bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sls1p Is a Membrane-Bound Regulator of Transcription-Coupled Processes Involved in Saccharomyces cerevisiae Mitochondrial Gene Expression
Authors: Bryan Anthony C , Rodeheffer Matthew S , Wearn Christopher M , Shadel Gerald S 
Published: April 2021

Abstract
1Mitochondrial translation is largely membrane-associated in S. cerevisiae. Recently, we discovered that the matrix protein Nam1p binds the amino-terminal domain of yeast mtRNA polymerase to couple translation and/or RNA-processing events to transcription. To gain additional insight into these transcription-coupled processes, we performed a genetic screen for genes that suppress the petite phenotype of a point mutation in mtRNA polymerase (rpo41-R129D) when overexpressed. One suppressor identified in this screen was SLS1, which encodes a mitochondrial membrane protein required for assembly of respiratory-chain enzyme complexes III and IV. The mtRNA-processing defects associated with the rpo41-R129D mutation were corrected in the suppressed strain, linking Sls1p to a pathway that includes mtRNA polymerase and Nam1p. This was supported by the observation that SLS1 overexpression rescued the petite phenotype of a NAM1 null mutation. In contrast, overexpression of Nam1p did not rescue the petite phenotype of a SLS1 null mutation, indicating that Nam1p and Sls1p are not functionally redundant but rather exist in an ordered pathway. On the basis of these data, a model in which Nam1p coordinates the delivery of newly synthesized transcripts to the membrane, where Sls1p directs or regulates their subsequent handling by membrane-bound factors involved in translation, is proposed.
Structure/Function Analysis of the Saccharomyces cerevisiae Trf4/Pol σ DNA Polymerase
Authors: Wang Zhenghe , Castaño Irene B , Adams Carrie , Vu Clemence , Fitzhugh David , Christman Michael F 
Published: April 2021

Abstract
The Trf4p/Pol σ DNA polymerase (formerly Trf4p/Pol κ) couples DNA replication to the establishment of sister chromatid cohesion. The polymerase is encoded by two redundant homologs in Saccharomyces cerevisiae, TRF4 and TRF5, that together define a fourth essential nuclear DNA polymerase in yeast and probably in all eukaryotes. Here we present a thorough genetic analysis of the founding member of this novel family of DNA polymerases, TRF4. Analyses of mutants carrying 1 of 34 “surface-targeted” alanine scanning mutations in TRF4 have identified those regions required for Pol σ's essential function, for its role in DNA double-strand break repair, and for its association with chromosomes. The data strongly support the importance of the regions of predicted structural similarity with the Pol β superfamily as critical for Trf4p/Pol σ's essential and repair functions. Surprisingly, five lethal mutations lie outside all polymerase homology in a C-terminal region. The protein possesses Mg2+-dependent 3′ to 5′ exonuclease activity. Cell cycle analysis reveals that Trf4p/Pol σ associates with chromosomes in G1, S, and G2 phases, but that association is abolished coincident with dissolution of cohesion at the metaphase-to-anaphase transition.
Schizosaccharomyces pombe Bir1p, a Nuclear Protein That Localizes to Kinetochores and the Spindle Midzone, Is Essential for Chromosome Condensation and Spindle Elongation During Mitosis
Authors: Rajagopalan Srividya , Balasubramanian Mohan K 
Published: April 2021

Abstract
The inhibitor of apoptosis (IAP) family of proteins contains a subset of members characterized by the presence of highly conserved baculoviral IAP repeat (BIR) domains. Recent work has shown that some of these BIR-domain proteins play a prominent role in the regulation of cell division, in particular at the stage of chromosome segregation and cytokinesis. We and others have shown that the Schizosaccharomyces pombe BIR-domain protein, Bir1p/Pbh1p/Cut17p, is important for the regulation of mitosis. Here we further characterize S. pombe Bir1p using methods of cell biology and genetics. We show that Bir1p is dispersed throughout the nucleus during the cell cycle. In addition, a significant part of Bir1p is also detected at the kinetochores and the spindle midzone during mitosis and meiosis. Time-lapse microscopy studies suggest that Bir1p relocates from the kinetochores to the spindle at the end of anaphase A. Bir1p colocalizes with the S. pombe Aurora kinase homolog Aim1p, a protein essential for mitosis, at the kinetochores as well as the spindle midzone during mitosis, and functional Bir1p is essential for localization of Aim1p to the kinetochores and the spindle midzone. Analyses of bir1 conditional mutants revealed that Bir1p is essential for chromosome condensation during mitosis. In addition, anaphase cells show the presence of lagging chromosomes and a defect in spindle elongation. We conclude that Bir1p is important for multiple processes that occur during mitosis in S. pombe.
Dimorphic Mating-Type Chromosomes in the Fungus Microbotryum violaceum
Authors: Hood Michael E 
Published: April 2021

Abstract
Fungi often mate as haploids, and sex chromosomes (i.e., mating-type chromosomes) that are dimorphic for their size or overall DNA content have never been reported in this kingdom. Using electrophoretic techniques for karyotype analysis, a highly dimorphic chromosome pair that determines mating compatibility is shown to occur in populations of the fungus Microbotryum violaceum. This substantiates the evolution of such dimorphism as a general feature associated with haploid determination of mating compatibility, which previously had been known only in haplodioecious plants (mosses and liverworts). Size-dimorphic sex chromosomes are present in a lineage of M. violaceum native to Europe, as well as a lineage native to North America. However, they are very different in size between these lineages, indicating either independent evolution of the dimorphism or a large degree of divergence since their isolation. Several DNA sequences that show sequence similarity to transposons were isolated from these sex chromosomes.
Roles for Caenorhabditis elegans rad-51 in Meiosis and in Resistance to Ionizing Radiation During Development
Authors: Rinaldo Cinzia , Bazzicalupo Paolo , Ederle Sara , Hilliard Massimo , La Volpe Adriana 
Published: April 2021

Abstract
We have investigated the role of Caenorhabditis elegans RAD-51 during meiotic prophase and embryogenesis, making use of the silencing effect of RNA interference (RNAi). rad-51 RNAi leads to severe defects in chromosome morphology in diakinesis oocytes. We have explored the effect of rad-51 RNAi in mutants lacking fundamental components of the recombination machinery. If double-strand breaks are prevented by spo-11 mutation, rad-51 RNAi does not affect chromosome appearance. This is consistent with a role for RAD-51 downstream of the initiation of recombination. In the absence of MRE-11, as in the absence of SPO-11, RAD-51 depletion has no effect on the chromosomes, which appear intact, thus indicating a role for MRE-11 in DSB induction. Intriguingly, rad-51 silencing in oocytes that lack MSH-5 leads to chromosome fragmentation, a novel trait that is distinct from that seen in msh-5 mutants and in rad-51 RNAi oocytes, suggesting new potential roles for the msh-5 gene. Silencing of the rad-51 gene also causes a reduction in fecundity, which is suppressed by mutation in the DNA damage checkpoint gene rad-5, but not in the cell death effector gene ced-3. Finally, RAD-51 depletion is also seen to affect the soma, resulting in hypersensitivity to ionizing radiation in late embryogenesis.
Unexpected Stability of mariner Transgenes in Drosophila
Authors: Lozovsky Elena R , Nurminsky Dmitry , Wimmer Ernst A , Hartl Daniel L 
Published: April 2021

Abstract
A number of mariner transformation vectors based on the mauritiana subfamily of transposable elements were introduced into the genome of Drosophila melanogaster and examined for their ability to be mobilized by the mariner transposase. Simple insertion vectors were constructed from single mariner elements into which exogenous DNA ranging in size from 1.3 to 4.5 kb had been inserted; composite vectors were constructed with partial or complete duplications of mariner flanking the exogenous DNA. All of the simple insertion vectors showed levels of somatic and germline excision that were at least 100-fold lower than the baseline level of uninterrupted mariner elements. Although composite vectors with inverted duplications were unable to be mobilized at detectable frequencies, vectors with large direct duplications of mariner could be mobilized. A vector consisting of two virtually complete elements flanking exogenous DNA yielded a frequency of somatic eye-color mosaicism of ~10% and a frequency of germline excision of 0.04%. These values are far smaller than those observed for uninterrupted elements. The results imply that efficient mobilization of mariner in vivo requires the presence and proper spacing of sequences internal to the element as well as the inverted repeats.
The Drosophila Gene taranis Encodes a Novel Trithorax Group Member Potentially Linked to the Cell Cycle Regulatory Apparatus
Authors: Calgaro Stéphane , Boube Muriel , Cribbs David L , Bourbon Henri-Marc 
Published: April 2021

Abstract
Genes of the Drosophila Polycomb and trithorax groups (PcG and trxG, respectively) influence gene expression by modulating chromatin structure. Segmental expression of homeotic loci (HOM) initiated in early embryogenesis is maintained by a balance of antagonistic PcG (repressor) and trxG (activator) activities. Here we identify a novel trxG family member, taranis (tara), on the basis of the following criteria: (i) tara loss-of-function mutations act as genetic antagonists of the PcG genes Polycomb and polyhomeotic and (ii) they enhance the phenotypic effects of mutations in the trxG genes trithorax (trx), brahma (brm), and osa. In addition, reduced tara activity can mimic homeotic loss-of-function phenotypes, as is often the case for trxG genes. tara encodes two closely related 96-kD protein isoforms (TARA-α/-β) derived from broadly expressed alternative promoters. Genetic and phenotypic rescue experiments indicate that the TARA-α/-β proteins are functionally redundant. The TARA proteins share evolutionarily conserved motifs with several recently characterized mammalian nuclear proteins, including the cyclin-dependent kinase regulator TRIP-Br1/p34SEI-1, the related protein TRIP-Br2/Y127, and RBT1, a partner of replication protein A. These data raise the possibility that TARA-α/-β play a role in integrating chromatin structure with cell cycle regulation.
Rough eye Is a Gain-of-Function Allele of amos That Disrupts Regulation of the Proneural Gene atonal During Drosophila Retinal Differentiation
Authors: Chanut Françoise , Woo Katherine , Pereira Shalini , Donohoe Terrence J , Chang Shang-Yu , Laverty Todd R , Jarman Andrew P , Heberlein Ulrike 
Published: April 2021

Abstract
The regular organization of the ommatidial lattice in the Drosophila eye originates in the precise regulation of the proneural gene atonal (ato), which is responsible for the specification of the ommatidial founder cells R8. Here we show that Rough eye (Roi), a dominant mutation manifested by severe roughening of the adult eye surface, causes defects in ommatidial assembly and ommatidial spacing. The ommatidial spacing defect can be ascribed to the irregular distribution of R8 cells caused by a disruption of the patterning of ato expression. Disruptions in the recruitment of other photoreceptors and excess Hedgehog production in differentiating cells may further contribute to the defects in ommatidial assembly. Our molecular characterization of the Roi locus demonstrates that it is a gain-of-function mutation of the bHLH gene amos that results from a chromosomal inversion. We show that Roi can rescue the retinal developmental defect of ato1 mutants and speculate that amos substitutes for some of ato's function in the eye or activates a residual function of the ato1 allele.
Assembly of Two Transgenes in an Artificial Chromatin Domain Gives Highly Coordinated Expression in Tobacco
Authors: Mlynárová Ludmila , Loonen Annelies , Mietkiewska Elzbieta , Jansen Ritsert C , Nap Jan-Peter 
Published: April 2021

Abstract
The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli β-glucuronidase gene and the firefly luciferase gene, driven by different promoters, were placed between copies of the chicken lysozyme A element, a member of the matrix-associated region (MAR) group of chromatin boundary elements, and introduced in tobacco (Nicotiana tabacum). In plants carrying A elements, quantitative enzyme activities and mRNA levels of both genes show high correlations compared to control plants. The A element thus creates an artificial chromatin domain that yields coordinated expression. Surprisingly, enzyme activities correlated poorly with their respective mRNA levels. We hypothesize that this indicates the occurrence of “error pipelines” in data generation: systematic errors of a given analytical method will point in the same direction and cancel out in correlation analysis, resulting in better correlations. In combining different methods of analysis, however, such errors do not cancel out and as a result relevant correlations can be masked. Such error pipelines will have to be taken into account when different types of (e.g., whole-genome) data sets are combined in quantitative analyses.
Likelihood-Based Estimation of the Effective Population Size Using Temporal Changes in Allele Frequencies: A Genealogical Approach
Authors: Berthier Pierre , Beaumont Mark A , Cornuet Jean-Marie , Luikart Gordon 
Published: April 2021

AbstractA new genetic estimator of the effective population size (Ne) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based Ne estimator () by using data from simulated populations with known Ne and real populations. The new likelihood-based estimator () showed narrower credible intervals and greater accuracy than () when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., Ne = 20 for five generations), as few as ~10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit &lt;50 using the LB method. In contrast, ~20 loci are required for the same precision when using the classical F-statistic approach. The estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates Ne than does and thus is less likely to erroneously suggest that a population is large and has a low extinction risk.
Joint Linkage and Linkage Disequilibrium Mapping of Quantitative Trait Loci in Natural Populations
Authors: Wu Rongling , Ma Chang-Xing , Casella George 
Published: April 2021

AbstractLinkage analysis and allelic association (also referred to as linkage disequilibrium) studies are two major approaches for mapping genes that control simple or complex traits in plants, animals, and humans. But these two approaches have limited utility when used alone, because they use only part of the information that is available for a mapping population. More recently, a new mapping strategy has been designed to integrate the advantages of linkage analysis and linkage disequilibrium analysis for genome mapping in outcrossing populations. The new strategy makes use of a random sample from a panmictic population and the open-pollinated progeny of the sample. In this article, we extend the new strategy to map quantitative trait loci (QTL), using molecular markers within the EM-implemented maximum-likelihood framework. The most significant advantage of this extension is that both linkage and linkage disequilibrium between a marker and QTL can be estimated simultaneously, thus increasing the efficiency and effectiveness of genome mapping for recalcitrant outcrossing species. Simulation studies are performed to test the statistical properties of the MLEs of genetic and genomic parameters including QTL allele frequency, QTL effects, QTL position, and the linkage disequilibrium of the QTL and a marker. The potential utility of our mapping strategy is discussed.
Timing and Targeting of P-Element Local Transposition in the Male Germline Cells of Drosophila melanogaster
Authors: Timakov Benjamin , Liu Xiaoru , Turgut Ismail , Zhang Ping 
Published: April 2021

Abstract
The P element in Drosophila melanogaster preferentially transposes into nearby sites. The local insertions display a preferential orientation toward the starting element. We investigated the mechanism of the P-element local transposition by isolating and characterizing local insertions in the male germline. We designed a genetic screen employing a marker gene that is carried in the P element and is dose sensitive. This dose effect allows isolation of flies containing newly transposed P elements in the presence of the starting element. A rapid molecular screen with PCR was used to identify 45 local insertions located within an ~40-kb genomic region on both sides of the starting element. Our system permits the isolation of the cluster progeny derived from a single insertion event, but none was isolated. The data suggest that local transposition occurs in the meiotic cell cycle. Nearly all of the local insertions were located within the promoter regions of the genes that were active in the male germline cells, suggesting that local insertions target predominantly active promoters. Our analysis shows that local transposition of the P element is highly regulated, displaying a cell-type specificity and a target specificity.
Multiple Effects of Genetic Background on Variegated Transgene Expression in Mice
Authors: Opsahl Margaret L , McClenaghan Margaret , Springbett Anthea , Reid Sarah , Lathe Richard , Colman Alan , Whitelaw C Bruce A 
Published: April 2021

Abstract
BLG/7 transgenic mice express an ovine β-lactoglobulin transgene during lactation. Unusually, transgene expression levels in milk differ between siblings. This variable expression is due to variegated transgene expression in the mammary gland and is reminiscent of position-effect variegation. The BLG/7 line was created and maintained on a mixed CBA × C57BL/6 background. We have investigated the effect on transgene expression of backcrossing for 13 generations into these backgrounds. Variable transgene expression was observed in all populations examined, confirming that it is an inherent property of the transgene array at its site of integration. There were also strain-specific effects on transgene expression that appear to be independent of the inherent variegation. The transgene, compared to endogenous milk protein genes, is specifically susceptible to inbreeding depression. Outcrossing restored transgene expression levels to that of the parental population; thus suppression was not inherited. Finally, no generation-dependent decrease in mean expression levels was observed in the parental population. Thus, although the BLG/7 transgene is expressed in a variegated manner, there was no generation-associated accumulated silencing of transgene expression.
Crossover Interference in the Mouse
Authors: Broman Karl W , Rowe Lucy B , Churchill Gary A , Paigen Ken 
Published: April 2021

AbstractWe present an analysis of crossover interference in the mouse genome, on the basis of high-density genotype data from two reciprocal interspecific backcrosses, comprising 188 meioses. Overwhelming evidence was found for strong positive crossover interference with average strength greater than that implied by the Carter-Falconer map function. There was some evidence for interchromosomal variation in the level of interference, with smaller chromosomes exhibiting stronger interference. We further compared the observed numbers of crossovers to previous cytological observations on the numbers of chiasmata and evaluated evidence for the obligate chiasma hypothesis.
The Colinearity of the Sh2/A1 Orthologous Region in Rice, Sorghum and Maize Is Interrupted and Accompanied by Genome Expansion in the Triticeae
Authors: Li Wanlong , Gill Bikram S 
Published: April 2021

Abstract
The Sh2/A1 orthologous region of maize, rice, and sorghum contains five genes in the order Sh2, X1, X2, and two A1 homologs in tandem duplication. The Sh2 and A1 homologs are separated by ~20 kb in rice and sorghum and by ~140 kb in maize. We analyzed the fate of the Sh2/A1 region in large-genome species of the Triticeae (wheat, barley, and rye). In the Triticeae, synteny in the Sh2/A1 region was interrupted by a break between the X1 and X2 genes. The A1 and X2 genes remained colinear in homeologous chromosomes as in other grasses. The Sh2 and X1 orthologs also remained colinear but were translocated to a nonhomeologous chromosome. Gene X1 was duplicated on two nonhomeologous chromosomes, and surprisingly, a paralog shared homology much higher than that of the orthologous copy to the X1 gene of other grasses. No tandem duplication of A1 homologs was detected but duplication of A1 on a nonhomeologous barley chromosome 6H was observed. Intergenic distances expanded greatly in wheat compared to rice. Wheat and barley diverged from each other 12 million years ago and both show similar changes in the Sh2/A1 region, suggesting that the break in colinearity as well as X1 duplications and genome expansion occurred in a common ancestor of the Triticeae species.
A Model-Based Method for Identifying Species Hybrids Using Multilocus Genetic Data
Authors: Anderson E C , Thompson E A 
Published: April 2021

AbstractWe present a statistical method for identifying species hybrids using data on multiple, unlinked markers. The method does not require that allele frequencies be known in the parental species nor that separate, pure samples of the parental species be available. The method is suitable for both markers with fixed allelic differences between the species and markers without fixed differences. The probability model used is one in which parentals and various classes of hybrids (F1's, F2's, and various backcrosses) form a mixture from which the sample is drawn. Using the framework of Bayesian model-based clustering allows us to compute, by Markov chain Monte Carlo, the posterior probability that each individual belongs to each of the distinct hybrid classes. We demonstrate the method on allozyme data from two species of hybridizing trout, as well as on two simulated data sets.
A Coalescent-Based Method for Detecting and Estimating Recombination From Gene Sequences
Authors: McVean Gil , Awadalla Philip , Fearnhead Paul 
Published: April 2021

Abstract
Determining the amount of recombination in the genealogical history of a sample of genes is important to both evolutionary biology and medical population genetics. However, recurrent mutation can produce patterns of genetic diversity similar to those generated by recombination and can bias estimates of the population recombination rate. Hudson (2001) has suggested an approximate-likelihood method based on coalescent theory to estimate the population recombination rate, 4Ner, under an infinite-sites model of sequence evolution. Here we extend the method to the estimation of the recombination rate in genomes, such as those of many viruses and bacteria, where the rate of recurrent mutation is high. In addition, we develop a powerful permutation-based method for detecting recombination that is both more powerful than other permutation-based methods and robust to misspecification of the model of sequence evolution. We apply the method to sequence data from viruses, bacteria, and human mitochondrial DNA. The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data.