journal
MENU ▼
Read by QxMD icon Read
search

Genome Research

journal
https://www.readbyqxmd.com/read/28522613/dehydration-stress-extends-mrna-3-untranslated-regions-with-noncoding-rna-functions-in-arabidopsis
#1
Hai-Xi Sun, Yan Li, Qi-Wen Niu, Nam-Hai Chua
The 3' untranslated regions (3' UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3' UTRs, but the involvement of this process in stress response has not yet been clarified. Here, we report that a subset of stress-related genes exhibits 3' UTR extensions of their mRNAs during dehydration stress. These extended 3' UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#2
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28522611/long-terminal-repeats-power-evolution-of-genes-and-gene-expression-programs-in-mammalian-oocytes-and-zygotes
#3
Vedran Franke, Sravya Ganesh, Rosa Karlic, Radek Malik, Josef Pasulka, Filip Horvat, Maja Kuzman, Helena Fulka, Marketa Cernohorska, Jana Urbanova, Eliska Svobodova, Jun Ma, Yutaka Suzuki, Fugaku Aoki, Richard M Schultz, Kristian Vlahovicek, Petr Svoboda
Retrotransposons are 'copy-and-paste' insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified >800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28512194/ancient-antagonism-between-celf-and-rbfox-families-tunes-mrna-splicing-outcomes
#4
Matthew R Gazzara, Michael J Mallory, Renat Roytenberg, John Lindberg, Anupama Jha, Kristen W Lynch, Yoseph Barash
Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic splicing code models, we find evidence of splicing antagonism between CELF2 and the RBFOX family of splicing factors...
May 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28512193/dna-replication-timing-during-development-anticipates-transcriptional-programs-and-parallels-enhancer-activation
#5
Joseph C Siefert, Constantin Georgescu, Jonathan D Wren, Amnon Koren, Christopher L Sansam
In dividing cells, DNA replication occurs in a precise order, but many questions remain regarding the mechanisms of replication timing establishment and regulation. We now have generated genome-wide, high-resolution replication timing maps throughout zebrafish development. Unexpectedly, in the rapid cell cycles preceding the midblastula transition, a defined timing program was present that predicted the initial wave of zygotic transcription. Replication timing was thereafter progressively and continuously remodeled across the majority of the genome, and epigenetic changes involved in enhancer activation frequently paralleled developmental changes in replication timing...
May 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28512192/human-mismatch-repair-system-balances-mutation-rates-between-strands-by-removing-more-mismatches-from-the-lagging-strand
#6
Maria Andrianova, Georgii Bazykin, Sergey Nikolaev, Vladimir Seplyarskiy
Mismatch repair (MMR) is one of the main systems maintaining fidelity of replication. Differences in correction of errors produced during replication of the leading and the lagging DNA strands were reported in yeast and in human cancers, but the causes of these differences remain unclear. Here, we analyze data on human cancers with somatic mutations in two of the major DNA polymerases, delta and epsilon, that replicate the genome. We show that these cancers demonstrate a substantial asymmetry of the mutations between the leading and the lagging strands...
May 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28487280/the-identification-and-functional-annotation-of-rna-structures-conserved-in-vertebrates
#7
Stefan E Seemann, Aashiq H Mirza, Claus Hansen, Claus H Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Elfar Torarinsson, Zizhen Yao, Christopher T Workman, Flemming Pociot, Henrik Nielsen, Niels Tommerup, Walter L Ruzzo, Jan Gorodkin
Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins (RBPs) or (ii) are transcribed in corresponding tissues...
May 9, 2017: Genome Research
https://www.readbyqxmd.com/read/28487279/single-cell-sequencing-deciphers-a-convergent-evolution-of-copy-number-alterations-from-primary-to-circulating-tumour-cells
#8
Yan Gao, Xiaohui Ni, Hua Guo, Zhe Su, Yi Ba, Zhongsheng Tong, Zhi Guo, Xin Yao, Xixi Chen, Jian Yin, Zhao Yan, Lin Guo, Ying Liu, Fan Bai, Xiaoliang Sunney Xie, Ning Zhang
Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here we studied genomic alterations in single primary tumour cells and circulating tumour cells (CTCs) from the same patient. Single-nucleotide variations (SNVs) in single cells from both samples occurred sporadically, whereas CNAs among primary tumour cells emerged accumulatively rather than abruptly, converging toward that of CTCs. Focal CNAs affecting MYC gene and PTEN gene were observed only in a minor portion of primary tumour cells but were present in all CTCs, suggesting a strong selection toward metastasis...
May 9, 2017: Genome Research
https://www.readbyqxmd.com/read/28483779/heritable-l1-retrotransposition-in-the-mouse-primordial-germline-and-early-embryo
#9
Sandra R Richardson, Patricia Gerdes, Daniel J Gerhardt, Francisco J Sanchez-Luque, Gabriela-Oana Bodea, Martin Munoz-Lopez, J Samuel Jesuadian, Marie-Jeanne H C Kempen, Patricia E Carreira, Jeffrey A Jeddeloh, Jose L Garcia-Perez, Haig H Kazazian, Adam D Ewing, Geoffrey J Faulkner
LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per 8 births...
May 8, 2017: Genome Research
https://www.readbyqxmd.com/read/28465312/a-comparative-analysis-of-whole-genome-sequencing-of-oesophageal-adenocarcinoma-pre-and-post-chemotherapy
#10
Ayesha Noorani, Jan Bornschein, Andy G Lynch, Maria Secrier, Achilleas Achilleos, Matthew Eldridge, Lawrence Bower, Jamie M J Weaver, Jason Crawte, Chin-Ann Ong, Nicholas Shannon, Shona MacRae, Nicola Grehan, Barbara Nutzinger, Maria O'Donovan, Richard Hardwick, Simon Tavaré, Rebecca C Fitzgerald, Rachael Fels Elliott, Paul A W Edwards, Xiaodun Li, Hamza Chettouh, Gianmarco Contini, Eleanor Gregson, Sebastian Zeki, Laura Smith, Zarah Abdullahi, Rachel de la Rue, Ahmad Miremadi, Shalini Malhotra, Mike L Smith, Jim Davies, Charles Crichton, Nick Carroll, Peter Safranek, Andrew Hindmarsh, Vijayendran Sujendran, Richard Turkington, Stephen J Hayes, Yeng Ang, Shaun R Preston, Sarah Oakes, Izhar Bagwan, Vicki Save, Richard J E Skipworth, Ted R Hupp, J Robert O'Neill, Olga Tucker, Andrew Beggs, Philippe Taniere, Timothy J Underwood, Fergus Noble, Jack Owsley, Hugh Barr, Neil Shepherd, Oliver Old, Jesper Lagergren, James Gossage, Andrew Davies, Fuju Chang, Janine Zylstra, Grant Sanders, Richard Berrisford, Catherine Harden, David Bunting, Mike Lewis, Ed Cheong, Bhaskar Kumar, Simon L Parsons, Irshad Soomro, Philip Kaye, Laurence Lovat, Rehan Haidry, Victor Eneh, Laszlo Igali, Michael Scott, Shamila Sothi, Sari Suortamo, Suzy Lishman
The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status...
May 2, 2017: Genome Research
https://www.readbyqxmd.com/read/28442558/gene-flow-ancient-polymorphism-and-ecological-adaptation-shape-the-genomic-landscape-of-divergence-among-darwin-s-finches
#11
Fan Han, Sangeet Lamichhaney, B Rosemary Grant, Peter R Grant, Leif Andersson, Matthew T Webster
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances...
April 25, 2017: Genome Research
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#12
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 Jean 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 data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 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
#13
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
#14
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/28420691/clustering-of-drosophila-housekeeping-promoters-facilitates-their-expression
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
journal
journal
32413
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"