spradling A C , Perrimon N
Published: June 2007

The orthodenticle (otd) locus of Drosophila is required for embryonic development, and null mutations of otd cause defects in head development and segmental patterning. We show here that otd is necessary for the formation of the embryonic central nervous system (CNS). otd mutations result in the formation of an abnormal neuropil and in the disappearance of identified neurons associated with the midline of the CNS. In addition, otd is allelic to ocelliless (oc), a mutation that causes the deletion of the ocelli of the adult fly. We have identified a transcription unit corresponding to the otd locus and find that it is expressed early in a stripe near the anterior pole of the cellular blastoderm and later in the region of the CNS from which these neurons normally arise. The predicted otd protein contains a well-conserved homeo domain and is therefore likely to be a transcriptional regulator involved in specifying cell fate both in the embryonic CNS and in the ocelli.
MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain.
Authors: Reith W , Herrero-Sanchez C , Kobr M , Silacci P , Berte C , Barras E , Fey S , Mach B
Published: June 2007

The regulation of MHC class II gene expression controls T-cell activation and, hence, the immune response. Among the nuclear factors observed to bind to conserved DNA sequences in human leukocyte antigen (HLA) class II gene promoters, RFX is of special interest: Its binding is defective in congenital HLA class II deficiency, a disease of class II gene regulation. The cloning of an RFX cDNA has allowed us to show by transfection of a plasmid directing the synthesis of antisense RFX RNA that RFX is a class II gene regulatory factor. RFX is a novel 979-amino-acid DNA-binding protein that contains three structurally and functionally separate domains. The 91-amino-acid DNA-binding domain is distinct from other known DNA-binding motifs but may be distantly related to the helix-loop-helix motif. The most striking property of RFX is that it can bind stably to the class II X box as either a monomer or a homodimer and that the domain responsible for dimerization is distant from and functionally independent of the DNA-binding domain. This distinguishes RFX from other known dimeric DNA-binding proteins. It also implies that an RFX homodimer has two potential DNA-binding sites. We therefore speculate that RFX could form a DNA loop by cross-linking the two X-box sequences found far apart upstream of MHC class II genes.
LAP, a novel member of the C/EBP gene family, encodes a liver-enriched transcriptional activator protein.
Authors: Descombes P , Chojkier M , Lichtsteiner S , Falvey E , Schibler U
Published: June 2007

A gene, encoding a liver-enriched transcriptional activator protein (LAP) has been isolated. LAP is a 32-kD protein that stimulates the transcription of chimeric genes containing albumin D-promoter elements both in vivo and in vitro. LAP shares extensive sequence homology (71%) in its DNA-binding and leucine zipper domains with C/EBP. As a consequence, these two proteins show an indistinguishable DNA-binding specificity and readily heterodimerize. In addition, both genes, lap and cebp, are devoid of intervening sequences. Although correctly initiated transcripts from the LAP gene accumulate in the six examined tissues--liver, lung, spleen, kidney, brain, and testis--LAP protein is highly enriched in liver nuclei. Thus, the preferential accumulation of LAP protein in liver appears to be regulated post-transcriptionally.
Cap-independent translation of encephalomyocarditis virus RNA: structural elements of the internal ribosomal entry site and involvement of a cellular 57-kD RNA-binding protein.
Authors: Jang S K , Wimmer E
Published: June 2007

Translation of encephalomyocarditis virus (EMCV) mRNA occurs by ribosomal internal entry into the 5'-nontranslated region (5' NTR) rather than by ribosomal scanning. The internal ribosomal entry site (IRES) in the EMCV 5' NTR was determined by in vitro translation with RNAs that were generated by in vitro transcription of EMCV cDNAs containing serial deletions from either the 5' or 3' end of the EMCV 5' NTR. Regions downstream of nucleotide 403 and upstream of nucleotide 811 of EMCV were required for efficient translation. Site-directed mutagenesis revealed that a stem-loop structure (400 nucleotides upstream of the initiation codon) was essential for IRES function. We discovered a 57-kD cellular protein whose specific interaction with this stem-loop appears to be prerequisite for IRES function. A A pyrimidine-rich stretch proximal to the initiation codon was also crucial for efficient translation of EMCV mRNA. We propose that ribosomes bind directly to the initiating AUG without scanning.
Modulation of the IgH enhancer's cell type specificity through a genetic switch.
Authors: Ruezinsky D , Beckmann H , Kadesch T
Published: June 2007

Using defined regions of the immunoglobulin heavy-chain enhancer linked to minimal promoters and cDNAs that encode the two helix-loop-helix transcription factors ITF-1 and TFE3, we demonstrate that activity of an otherwise repressed enhancer can be stimulated in nonlymphoid cells. Repression in non-B cells is mediated by the microE5 motif. Derepression occurs at two levels. First, overexpression of ITF-1, and E12/E47-related protein that binds the microE5 motif, leads to transcriptional activation itself. Second, binding of ITF-1 physically displaces a repressor that normally blocks the stimulatory activity of TFE3, which binds the neighboring microE3 motif. TFE3 can only stimulate enhancer activity in the presence of ITF-1 or in the absence of a microE5 motif. Hence, one component of the enhancer's cell type specificity can be artificially modulated through a "genetic switch" in which activity is dictated by the relative levels of ITF-1 and a competing repressor.
Germ-line intrachromosomal recombination restores fertility in transgenic MyK-103 male mice.
Authors: Wilkie T M , Braun R E , Ehrman W J , Palmiter R D , Hammer R E
Published: June 2007

Males of the MyK-103 line of transgenic mice are fertile and sire litters of normal size, but they never transmit the transgene, whereas females transmit the transgene with normal frequency. The chromosome originally bearing the transgene can be transmitted through the male germ line, but only after the transgene is deleted or rearranged by intrachromosomal recombination. The transgene encodes a functional herpes simplex virus (HSV) thymidine kinase gene that causes sperm infertility when expressed in postmeiotic germ cells. Immunocytochemistry revealed clones of germ cells that fail to express HSV thymidine kinase. We postulate that these cells arose by transgene deletion in embryonic germ cells and postnatal spermatogonial stem cells and that they are responsible for the normal fertility of MyK-103 males. The frequency of recombination events at the integration locus suggests that it contains a hotspot for mitotic recombination.
Fission yeast genes that confer resistance to staurosporine encode an AP-1-like transcription factor and a protein kinase related to the mammalian ERK1/MAP2 and budding yeast FUS3 and KSS1 kinases.
Authors: Toda T , Shimanuki M , Yanagida M
Published: June 2007

Staurosporine, a potent inhibitor of protein kinase C, arrests fission yeast cell elongation specifically at a stage immediately after cell division. We isolated two genes, which, when carried on multicopy plasmids, confer drug resistance in fission yeast. One, spk1+, encodes a protein kinase highly similar (54% identity) to those encoded by the mammalian ERK1/MAP2 kinase and the budding yeast KSS1 and FUS3 genes. It is not essential for vegetative growth of Schizosaccharomyces pombe cells but is required for conjugation. The spk1+ gene product is a 45-kD protein enriched in the nucleus, and its level increases 10-fold after addition of staurosporine. The other gene pap1+ encodes an AP-1-like transcription factor that contains a region rich in basic amino acids followed by a "leucine zipper" motif. The pap1+ gene is required for spk1(+)-conferred staurosporine resistance. These two genes appear to function as a part of the fission yeast growth control pathway.
A retinoic acid receptor expressed in the early development of Xenopus laevis.
Authors: Ellinger-Ziegelbauer H , Dreyer C
Published: June 2007

We have isolated cDNAs coding for a putative retinoic acid receptor (RAR) of the gamma-type from a Xenopus laevis neurula cDNA library. By transient cotransfection of COS cells with an expression vector and a reporter plasmid, this cDNA is shown to direct the synthesis of a retinoic acid-dependent transcription factor. In embryos of X. laevis, transcription of the corresponding gene is greatly enhanced during gastrulation and early neurulation. Two distinct areas with high abundance of RAR gamma mRNA are located at the anterior and at the posterior end of the neurula. The two maxima have emerged by the end of gastrulation and they become more pronounced during neurulation. At tailbud and early tadpole stages, the RAR transcripts are found mainly in the head mesenchyme and in the tailbud. The expression of this RAR is region-specific but not germ-layer-specific. The strong and stage-specific activation of zygotic transcription of this RAR gene, and the specific localization of the mRNA are consistent with the temporal and spatial pattern of retinoic acid sensitivity of X. laevis embryos. Therefore it is likely that the gene product mediates the effects of endogenous and of exogenous retinoic acid on early embryogenesis of Xenopus. The significance of these findings for the specification of the anteroposterior axis is discussed.
TEF, a transcription factor expressed specifically in the anterior pituitary during embryogenesis, defines a new class of leucine zipper proteins.
Authors: Drolet D W , Scully K M , Simmons D M , Wegner M , Chu K T , Swanson L W , Rosenfeld M G
Published: June 2007

We have identified and characterized a new member of the leucine zipper (bZIP) gene family of transcription factors, thyrotroph embryonic factor (TEF). Analysis of the ontogeny of TEF gene expression reveals the presence of TEF transcripts, beginning on embryonic day 14, only in the region of the rat anterior pituitary gland in which thyrotrophs arise. This pattern of gene expression corresponds temporally and spatially to the onset of thyroid-stimulating hormone (TSH beta) gene expression, which defines the thyrotroph phenotype. Coupled with this observation, we find that TEF can bind to and trans-activate the TSH beta promoter. In contrast to this restricted pattern of expression during embryogenesis, TEF transcripts appear in several tissues in the mature organism. We propose that TEF belongs to a new class of bZIP proteins on the basis of the unique homology between TEF and another member of the bZIP gene family, the albumin D box-binding protein (DBP). TEF and DBP transcripts are coexpressed in a pituitary cell line, and these two proteins can readily form heterodimers. The DNA-binding and dimerization domains of TEF correspond to those found in other bZIP proteins. We have however, identified a cluster of basic amino acids, found only in TEF and DBP, that is necessary for the proper DNA-binding site specificity of TEF. A major trans-activation domain of TEF resides outside the region of homology to other bZIP proteins. These data are consistent with a role for a member of a new class of bZIP transcription factors in activating gene expression in the developing thyrotroph.
cAMP stimulates the C/EBP-related transcription factor rNFIL-6 to trans-locate to the nucleus and induce c-fos transcription.
Authors: Metz R , Ziff E
Published: June 2007

The c-fos serum response element (SRE) is a multifunctional regulatory region of the c-fos promoter that responds to a variety of inducers. Recently, we have demonstrated that the SRE binds the C/EBP-related transcription factor rat NFIL-6 (rNFIL-6). In this study we show that rNFIL-6 is regulated by the cAMP second messenger pathway in the rat pheochromocytoma PC12 cell line. Following forskolin treatment, rNFIL-6 binding to the SRE is increased, and the factor becomes phosphorylated and undergoes a trans-location to the nucleus. In transient cotransfection assays, rNFIL-6 is capable of trans-activating the c-fos promoter in a manner dependent on the SRE. These data show that rNFIL-6 undergoes a novel activation in which cAMP-induced nuclear trans-location allows rNFIL-6 to bind to the SRE and contribute to c-fos activation. We propose that rNFIL-6 is an additional regulatory component of the c-fos gene, which provides cAMP responsiveness to the multifunctional SRE.
The carboxy-terminal catalytic domain of the GTPase-activating protein inhibits nuclear signal transduction and morphological transformation mediated by the CSF-1 receptor.
Authors: Bortner D M , Ulivi M , Roussel M F , Ostrowski M C
Published: June 2007

To determine whether ras p21 products are necessary for signal transduction mediated by the colony stimulating factor-1 receptor (CSF-1R, the c-fms proto-oncogene product), we determined whether CSF-1R and ras activate a common nuclear target and whether the interruption of ras action affects CSF-1R signal transduction. Expression of the NVL3 retrotransposon was activated to the same extent in NIH-3T3 cells by both ras and v-fms oncogenes, and the ras-responsive element located in the long terminal repeat of NVL3 was demonstrated to be a common target for oncogene action. Human recombinant CSF-1 stimulated expression of the NVL3 element 30-fold in NIH-3T3 cells that contained human CSF-1R. Expression of the carboxy-terminal 374 amino acid residues of the human ras GTPase-activating protein (GAP) in cells containing CSF-1R was able to inhibit CSF-1 induction of NVL3 expression by 90%. Expression of the catalytic domain of GAP was also able to suppress transformation by either v-fms or ligand-activated CSF-1R. Expression of the c-jun proto-oncogene was activated by CSF-1R but was insensitive to the action of the catalytic domain of GAP. These results provide genetic evidence that in NIH-3T3 cells, ras p21 is involved in signal transduction mediated by CSF-1R.