Genome Biology最新文献

{"title":"A novel cause for primordial dwarfism revealed: defective tRNA modification.","authors":"Liudmila Filonava,&nbsp;Adrian Gabriel Torres,&nbsp;Lluis Ribas de Pouplana","doi":"10.1186/s13059-015-0786-y","DOIUrl":"https://doi.org/10.1186/s13059-015-0786-y","url":null,"abstract":"<p><p>A mutation in the WDR4 gene, coding for a tRNA-modifying enzyme, leads to reduced levels of guanosine methylation in tRNA in patients with primordial dwarfism.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"216"},"PeriodicalIF":12.3,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0786-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34054056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment.","authors":"Zheya Sheng,&nbsp;Mats E Pettersson,&nbsp;Christa F Honaker,&nbsp;Paul B Siegel,&nbsp;Örjan Carlborg","doi":"10.1186/s13059-015-0785-z","DOIUrl":"https://doi.org/10.1186/s13059-015-0785-z","url":null,"abstract":"<p><strong>Background: </strong>Artificial selection provides a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions where allele-frequencies have diverged during selection. To avoid false positive signatures of selection, it is necessary to show that a sweep affects a selected trait before it can be considered adaptive. Here, we confirm candidate, genome-wide distributed selective sweeps originating from the standing genetic variation in a long-term selection experiment on high and low body weight of chickens.</p><p><strong>Results: </strong>Using an intercross between the two divergent chicken lines, 16 adaptive selective sweeps were confirmed based on their association with the body weight at 56 days of age. Although individual additive effects were small, the fixation for alternative alleles across the loci contributed at least 40 % of the phenotypic difference for the selected trait between these lines. The sweeps contributed about half of the additive genetic variance present within and between the lines after 40 generations of selection, corresponding to a considerable portion of the additive genetic variance of the base population.</p><p><strong>Conclusions: </strong>Long-term, single-trait, bi-directional selection in the Virginia chicken lines has resulted in a gradual response to selection for extreme phenotypes without a drastic reduction in the genetic variation. We find that fixation of several standing genetic variants across a highly polygenic genetic architecture made a considerable contribution to long-term selection response. This provides new fundamental insights into the dynamics of standing genetic variation during long-term selection and adaptation.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"219"},"PeriodicalIF":12.3,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0785-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34062926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harvesting rice's dispensable genome.","authors":"Rod A Wing","doi":"10.1186/s13059-015-0787-x","DOIUrl":"https://doi.org/10.1186/s13059-015-0787-x","url":null,"abstract":"<p><p>A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome assemblies.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"217"},"PeriodicalIF":12.3,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0787-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34224525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New genes drive the evolution of gene interaction networks in the human and mouse genomes.","authors":"Wenyu Zhang,&nbsp;Patrick Landback,&nbsp;Andrea R Gschwend,&nbsp;Bairong Shen,&nbsp;Manyuan Long","doi":"10.1186/s13059-015-0772-4","DOIUrl":"https://doi.org/10.1186/s13059-015-0772-4","url":null,"abstract":"<p><strong>Background: </strong>The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. The mechanisms by which new genes are integrated into ancestral networks, and their evolutionary significance, are yet to be characterized. Herein, we present a study investigating the rates and patterns of new gene-driven evolution of GGI networks in the human and mouse genomes.</p><p><strong>Results: </strong>We examine the network topological and functional evolution of new genes that originated at various stages in the human and mouse lineages by constructing and analyzing three different GGI datasets. We find a large number of new genes integrated into GGI networks throughout vertebrate evolution. These genes experienced a gradual integration process into GGI networks, starting on the network periphery and gradually becoming highly connected hubs, and acquiring pleiotropic and essential functions. We identify a few human lineage-specific hub genes that have evolved brain development-related functions. Finally, we explore the possible underlying mechanisms driving the GGI network evolution and the observed patterns of new gene integration process.</p><p><strong>Conclusions: </strong>Our results unveil a remarkable network topological integration process of new genes: over 5000 new genes were integrated into the ancestral GGI networks of human and mouse; new genes gradually acquire increasing number of gene partners; some human-specific genes evolved into hub structure with critical phenotypic effects. Our data cast new conceptual insights into the evolution of genetic networks.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"202"},"PeriodicalIF":12.3,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0772-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34219704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determining exon connectivity in complex mRNAs by nanopore sequencing.","authors":"Mohan T Bolisetty,&nbsp;Gopinath Rajadinakaran,&nbsp;Brenton R Graveley","doi":"10.1186/s13059-015-0777-z","DOIUrl":"https://doi.org/10.1186/s13059-015-0777-z","url":null,"abstract":"<p><p>Short-read high-throughput RNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maximum read length. Here, we use the Oxford Nanopore MinION sequencer to identify 7,899 'full-length' isoforms expressed from four Drosophila genes, Dscam1, MRP, Mhc, and Rdl. These results demonstrate that nanopore sequencing can be used to deconvolute individual isoforms and that it has the potential to be a powerful method for comprehensive transcriptome characterization.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"204"},"PeriodicalIF":12.3,"publicationDate":"2015-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0777-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34115148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome.","authors":"Da-Hai Yu,&nbsp;Manasi Gadkari,&nbsp;Quan Zhou,&nbsp;Shiyan Yu,&nbsp;Nan Gao,&nbsp;Yongtao Guan,&nbsp;Deborah Schady,&nbsp;Tony N Roshan,&nbsp;Miao-Hsueh Chen,&nbsp;Eleonora Laritsky,&nbsp;Zhongqi Ge,&nbsp;Hui Wang,&nbsp;Rui Chen,&nbsp;Caroline Westwater,&nbsp;Lynn Bry,&nbsp;Robert A Waterland,&nbsp;Chelsea Moriarty,&nbsp;Cindy Hwang,&nbsp;Alton G Swennes,&nbsp;Sean R Moore,&nbsp;Lanlan Shen","doi":"10.1186/s13059-015-0763-5","DOIUrl":"https://doi.org/10.1186/s13059-015-0763-5","url":null,"abstract":"<p><strong>Background: </strong>DNA methylation is an epigenetic mechanism central to development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited.</p><p><strong>Results: </strong>We use whole genome bisulfite sequencing, and find that differentiation of mouse colonic intestinal stem cells to intestinal epithelium is not associated with major changes in DNA methylation. However, we detect extensive dynamic epigenetic changes in intestinal stem cells and their progeny during the suckling period, suggesting postnatal epigenetic development in this stem cell population. We find that postnatal DNA methylation increases at 3' CpG islands (CGIs) correlate with transcriptional activation of glycosylation genes responsible for intestinal maturation. To directly test whether 3' CGI methylation regulates transcription, we conditionally disrupted two major DNA methyltransferases, Dnmt1 or Dnmt3a, in fetal and adult intestine. Deficiency of Dnmt1 causes severe intestinal abnormalities in neonates and disrupts crypt homeostasis in adults, whereas Dnmt3a loss was compatible with intestinal development. These studies reveal that 3' CGI methylation is functionally involved in the regulation of transcriptional activation in vivo, and that Dnmt1 is a critical regulator of postnatal epigenetic changes in intestinal stem cells. Finally, we show that postnatal 3' CGI methylation and associated gene activation in intestinal epithelial cells are significantly altered by germ-free conditions.</p><p><strong>Conclusions: </strong>Our results demonstrate that the suckling period is critical for epigenetic development of intestinal stem cells, with potential important implications for lifelong gut health, and that the gut microbiome guides and/or facilitates these postnatal epigenetic processes.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"211"},"PeriodicalIF":12.3,"publicationDate":"2015-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0763-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34115131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.","authors":"A Rasim Barutcu,&nbsp;Bryan R Lajoie,&nbsp;Rachel P McCord,&nbsp;Coralee E Tye,&nbsp;Deli Hong,&nbsp;Terri L Messier,&nbsp;Gillian Browne,&nbsp;Andre J van Wijnen,&nbsp;Jane B Lian,&nbsp;Janet L Stein,&nbsp;Job Dekker,&nbsp;Anthony N Imbalzano,&nbsp;Gary S Stein","doi":"10.1186/s13059-015-0768-0","DOIUrl":"https://doi.org/10.1186/s13059-015-0768-0","url":null,"abstract":"<p><strong>Background: </strong>Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines.</p><p><strong>Results: </strong>Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16-22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16-22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells.</p><p><strong>Conclusions: </strong>We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"214"},"PeriodicalIF":12.3,"publicationDate":"2015-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0768-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34111586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells.","authors":"Anna Mattout,&nbsp;Yair Aaronson,&nbsp;Badi Sri Sailaja,&nbsp;Edupuganti V Raghu Ram,&nbsp;Arigela Harikumar,&nbsp;Jan-Philipp Mallm,&nbsp;Kae Hwan Sim,&nbsp;Malka Nissim-Rafinia,&nbsp;Emmanuelle Supper,&nbsp;Prim B Singh,&nbsp;Siu Kwan Sze,&nbsp;Susan M Gasser,&nbsp;Karsten Rippe,&nbsp;Eran Meshorer","doi":"10.1186/s13059-015-0760-8","DOIUrl":"https://doi.org/10.1186/s13059-015-0760-8","url":null,"abstract":"<p><strong>Background: </strong>Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown.</p><p><strong>Results: </strong>Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. In pluripotent and differentiated cells HP1β is differentially localized and differentially associated with chromatin. Deletion of HP1β, but not HP1α, in ESCs provokes a loss of the morphological and proliferative characteristics of embryonic pluripotent cells, reduces expression of pluripotency factors and causes aberrant differentiation. However, in differentiated cells, loss of HP1β has the opposite effect, perturbing maintenance of the differentiation state and facilitating reprogramming to an induced pluripotent state. Microscopy, biochemical fractionation and chromatin immunoprecipitation reveal a diffuse nucleoplasmic distribution, weak association with chromatin and high expression levels for HP1β in ESCs. The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated cells, where it binds heterochromatic satellite repeats and chromocenters.</p><p><strong>Conclusions: </strong>We demonstrate an unexpected duality in the role of HP1β: it is essential in ESCs for maintaining pluripotency, while it is required for proper differentiation in differentiated cells. Thus, HP1β function both depends on, and regulates, the pluripotent state.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"213"},"PeriodicalIF":12.3,"publicationDate":"2015-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0760-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34111580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages.","authors":"Shruthi Sridhar Vembar,&nbsp;Cameron Ross Macpherson,&nbsp;Odile Sismeiro,&nbsp;Jean-Yves Coppée,&nbsp;Artur Scherf","doi":"10.1186/s13059-015-0771-5","DOIUrl":"https://doi.org/10.1186/s13059-015-0771-5","url":null,"abstract":"<p><strong>Background: </strong>Transcriptome-wide ribosome occupancy studies have suggested that during the intra-erythrocytic lifecycle of Plasmodium falciparum, select mRNAs are post-transcriptionally regulated. A subset of these encodes parasite virulence factors required for invading host erythrocytes, and are currently being developed as vaccine candidates. However, the molecular mechanisms that govern post-transcriptional regulation are currently unknown.</p><p><strong>Results: </strong>We explore the previously identified DNA/RNA-binding protein PfAlba1, which localizes to multiple foci in the cytoplasm of P. falciparum trophozoites. We establish that PfAlba1 is essential for asexual proliferation, and subsequently investigate parasites overexpressing epitope-tagged PfAlba1 to identify its RNA targets and effects on mRNA homeostasis and translational regulation. Using deep sequencing of affinity-purified PfAlba1-associated RNAs, we identify 1193 transcripts that directly bind to PfAlba1 in trophozoites. For 105 such transcripts, 43 % of which are uncharacterized and 13 % of which encode erythrocyte invasion components, the steady state levels significantly change at this stage, evidencing a role for PfAlba1 in maintaining mRNA homeostasis. Additionally, we discover that binding of PfAlba1 to four erythrocyte invasion mRNAs, Rap1, RhopH3, CDPK1, and AMA1, is linked to translation repression in trophozoites whereas release of these mRNAs from a PfAlba1 complex in mature stages correlates with protein synthesis.</p><p><strong>Conclusions: </strong>We show that PfAlba1 binds to a sub-population of asexual stage mRNAs and fine-tunes the timing of translation. This mode of post-transcriptional regulation may be especially important for P. falciparum erythrocyte invasion components that have to be assembled into apical secretory organelles in a highly time-dependent manner towards the end of the parasite's asexual lifecycle.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"212"},"PeriodicalIF":12.3,"publicationDate":"2015-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0771-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34214399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism.","authors":"Ranad Shaheen,&nbsp;Ghada M H Abdel-Salam,&nbsp;Michael P Guy,&nbsp;Rana Alomar,&nbsp;Mohamed S Abdel-Hamid,&nbsp;Hanan H Afifi,&nbsp;Samira I Ismail,&nbsp;Bayoumi A Emam,&nbsp;Eric M Phizicky,&nbsp;Fowzan S Alkuraya","doi":"10.1186/s13059-015-0779-x","DOIUrl":"https://doi.org/10.1186/s13059-015-0779-x","url":null,"abstract":"<p><strong>Background: </strong>Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity.</p><p><strong>Results: </strong>Two presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m(7)G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m(7)G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m(7)G46 modification causes a growth deficiency phenotype in yeast.</p><p><strong>Conclusion: </strong>Our study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"210"},"PeriodicalIF":12.3,"publicationDate":"2015-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0779-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34111599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}