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Genome Biology

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https://www.readbyqxmd.com/read/28302177/cepip-context-dependent-epigenomic-weighting-for-prioritization-of-regulatory-variants-and-disease-associated-genes
#1
Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S Liu, Junwen Wang
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential. We present cepip, a joint likelihood framework, for estimating a variant's regulatory probability in a context-dependent manner. Our method exhibits significant GWAS signal enrichment and is superior to existing cell type-specific methods...
March 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28298237/irfinder-assessing-the-impact-of-intron-retention-on-mammalian-gene-expression
#2
Robert Middleton, Dadi Gao, Aubin Thomas, Babita Singh, Amy Au, Justin J-L Wong, Alexandra Bomane, Bertrand Cosson, Eduardo Eyras, John E J Rasko, William Ritchie
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene...
March 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28283040/functional-variation-in-allelic-methylomes-underscores-a-strong-genetic-contribution-and-reveals-novel-epigenetic-alterations-in-the-human-epigenome
#3
Warren A Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Marie-Michelle Simon, Elodie Boulier, Adriana Redensek, Stephen Watt, Avik Datta, Laura Clarke, Paul Flicek, Daniel Mead, Dirk S Paul, Stephan Beck, Guillaume Bourque, Mark Lathrop, André Tchernof, Marie-Claude Vohl, Florence Demenais, Isabelle Pin, Kate Downes, Hendrick G Stunnenberg, Nicole Soranzo, Tomi Pastinen, Elin Grundberg
BACKGROUND: The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples. RESULTS: We describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution...
March 10, 2017: Genome Biology
https://www.readbyqxmd.com/read/28279197/the-birth-of-a-human-specific-neural-gene-by-incomplete-duplication-and-gene-fusion
#4
Max L Dougherty, Xander Nuttle, Osnat Penn, Bradley J Nelson, John Huddleston, Carl Baker, Lana Harshman, Michael H Duyzend, Mario Ventura, Francesca Antonacci, Richard Sandstrom, Megan Y Dennis, Evan E Eichler
BACKGROUND: Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing...
March 9, 2017: Genome Biology
https://www.readbyqxmd.com/read/28274275/whole-exome-sequencing-coupled-with-unbiased-functional-analysis-reveals-new-hirschsprung-disease-genes
#5
Hongsheng Gui, Duco Schriemer, William W Cheng, Rajendra K Chauhan, Guillermo Antiňolo, Courtney Berrios, Marta Bleda, Alice S Brooks, Rutger W W Brouwer, Alan J Burns, Stacey S Cherny, Joaquin Dopazo, Bart J L Eggen, Paola Griseri, Binta Jalloh, Thuy-Linh Le, Vincent C H Lui, Berta Luzón-Toro, Ivana Matera, Elly S W Ngan, Anna Pelet, Macarena Ruiz-Ferrer, Pak C Sham, Iain T Shepherd, Man-Ting So, Yunia Sribudiani, Clara S M Tang, Mirjam C G N van den Hout, Herma C van der Linde, Tjakko J van Ham, Wilfred F J van IJcken, Joke B G M Verheij, Jeanne Amiel, Salud Borrego, Isabella Ceccherini, Aravinda Chakravarti, Stanislas Lyonnet, Paul K H Tam, Maria-Mercè Garcia-Barceló, Robert M W Hofstra
BACKGROUND: Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human...
March 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28270225/post-transcriptional-regulation-of-fruit-ripening-and-disease-resistance-in-tomato-by-the-vacuolar-protease-slvpe3
#6
Weihao Wang, Jianghua Cai, Peiwen Wang, Shiping Tian, Guozheng Qin
BACKGROUND: Proteases represent one of the most abundant classes of enzymes in eukaryotes and are known to play key roles in many biological processes in plants. However, little is known about their functions in fruit ripening and disease resistance, which are unique to flowering plants and required for seed maturation and dispersal. Elucidating the genetic mechanisms of fruit ripening and disease resistance is an important goal given the biological and dietary significance of fruit. RESULTS: Through expression profile analyses of genes encoding tomato (Solanum lycopersicum) cysteine proteases, we identify a number of genes whose expression increases during fruit ripening...
March 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/28260531/defining-the-diverse-spectrum-of-inversions-complex-structural-variation-and-chromothripsis-in-the-morbid-human%C3%A2-genome
#7
Ryan L Collins, Harrison Brand, Claire E Redin, Carrie Hanscom, Caroline Antolik, Matthew R Stone, Joseph T Glessner, Tamara Mason, Giulia Pregno, Naghmeh Dorrani, Giorgia Mandrile, Daniela Giachino, Danielle Perrin, Cole Walsh, Michelle Cipicchio, Maura Costello, Alexei Stortchevoi, Joon-Yong An, Benjamin B Currall, Catarina M Seabra, Ashok Ragavendran, Lauren Margolin, Julian A Martinez-Agosto, Diane Lucente, Brynn Levy, Stephan J Sanders, Ronald J Wapner, Fabiola Quintero-Rivera, Wigard Kloosterman, Michael E Talkowski
BACKGROUND: Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. RESULTS: We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution...
March 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28249593/ddclone-joint-statistical-inference-of-clonal-populations-from-single-cell-and-bulk-tumour-sequencing-data
#8
Sohrab Salehi, Adi Steif, Andrew Roth, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P Shah
Next-generation sequencing (NGS) of bulk tumour tissue can identify constituent cell populations in cancers and measure their abundance. This requires computational deconvolution of allelic counts from somatic mutations, which may be incapable of fully resolving the underlying population structure. Single cell sequencing (SCS) is a more direct method, although its replacement of NGS is impeded by technical noise and sampling limitations. We propose ddClone, which analytically integrates NGS and SCS data, leveraging their complementary attributes through joint statistical inference...
March 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28249590/erratum-to-tumor-immune-microenvironment-characterization-in-clear-cell-renal-cell-carcinoma-identifies-prognostic-and-immunotherapeutically-relevant-messenger-rna-signatures
#9
Yasin Şenbabaoğlu, Ron S Gejman, Andrew G Winer, Ming Liu, Eliezer M Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J Manley, Danny N Khalil, Samuel D Kaffenberger, Yingbei Chen, Ludmila Danilova, Martin H Voss, Jonathan A Coleman, Paul Russo, Victor E Reuter, Timothy A Chan, Emily H Cheng, David A Scheinberg, Ming O Li, Toni K Choueiri, James J Hsieh, Chris Sander, A Ari Hakimi
No abstract text is available yet for this article.
March 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28249587/single-cell-transcriptome-conservation-in-cryopreserved-cells-and-tissues
#10
Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego A Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos, Hadas Keren-Shaul, Simon Heath, Marta Gut, Ido Amit, Ivo Gut, Holger Heyn
A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps. We sequence single-cell transcriptomes from >1000 fresh and cryopreserved cells using 3'-end and full-length RNA preparation methods. Our results confirm that the conservation process did not alter transcriptional profiles...
March 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28245842/knocking-out-consumer-concerns-and-regulator-s-rules-efficient-use-of-crispr-cas-ribonucleoprotein-complexes-for-genome-editing-in-cereals
#11
Felix Wolter, Holger Puchta
Selection-free genome editing using Cas9 ribonucleoprotein embryo bombardment has been achieved for maize and wheat. This is a breakthrough that should make new breeding technologies more acceptable for worldwide use.
February 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28241876/erratum-to-methylome-evolution-in-plants
#12
Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier, Frank Johannes
No abstract text is available yet for this article.
February 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28241850/accurate-and-equitable-medical-genomic-analysis-requires-an-understanding-of-demography-and-its-influence-on-sample-size-and-ratio
#13
Michael D Kessler, Timothy D O'Connor
In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggregation Consortium (ExAC) data to show that sample size and ratio interact to influence the number of these singletons identified in a cohort. These interactions are different across ancestries and can lead to the same number of identified singletons in both Europeans and non-Europeans without an equal number of samples...
February 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28241843/erratum-to-retrozymes-are-a-unique-family-of-non-autonomous-retrotransposons-with-hammerhead-ribozymes-that-propagate-in-plants-through-circular-rnas
#14
Amelia Cervera, Denisse Urbina, Marcos de la Peña
No abstract text is available yet for this article.
February 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28235418/baalchip-bayesian-analysis-of-allele-specific-transcription-factor-binding-in-cancer-genomes
#15
Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A J Ponder, Kerstin B Meyer, Florian Markowetz
Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts...
February 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28222791/epig-statistical-inference-and-profiling-of-dna-methylation-from-whole-genome-bisulfite-sequencing-data
#16
Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen, Carsten Wiuf
The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data...
February 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28219439/rnas-competing-for-micrornas-mutually-influence-their-fluctuations-in-a-highly-non-linear-microrna-dependent-manner-in-single-cells
#17
Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani, Riccardo Zecchina
BACKGROUND: Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other's expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are coupled through miRNAs. This may result in striking effects on a broad range of cellular processes, such as cell differentiation and proliferation...
February 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28219438/genomic-insights-into-divergence-and-dual-domestication-of-cultivated-allotetraploid-cottons
#18
Lei Fang, Hao Gong, Yan Hu, Chunxiao Liu, Baoliang Zhou, Tao Huang, Yangkun Wang, Shuqi Chen, David D Fang, Xiongming Du, Hong Chen, Jiedan Chen, Sen Wang, Qiong Wang, Qun Wan, Bingliang Liu, Mengqiao Pan, Lijing Chang, Huaitong Wu, Gaofu Mei, Dan Xiang, Xinghe Li, Caiping Cai, Xiefei Zhu, Z Jeffrey Chen, Bin Han, Xiaoya Chen, Wangzhen Guo, Tianzhen Zhang, Xuehui Huang
BACKGROUND: Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown. RESULTS: We resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species...
February 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28219395/efficient-precise-knockin-with-a-double-cut-hdr-donor-after-crispr-cas9-mediated-double-stranded-dna-cleavage
#19
Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng, Xiao-Bing Zhang
BACKGROUND: Precise genome editing via homology-directed repair (HDR) after double-stranded DNA (dsDNA) cleavage facilitates functional genomic research and holds promise for gene therapy. However, HDR efficiency remains low in some cell types, including some of great research and clinical interest, such as human induced pluripotent stem cells (iPSCs). RESULTS: Here, we show that a double cut HDR donor, which is flanked by single guide RNA (sgRNA)-PAM sequences and is released after CRISPR/Cas9 cleavage, increases HDR efficiency by twofold to fivefold relative to circular plasmid donors at one genomic locus in 293 T cells and two distinct genomic loci in iPSCs...
February 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28219390/the-genome-landscape-of-indigenous-african-cattle
#20
Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Salim Bashir, Boubacar Diallo, Morris Agaba, Kwondo Kim, Woori Kwak, Samsun Sung, Minseok Seo, Hyeonsoo Jeong, Taehyung Kwon, Mengistie Taye, Ki-Duk Song, Dajeong Lim, Seoae Cho, Hyun-Jeong Lee, Duhak Yoon, Sung Jong Oh, Stephen Kemp, Hak-Kyo Lee, Heebal Kim
BACKGROUND: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. RESULTS: We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds...
February 20, 2017: Genome Biology
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