bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escape From Repeat-Induced Point Mutation of a Gene-Sized Duplication in Neurospora crassa Crosses That Are Heterozygous for a Larger Chromosome Segment Duplication
Authors: Bhat Ashwin , Kasbekar Durgadas P 
Published: April 2021

Abstract
In Neurospora crassa the ability of an ectopic gene-sized duplication to induce repeat-induced point mutation (RIP) in its target gene was suppressed in crosses that were heterozygous for another larger chromosome segment duplication. Specifically, the frequency of RIP in the erg-3 gene due to a 1.3-kb duplication was reduced if the chromosome segment duplications Dp(IIIR &gt; [I;II]) AR17, Dp(VIR &gt; IIIR) OY329, or Dp(IVR &gt; VII) S1229 were present in either the same or the other parental nucleus of the premeiotic dikaryon. We suggest that the larger duplications act as sinks to titrate the RIP machinery away from the smaller duplication. In contrast, RIP efficiency was relatively unaffected in comparably unproductive interspecies crosses with N. intermedia and N. tetrasperma. These findings offer a novel explanation for the observed persistence of the transposable element Tad in only a subset of Neurospora strains.
The Mutant Phenotype Associated With P-Element Alleles of the vestigial Locus in Drosophila melanogaster May Be Caused by a Readthrough Transcript Initiated at the P-Element Promoter
Authors: Hodgetts Ross B , O'Keefe Sandra L 
Published: April 2021

Abstract
We report here the isolation of a new P-element-induced allele of the vestigial locus vg2a33, the molecular characterization of which allows us to propose a unifying explanation of the phenotypes of the large number of vestigial P-element alleles that now exists. The first P-element allele of vestigial to be isolated was vg21, which results in a very weak mutant wing phenotype that is suppressed in the P cytotype. By destabilizing vg2a33 in a dysgenic cross, we isolated the vg2a33 allele, which exhibits a moderate mutant wing phenotype and is not suppressed by the P cytotype. The new allele is characterized by a 46-bp deletion that removes the 3′-proximal copy of the 11-bp internal repeat from the P element of vg21. To understand how this subtle difference between the two alleles leads to a rather pronounced difference in their phenotypes, we mapped both the vg and P-element transcription units present in wild type and mutants. Using both 5′-RACE and S1 protection, we found that P-element transcription is initiated 19 bp farther upstream than previously thought. Using primer extension, the start of vg transcription was determined to lie 435 bp upstream of the longest cDNA recovered to date and upstream of the P-element insertion site. Our discovery that the P element is situated within the first vg exon has prompted a reassessment of the large body of genetic data on a series of alleles derived from vg21. Our current hypothesis to explain the degree of variation in the mutant phenotypes and their response to the P repressor invokes a critical RNA secondary structure in the vg transcript, the formation of which is hindered by a readthrough transcript initiated at the P-element promoter.
Expansions and Contractions in 36-bp Minisatellites by Gene Conversion in Yeast
Authors: Pâques Frédéric , Richard Guy-Franck , Haber James E 
Published: April 2021

Abstract
The instability of simple tandem repeats, such as human minisatellite loci, has been suggested to arise by gene conversions. In Saccharomyces cerevisiae, a double-strand break (DSB) was created by the HO endonuclease so that DNA polymerases associated with gap repair must traverse an artificial minisatellite of perfect 36-bp repeats or a yeast Y′ minisatellite containing diverged 36-bp repeats. Gene conversions are frequently accompanied by changes in repeat number when the template contains perfect repeats. When the ends of the DSB have nonhomologous tails of 47 and 70 nucleotides that must be removed before repair DNA synthesis can begin, 16% of gene conversions had rearrangements, most of which were contractions, almost always in the recipient locus. When efficient removal of nonhomologous tails was prevented in rad1 and msh2 strains, repair was reduced 10-fold, but among survivors there was a 10-fold reduction in contractions. Half the remaining events were expansions. A similar decrease in the contraction rate was observed when the template was modified so that DSB ends were homologous to the template; and here, too, half of the remaining rearrangements were expansions. In this case, efficient repair does not require RAD1 and MSH2, consistent with our previous observations. In addition, without nonhomologous DSB ends, msh2 and rad1 mutations did not affect the frequency or the distribution of rearrangements. We conclude that the presence of nonhomologous ends alters the mechanism of DSB repair, likely through early recruitment of repair proteins including Msh2p and Rad1p, resulting in more frequent contractions of repeated sequences.
Multiple Functional Interactions Between Components of the Lsm2-Lsm8 Complex, U6 snRNA, and the Yeast La Protein
Authors: Pannone Barbara K , Kim Sang Do , Noe Dennis A , Wolin Sandra L 
Published: April 2021

Abstract
The U6 small nuclear ribonucleoprotein is a critical component of the eukaryotic spliceosome. The first protein that binds the U6 snRNA is the La protein, an abundant phosphoprotein that binds the 3′ end of many nascent small RNAs. A complex of seven Sm-like proteins, Lsm2-Lsm8, also binds the 3′ end of U6 snRNA. A mutation within the Sm motif of Lsm8p causes Saccharomyces cerevisiae cells to require the La protein Lhp1p to stabilize nascent U6 snRNA. Here we describe functional interactions between Lhp1p, the Lsm proteins, and U6 snRNA. LSM2 and LSM4, but not other LSM genes, act as allele-specific, low-copy suppressors of mutations in Lsm8p. Overexpression of LSM2 in the lsm8 mutant strain increases the levels of both Lsm8p and U6 snRNPs. In the presence of extra U6 snRNA genes, LSM8 becomes dispensable for growth, suggesting that the only essential function of LSM8 is in U6 RNA biogenesis or function. Furthermore, deletions of LSM5, LSM6, or LSM7 cause LHP1 to become required for growth. Our experiments are consistent with a model in which Lsm2p and Lsm4p contact Lsm8p in the Lsm2-Lsm8 ring and suggest that Lhp1p acts redundantly with the entire Lsm2-Lsm8 complex to stabilize nascent U6 snRNA.
Long-Range Repression by Multiple Polycomb Group (PcG) Proteins Targeted by Fusion to a Defined DNA-Binding Domain in Drosophila
Authors: Roseman Robin R , Morgan Kelly , Mallin Daniel R , Roberson Rachel , Parnell Timothy J , Bornemann Douglas J , Simon Jeffrey A , Geyer Pamela K 
Published: April 2021

Abstract
A tethering assay was developed to study the effects of Polycomb group (PcG) proteins on gene expression in vivo. This system employed the Su(Hw) DNA-binding domain (ZnF) to direct PcG proteins to transposons that carried the white and yellow reporter genes. These reporters constituted naive sensors of PcG effects, as bona fide PcG response elements (PREs) were absent from the constructs. To assess the effects of different genomic environments, reporter transposons integrated at nearly 40 chromosomal sites were analyzed. Three PcG fusion proteins, ZnF-PC, ZnF-SCM, and ZnF-ESC, were studied, since biochemical analyses place these PcG proteins in distinct complexes. Tethered ZnF-PcG proteins repressed white and yellow expression at the majority of sites tested, with each fusion protein displaying a characteristic degree of silencing. Repression by ZnF-PC was stronger than ZnF-SCM, which was stronger than ZnF-ESC, as judged by the percentage of insertion lines affected and the magnitude of the conferred repression. ZnF-PcG repression was more effective at centric and telomeric reporter insertion sites, as compared to euchromatic sites. ZnF-PcG proteins tethered as far as 3.0 kb away from the target promoter produced silencing, indicating that these effects were long range. Repression by ZnF-SCM required a protein interaction domain, the SPM domain, which suggests that this domain is not primarily used to direct SCM to chromosomal loci. This targeting system is useful for studying protein domains and mechanisms involved in PcG repression in vivo.
Sequence Diversity in the Tetraploid Zea perennis and the Closely Related Diploid Z. diploperennis: Insights From Four Nuclear Loci
Authors: Tiffin Peter , Gaut Brandon S 
Published: April 2021

Abstract
Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.
Recognition and Specific Degradation of Bacteriophage T4 mRNAs
Authors: Ueno Hiroyuki , Yonesaki Tetsuro 
Published: April 2021

Abstract
Gene 61.5 of bacteriophage T4 has a unique role in gene expression. When this gene is mutated, mRNAs of many late genes are rapidly degraded, resulting in late-gene silencing. Here, we characterize an extragenic suppressor, ssf5, of a gene 61.5 mutation. ssf5 was found to be an amber mutation in motA, which encodes a transcription activator for T4 middle genes. When this gene is mutated, both degradation and specific cleavage of late-gene mRNA is induced after a delay, as exemplified by soc mRNA. Consequently, partial late-gene expression occurs. In an ssf5 genetic background, a gene 61.5 mutation exhibits a novel phenotype: in contrast to late-gene mRNA, middle-gene mRNA is stabilized and the expression of middle genes is prolonged. This is attributable to an activity of gene 61.5 specific for degradation of middle-gene mRNA. The degradation of middle-gene mRNA in the presence of a normal gene 61.5 appears in parallel with the degradation of late-gene mRNA in its absence. This observation suggests that the mRNA-degrading activity that silences late genes in cells infected with a gene 61.5 mutant is targeted to middle-gene mRNA when gene 61.5 is wild type. These results and the results obtained in the presence of a normal motA gene suggest that gene 61.5 protein functions to discriminate mRNAs for degradation in a stage-dependent manner.
A Systematic Screen for Dominant Second-Site Modifiers of Merlin/NF2 Phenotypes Reveals an Interaction With blistered/DSRF and scribbler
Authors: LaJeunesse Dennis R , McCartney Brooke M , Fehon Richard G 
Published: April 2021

Abstract
Merlin, the Drosophila homologue of the human tumor suppressor gene Neurofibromatosis 2 (NF2), is required for the regulation of cell proliferation and differentiation. To better understand the cellular functions of the NF2 gene product, Merlin, recent work has concentrated on identifying proteins with which it interacts either physically or functionally. In this article, we describe genetic screens designed to isolate second-site modifiers of Merlin phenotypes from which we have identified five multiallelic complementation groups that modify both loss-of-function and dominant-negative Merlin phenotypes. Three of these groups, Group IIa/scribbler (also known as brakeless), Group IIc/blistered, and Group IId/net, are known genes, while two appear to be novel. In addition, two genes, Group IIa/scribbler and Group IIc/blistered, alter Merlin subcellular localization in epithelial and neuronal tissues, suggesting that they regulate Merlin trafficking or function. Furthermore, we show that mutations in scribbler and blistered display second-site noncomplementation with one another. These results suggest that Merlin, blistered, and scribbler function together in a common pathway to regulate Drosophila wing epithelial development.
AFLP-Based Genetic Linkage Map of the Colorado Potato BeetleLeptinotarsa decemlineata: Sex Chromosomes and a Pyrethroid-Resistance Candidate Gene
Authors: Hawthorne David J 
Published: April 2021

AbstractA genetic linkage map was constructed from an intraspecific cross of the Colorado potato beetle, Leptinotarsa decemlineata. This is an initial step toward mapping the loci that underlie important phenotypes associated with insect adaptation to an agroecosystem. The map was made with 172 AFLP and 10 anonymous codominant markers segregating among 74 backcross (BC1) individuals. Markers were mapped to 18 linkage groups and a subset of the markers with a mean intermarker distance of 11.1 cM is presented. A pyrethroid-resistance candidate gene, LdVssc1, was placed onto the map as well. The sex chromosome was identified by exploiting the XO nature of sex determination in this species using patterns of variation at LdVssc1 and the codominant markers.
An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion
Authors: Cantrell Michael A , Filanoski Brian J , Ingermann Angela R , Olsson Katherine , DiLuglio Nicole , Lister Zach , Wichman Holly A 
Published: April 2021

Abstract
Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers.
Tracing Evolutionary and Developmental Implications of Mitochondrial Stoichiometric Shifting in the Common Bean
Authors: Arrieta-Montiel Maria , Lyznik Anna , Woloszynska Magdalena , Janska Hanna , Tohme Joe , Mackenzie Sally 
Published: April 2021

AbstractThe recombination and copy number shifting activities of the plant mitochondrial genome are widely documented across plant genera, but these genome processes have not been as well examined with regard to their roles in plant evolution. Because of the extensive plant collections of Phaseolus spp and the degree to which cytoplasmic male sterility (cms) has been characterized in the common bean, this system would be valuable for investigating mitochondrial genome dynamics in natural populations. We have used the cms-associated sequence pvs-orf239 as a mitochondrial genetic marker for these studies and have demonstrated its universal presence throughout a diversity of undomesticated Phaseolus lines. Within these populations, the pvs-orf239 sequence is present in high copy number in ∼10% of the lines, but substoichiometric in all others. This mitochondrial sequence, derived apparently by at least two recombination events, is well conserved with two point mutations identified that are both apparently silent with regard to the sterility phenotype. A putative progenitor sequence was identified in Phaseolus glabelus in substoichiometric levels, suggesting that the present-day pvs-orf239 sequence was likely introduced substoichiometrically. Copy number shifting within the mitochondrial genome results in a 1000- to 2000-fold change, so that substoichiometric forms are estimated at less than one copy per every 100 cells. On the basis of PCR analysis of root tips, we postulate that a mitochondrial “transmitted form” resides within the meristem to assure transmission of a complete genetic complement to progeny.
Characterization of the EYE2 Gene Required for Eyespot Assembly in Chlamydomonas reinhardtii
Authors: Roberts Douglas G W , Lamb Mary Rose , Dieckmann Carol L 
Published: April 2021

Abstract
The unicellular biflagellate green alga Chlamydomonas reinhardtii can perceive light and respond by altering its swimming behavior. The eyespot is a specialized structure for sensing light, which is assembled de novo at every cell division from components located in two different cellular compartments. Photoreceptors and associated signal transduction components are localized in a discrete patch of the plasma membrane. This patch is tightly packed against an underlying sandwich of chloroplast membranes and carotenoid-filled lipid granules, which aids the cell in distinguishing light direction. In a prior screen for mutant strains with eyespot defects, the EYE2 locus was defined by the single eye2-1 allele. The mutant strain has no eyespot by light microscopy and has no organized carotenoid granule layers as judged by electron microscopy. Here we demonstrate that the eye2-1 mutant is capable of responding to light, although the strain is far less sensitive than wild type to low light intensities and orients imprecisely. Therefore, pigment granule layer assembly in the chloroplast is not required for photoreceptor localization in the plasma membrane. A plasmid-insertion mutagenesis screen yielded the eye2-2 allele, which allowed the isolation and characterization of the EYE2 gene. The EYE2 protein is a member of the thioredoxin superfamily. Site-directed mutagenesis of the active site cysteines demonstrated that EYE2 function in eyespot assembly is redox independent, similar to the auxiliary functions of other thioredoxin family members in protein folding and complex assembly.
Mutants of Chlamydomonas reinhardtii Deficient in Mitochondrial Complex I: Characterization of Two Mutations Affecting the nd1 Coding Sequence
Authors: Remacle Claire , Baurain Denis , Cardol Pierre , Matagne René F 
Published: April 2021

Abstract
The mitochondrial rotenone-sensitive NADH:ubiquinone oxidoreductase (complex I) comprises more than 30 subunits, the majority of which are encoded by the nucleus. In Chlamydomonas reinhardtii, only five components of complex I are coded for by mitochondrial genes. Three mutants deprived of complex I activity and displaying slow growth in the dark were isolated after mutagenic treatment with acriflavine. A genetical analysis demonstrated that two mutations (dum20 and dum25) affect the mitochondrial genome whereas the third mutation (dn26) is of nuclear origin. Recombinational analyses showed that dum20 and dum25 are closely linked on the genetic map of the mitochondrial genome and could affect the nd1 gene. A sequencing analysis confirmed this conclusion: dum20 is a deletion of one T at codon 243 of nd1; dum25 corresponds to a 6-bp deletion that eliminates two amino acids located in a very conserved hydrophilic segment of the protein.
Terminal Retrotransposons Activate a Subtelomeric white Transgene at the 2L Telomere in Drosophila
Authors: Golubovsky Mikhail D , Konev Alexander Y , Walter Marika F , Biessmann Harald , Mason James M 
Published: April 2021

Abstract
Genetically marked P elements inserted into the subtelomeric satellites of Drosophila show repression and variegation of the reporter gene. One such white+ reporter, inserted between the subtelomeric satellite and the terminal HeT-A array in the left arm of chromosome 2 (2L), is sensitive to its context; changes in the structure of the telomere region can be identified by changes in eye color. Addition of HeT-A or TART elements to the 2L terminus increases w+ expression, and loss of sequence from the end decreases expression. This indicates that the telomeric retrotransposons in Drosophila have an activating influence on the repressed subterminal reporter gene. Changes in eye color due to altered expression of the transgene also allow the detection of interactions between homologous telomeres. The 2L arms that terminate in long HeT-A/TART arrays showed increased expression of the subterminal w+ transgene when the terminal repeats on the homologue are absent or markedly shorter. We propose that the chromatin structure of the terminal HeT-A/TART array and the activity of a putative promoter/enhancer element on HeT-A are affected by telomeric interactions. Such trans-activation may reflect control over HeT-A transcription and, thus, transposition activity.
Inbreeding Changes the Shape of the Genetic Covariance Matrix inDrosophila melanogaster
Authors: Phillips Patrick C , Whitlock Michael C , Fowler Kevin 
Published: April 2021

AbstractThe pattern of genetic covariation among traits (the G matrix) plays a central role in determining the pattern of evolutionary change from both natural selection and random genetic drift. Here we measure the effect of genetic drift on the shape of the G matrix using a large data set on the inheritance of wing characteristics in Drosophila melanogaster. Fifty-two inbred lines with a total of 4680 parent-offspring families were generated by one generation of brother-sister mating and compared to an outbred control population of 1945 families. In keeping with the theoretical expectation for a correlated set of additively determined traits, the average G matrix of the inbred lines remained proportional to the outbred control G matrix with a proportionality constant approximately equal to (1 – F), where F is the inbreeding coefficient. Further, the pattern of covariance among the means of the inbred lines induced by inbreeding was also proportional to the within-line G matrix of the control population with a constant very close to the expectation of 2F. Although the average G of the inbred lines did not show change in overall structure relative to the outbred controls, separate analysis revealed a great deal of variation among inbred lines around this expectation, including changes in the sign of genetic correlations. Since any given line can be quite different from the outbred control, it is likely that in nature unreplicated drift will lead to changes in the G matrix. Thus, the shape of G is malleable under genetic drift, and the evolutionary response of any particular population is likely to depend on the specifics of its evolutionary history.