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Genome Research

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https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#1
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28424353/constrained-release-of-lamina-associated-enhancers-and-genes-from-the-nuclear-envelope-during-t-cell-activation-facilitates-their-association-in-chromosome-compartments
#2
Michael I Robson, Jose I de Las Heras, Rafal Czapiewski, Aishwarya Sivakumar, Alastair R W Kerr, Eric Schirmer
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically-associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome re-organization at the nuclear periphery dominated by release of loci frequently important for T-cell function...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28424352/chromatin-module-inference-on-cellular-trajectories-identifies-key-transition-points-and-poised-epigenetic-states-in-diverse-developmental-processes
#3
Sushmita Roy, Rupa Sridharan
Changes in chromatin state play important roles in cell fate transitions. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Compared to existing approaches, CMINT can handle complex lineage topologies, capture higher quality clusters, and reliably detect chromatin transitions between cell types...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28420692/an-improved-assembly-and-annotation-of-the-allohexaploid-wheat-genome-identifies-complete-families-of-agronomic-genes-and-provides-genomic-evidence-for-chromosomal-translocations
#4
Bernardo J Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman, James Lipscombe, Tom Barker, Fu-Hao Lu, Neil McKenzie, Dina Raats, Ricardo H Ramirez-Gonzalez, Aurore Coince, Ned Peel, Lawrence Percival-Alwyn, Owen Duncan, Josua Trösch, Guotai Yu, Dan M Bolser, Guy Namaati, Arnaud Kerhornou, Manuel Spannagl, Heidrun Gundlach, Georg Haberer, Robert P Davey, Christine Fosker, Federica Di Palma, Andrew Phillips, A Harvey Millar, Paul J Kersey, Cristobal Uauy, Ksenia V Krasileva, David Swarbreck, Michael W Bevan, Matthew D Clark
Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28420691/clustering-of-drosophila-housekeeping-promoters-facilitates-their-expression
#5
Marc Corrales-Berjano, Aranzazu Rosado Diez, Ruggero Cortini, Joris van Arensbergen, Bas van Steensel, Guillaume J Filion
Housekeeping genes of animal genomes cluster in the same chromosomal regions. It has long been suggested that this organization contributes to their steady expression across all the tissues of the organism. Here we show that the activity of Drosophila housekeeping gene promoters depends on the expression of their neighbours. By measuring the expression of ~ 85,000 reporters integrated in Kc167 cells, we identified the best predictors of expression as chromosomal contacts with the promoters and terminators of active genes...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28420690/identification-of-protein-features-encoded-by-alternative-exons-using-exon-ontology
#6
Léon-Charles Tranchevent, Fabien Aubé, Louis Dulaurier, Clara Benoit-Pilven, Amandine Rey, Arnaud Poret, Emilie Chautard, Hussein Mortada, François-Olivier Desmet, Fatima Zahra Chakrama, Maira Alejandra Moreno-Garcia, Evelyne Goillot, Stéphane Janczarski, Franck Mortreux, Cyril F Bourgeois, Didier Auboeuf
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named Exon Ontology, based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28416533/capturing-in-vivo-rna-transcriptional-dynamics-from-the-malaria-parasite-plasmodium-falciparum
#7
Heather J Painter, Manuela Carrasquilla, Manuel Llinás
To capture the transcriptional dynamics within proliferating cells, methods to differentiate nascent transcription from pre-existing mRNAs are desired. One approach is to label newly synthesized mRNA transcripts in vivo through the incorporation of modified pyrimidines. However, the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine deaminase/uracil phosphoribosyltransferase (FCU)...
April 17, 2017: Genome Research
https://www.readbyqxmd.com/read/28411194/systematic-characterization-of-a-to-i-rna-editing-hotspots-in-micrornas-across-human-cancers
#8
Yumeng Wang, Xiaoyan Xu, Shuangxing Yu, Kang Jin Kang, Zhicheng Zhou, Leng Han, Yiu Huen Tsang, Jun Li, Hu Chen, Lingegowda S Mangala, Yuan Yuan, A Karina Eterovic, Yiling Lu, Anil K Sood, Kenneth L Scott, Gordon B Mills, Han Liang
RNA editing, a widespread posttranscriptional mechanism, has emerged as a new player in cancer biology. Recent studies have reported key roles for individual miRNA editing events, but a comprehensive picture of miRNA editing in human cancers remains largely unexplored. Here we systematically characterized the miRNA editing profiles of 8,595 samples across 20 cancer types from miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RNA editing hotspots. We independently validated 15 of them by perturbation experiments in several cancer cell lines...
April 14, 2017: Genome Research
https://www.readbyqxmd.com/read/28408382/extending-the-spectrum-of-dna-sequences-retrieved-from-ancient-bones-and-teeth
#9
Isabelle Glocke, Matthias Meyer
The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than approximately 35 base pairs (bp). Here we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction...
April 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28404620/accumulation-of-rna-on-chromatin-disrupts-heterochromatic-silencing
#10
Cornelia Brönner, Luca Salvi, Manuel Zocco, Ilaria Ugolini, Mario Halic
Long non-coding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe, that heterochromatin is lost at transcribed regions in absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA:RNA hybrids and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing...
April 12, 2017: Genome Research
https://www.readbyqxmd.com/read/28400425/the-logic-of-transcriptional-regulator-recruitment-architecture-at-cis-regulatory-modules-controlling-liver-functions
#11
Julie Dubois-Chevalier, Vanessa Dubois, Hélène Dehondt, Parisa Mazrooei, Claire Mazuy, Aurélien A Sérandour, Céline Gheeraert, Guillaume Penderia, Eric Baugé, Bruno Derudas, Nathalie Hennuyer, Réjane Paumelle, Guillemette Marot, Jason S Carroll, Mathieu Lupien, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute
Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TR). However, how recruitment of a myriad of TR is orchestrated at cis-regulatory modules (CRM) to account for co-regulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRM involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRM), which consist of subsets of preferentially and co-ordinately co-recruited TR, assemble into hierarchical combinations at hepatic CRM...
April 11, 2017: Genome Research
https://www.readbyqxmd.com/read/28400424/increased-taxon-sampling-reveals-thousands-of-hidden-orthologs-in-flatworms
#12
Jose M Martin-Duran, Joseph F Ryan, Bruno Vellutini, Kevin Pang, Andreas Hejnol
Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages - mistakenly considered new genes - but actually representing rapidly evolving orthologs or undetected paralogs...
April 11, 2017: Genome Research
https://www.readbyqxmd.com/read/28396522/de-novo-assembly-of-viral-quasispecies-using-overlap-graphs
#13
Jasmijn A Baaijens, Amal Zine El Aabidine, Eric Rivals, Alexander Schönhuth
A viral quasispecies, the ensemble of viral strains populating an infected person, can be highly diverse. For optimal assessment of virulence, pathogenesis, and therapy selection, determining the haplotypes of the individual strains can play a key role. As many viruses are subject to high mutation and recombination rates, high-quality reference genomes are often not available at the time of a new disease outbreak. We present SAVAGE, a computational tool for reconstructing individual haplotypes of intra-host virus strains without the need for a high-quality reference genome...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28396521/evaluation-of-grch38-and-de-novo-haploid-genome-assemblies-demonstrates-the-enduring-quality-of-the-reference-assembly
#14
Valerie A Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul A Kitts, Terence D Murphy, Kim D Pruitt, Françoise Thibaud-Nissen, Derek Albracht, Robert S Fulton, Milinn Kremitzki, Vincent Magrini, Chris Markovic, Sean McGrath, Karyn Meltz Steinberg, Kate Auger, William Chow, Joanna Collins, Glenn Harden, Timothy Hubbard, Sarah Pelan, Jared T Simpson, Glen Threadgold, James Torrance, Jonathan M Wood, Laura Clarke, Sergey Koren, Matthew Boitano, Paul Peluso, Heng Li, Chen-Shan Chin, Adam M Phillippy, Richard Durbin, Richard K Wilson, Paul Flicek, Evan E Eichler, Deanna M Church
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28396520/cytosine-modifications-modulate-the-chromatin-architecture-of-transcriptional-enhancers
#15
Elise A Mahé, Thierry Madigou, Aurélien A Sérandour, Maud Bizot, Stéphane Avner, Frédéric Chalmel, Gaëlle Palierne, Raphaël Métivier, Gilles Salbert
Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten Eleven Translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28396519/high-confidence-coding-and-noncoding-transcriptome-maps
#16
Bo-Hyun You, Sang-Ho Yoon, Jin-Wu Nam
The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps...
April 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28385713/genome-wide-top2a-dna-cleavage-is-biased-towards-translocated-and-highly-transcribed-loci
#17
Xiang Yu, James W Davenport, Karen A Urtishak, Marie L Carillo, Sager J Gosai, Christos P Kolaris, Jo Ann W Byl, Eric F Rappaport, Neil Osheroff, Brian D Gregory, Carolyn Ann Felix
Type II topoisomerases orchestrate proper DNA topology and they are the targets of anticancer drugs that cause treatment-related leukemias with balanced translocations. Here, we develop a high-throughput sequencing technology to define TOP2 cleavage sites at single base precision and use the technology to characterize TOP2A cleavage genome-wide in the human K562 leukemia cell line. We find that TOP2A cleavage has functionally conserved local sequence preferences, occurs in cleavage cluster regions (CCRs) and is enriched in introns and lincRNA loci...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28385712/asian-wild-rice-is-a-hybrid-swarm-with-extensive-gene-flow-and-feralization-from-domesticated-rice
#18
Hongru Wang, Filipe G Vieira, Jacob E Crawford, Chengcai Chu, Rasmus Nielsen
The domestication history of rice remains controversial with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 446 wild rice accessions...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28385711/microbiota-regulate-intestinal-epithelial-gene-expression-by-suppressing-the-transcription-factor-hepatocyte-nuclear-factor-4-alpha
#19
James M Davison, Colin R Lickwar, Lingyun Song, Ghislain Breton, Gregory E Crawford, John F Rawls
Microbiota influence diverse aspects of intestinal physiology and disease in part by controlling tissue-specific transcription of host genes. However, host genomic mechanisms mediating microbial control of intestinal gene expression are poorly understood. Hepatocyte nuclear factor 4 (HNF4) is the most ancient family of nuclear receptor transcription factors with important roles in human metabolic and inflammatory bowel diseases, but a role in host response to microbes is unknown. Using an unbiased screening strategy, we found that zebrafish Hnf4a specifically binds and activates a microbiota-suppressed intestinal epithelial transcriptional enhancer...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28385710/non-random-domain-organization-of-the-arabidopsis-genome-at-the-nuclear-periphery
#20
Xiuli Bi, Yingjuan Cheng, Bo Hu, Xiaoli Ma, Rui Wu, Jiawei Wang, Chang Liu
The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the non-random positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants...
April 6, 2017: Genome Research
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