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Genome Research

Xin Li, Yun Liu, Tal Salz, Kasper D Hansen, Andrew P Feinberg
DNA methylation at the 5-postion of cytosine (5mC) is an epigenetic modification that regulates gene expression and cellular plasticity in development and disease. The ten-eleven translocation (TET) gene family oxidizes 5mC to 5-hydroxymethylcytosine (5hmC), providing an active mechanism for DNA demethylation, and may also provide its own regulatory function. Here we applied oxidative bisulfite sequencing to generate whole-genome DNA methylation and hydroxymethylation maps at single-base resolution in paired human liver and lung normal and cancer...
October 13, 2016: Genome Research
Haihui Fu, Dewei Yang, Wenyue Su, Liuyin Ma, Yingjia Shen, Guoli Ji, Xingfu Ye, Xiaohui Wu, Qingshun Quinn Li
Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3'-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the Poly(A) Tag Sequencing (PAT-Seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression...
October 12, 2016: Genome Research
Sophia David, Christophe Rusniok, Massimo Mentasti, Laura Gomez-Valero, Simon R Harris, Pierre Lechat, John Lees, Christophe Ginevra, Philippe Glaser, Laurence Ma, Christiane Bouchier, Anthony Underwood, Sophie Jarraud, Timothy G Harrison, Julian Parkhill, Carmen Buchrieser
Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from >2000 currently described, cause nearly half of disease cases in North West Europe. Here we report the sequence and analyses of 364 L. pneumophila genomes including 337 from the five disease-associated STs and 27 representative of the species diversity. Phylogenetic analyses revealed that the five STs have independent origins within a highly diverse species. The number of de novo mutations is extremely low with maximum pairwise single nucleotide polymorphisms (SNPs) ranging from 19 (ST47) to 127 (ST1), which suggests emergences within the last century...
September 23, 2016: Genome Research
Sara González, Alicia García, Enrique Vázquez, Rebeca Serrano, Mar Sánchez, Luis Quintales, Francisco Antequera
In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae...
September 23, 2016: Genome Research
Marco-Antonio Mendoza-Parra, Valeriya Malysheva, Mohamed Ashick Mohamed Saleem, Michele Lieb, Aurelie Godel, Hinrich Gronemeyer
Cell lineages, which shape the body architecture and specify cell functions, derive from the integration of a plethora of cell intrinsic and extrinsic signals. These signals trigger a multiplicity of decisions at several levels to modulate the activity of dynamic gene regulatory networks (GRNs), which ensure both general and cell-specific functions within a given lineage, thereby establishing cell fates. Significant knowledge about these events and the involved key drivers comes from homogeneous cell differentiation models...
September 20, 2016: Genome Research
David Porubsky, Ashley D Sanders, Niek van Wietmarschen, Ester Falconer, Mark Hills, Diana C J Spierings, Marianna R Bevova, Victor Guryev, Peter Michael Lansdorp
Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype for HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference...
September 19, 2016: Genome Research
Mingzhou Li, Lei Chen, Shilin Tian, Yu Lin, Qianzi Tang, Xuming Zhou, Diyan Li, Carol Kl Yeung, Tiandong Che, Long Jin, Yuhua Fu, Jideng Ma, Xun Wang, Anan Jiang, Jing Lan, Qi Pan, Yingkai Liu, Zonggang Luo, Zongyi Guo, Haifeng Liu, Li Zhu, Surong Shuai, Guoqing Tang, Jiugang Zhao, Yanzhi Jiang, Lin Bai, Shunhua Zhang, Miaomiao Mai, Changchun Li, Dawei Wang, Yiren Gu, Guosong Wang, Hongfeng Lu, Yan Li, Haihao Zhu, Zongwen Li, Ming Li, Vadim N Gladyshev, Zhi Jiang, Shuhong Zhao, Jinyong Wang, Ruiqiang Li, Xuewei Li
Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs, structural variations, as well as 137...
September 19, 2016: Genome Research
Sujatha Jagannathan, Robert K Bradley
Genetic variants that disrupt protein-coding DNA are ubiquitous in the human population, with ~100 such loss-of-function variants per individual. While most loss-of-function variants are rare, a subset have risen to high frequency and occur in a homozygous state in healthy individuals. It is unknown why these common variants are well-tolerated, even though some affect essential genes implicated in Mendelian disease. Here, we combine genomic, proteomic, and biochemical data to demonstrate that many common nonsense variants do not ablate protein production from their host genes...
September 19, 2016: Genome Research
Isabel X Wang, Christopher Grunseich, Youree G Chung, Hojoong Kwak, Girish Ramrattan, Zhengwei Zhu, Vivian G Cheung
Alterations of RNA sequences and structures, such as those from editing and alternative splicing, result in two or more RNA transcripts from a DNA template. It was thought that in yeast, RNA editing only occurs in tRNAs. Here, we found that Saccharomyces cerevisiae have all 12 types of RNA-DNA sequence differences (RDDs) in the mRNA. We showed these sequence differences are propagated to proteins, as we identified peptides encoded by the RNA sequences in addition to those by the DNA sequences at RDD sites. RDDs are significantly enriched at regions with R-loops...
September 16, 2016: Genome Research
Petros Kolovos, Theodore Georgomanolis, Anna Koeferle, Joshua D Larkin, Lilija Brant, Miloš Nikolić, Eduardo G Gusmao, Anne Zirkel, Tobias A Knoch, Wilfred F van Ijcken, Peter R Cook, Ivan G Costa, Frank G Grosveld, Argyris Papantonis
Mammalian cells have developed intricate mechanisms to interpret, integrate, and respond to extracellular stimuli. For example, tumor necrosis factor (TNF) rapidly activates proinflammatory genes, but our understanding of how this occurs against the ongoing transcriptional program of the cell is far from complete. Here, we monitor the early phase of this cascade at high spatiotemporal resolution in TNF-stimulated human endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters...
September 15, 2016: Genome Research
Susanna Teppo, Saara Laukkanen, Thomas Liuksiala, Jessica Nordlund, Mikko Oittinen, Kaisa Teittinen, Toni Grönroos, Pascal St-Onge, Daniel Sinnett, Ann-Christine Syvänen, Matti Nykter, Keijo Viiri, Merja Heinäniemi, Olli Lohi
Approximately 20%-25% of childhood acute lymphoblastic leukemias carry the ETV6-RUNX1 (E/R) fusion gene, a fusion of two central hematopoietic transcription factors, ETV6 (TEL) and RUNX1 (AML1). Despite its prevalence, the exact genomic targets of E/R have remained elusive. We evaluated gene loci and enhancers targeted by E/R genome-wide in precursor B acute leukemia cells using global run-on sequencing (GRO-seq). We show that expression of the E/R fusion leads to widespread repression of RUNX1 motif-containing enhancers at its target gene loci...
September 12, 2016: Genome Research
Steven R Eichten, Tim Stuart, Akanksha Srivastava, Ryan Lister, Justin O Borevitz
DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines...
September 9, 2016: Genome Research
Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M Barr, Ruth Halaban, Ehud Shapiro
Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single cell sequencing, which is not scalable and could be biased by functional dependencies. Here we show an integrated biochemical-computational platform for generic single-cell lineage analysis that is retrospective, cost-effective and scalable. It consists of a biochemical-computational pipeline that inputs individual cells, produces targeted single-cell sequencing data and uses it to generate a lineage tree of the input cells...
August 24, 2016: Genome Research
Ashley D Sanders, Mark Hills, David Porubský, Victor Guryev, Ester Falconer, Peter M Lansdorp
Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively...
July 29, 2016: Genome Research
Arkarachai Fungtammasan, Erin Walsh, Francesca Chiaromonte, Kristin A Eckert, Kateryna D Makova
No abstract text is available yet for this article.
October 2016: Genome Research
Carole Charlier, Wanbo Li, Chad Harland, Mathew Littlejohn, Wouter Coppieters, Frances Creagh, Steve Davis, Tom Druet, Pierre Faux, François Guillaume, Latifa Karim, Mike Keehan, Naveen Kumar Kadri, Nico Tamma, Richard Spelman, Michel Georges
We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome...
October 2016: Genome Research
Kevin Roy, Jason Gabunilas, Abigail Gillespie, Duy Ngo, Guillaume F Chanfreau
RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for the production of stable noncoding RNAs and the control of pervasive transcription in Saccharomyces cerevisiae To uncover determinants of NNS termination, we mapped the 3'-ends of NNS-terminated transcripts genome-wide. We found that nucleosomes and specific DNA-binding proteins, including the general regulatory factors (GRFs) Reb1p, Rap1p, and Abf1p, and Pol III transcription factors enhance the efficiency of NNS termination by physically blocking Pol II progression...
October 2016: Genome Research
Max E Boeck, Chau Huynh, Lou Gevirtzman, Owen A Thompson, Guilin Wang, Dionna M Kasper, Valerie Reinke, LaDeana W Hillier, Robert H Waterston
We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post-embryonic stages across the life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period during which histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle...
October 2016: Genome Research
Kathy E Raven, Sandra Reuter, Rosy Reynolds, Hayley J Brodrick, Julie E Russell, M Estée Török, Julian Parkhill, Sharon J Peacock
Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree...
October 2016: Genome Research
K Melodi McSweeney, Ayal B Gussow, Shelton S Bradrick, Sarah A Dugger, Sahar Gelfman, Quanli Wang, Slavé Petrovski, Wayne N Frankel, Michael J Boland, David B Goldstein
Cultured neuronal networks monitored with microelectrode arrays (MEAs) have been used widely to evaluate pharmaceutical compounds for potential neurotoxic effects. A newer application of MEAs has been in the development of in vitro models of neurological disease. Here, we directly evaluated the utility of MEAs to recapitulate in vivo phenotypes of mature microRNA-128 (miR-128) deficiency, which causes fatal seizures in mice. We show that inhibition of miR-128 results in significantly increased neuronal activity in cultured neuronal networks derived from primary mouse cortical neurons...
October 2016: Genome Research
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