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Genome Biology

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https://www.readbyqxmd.com/read/28535802/n-blr-a-primate-specific-non-coding-transcript-leads-to-colorectal-cancer-invasion-and-migration
#1
Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M Clark, Hui Ling, Masayoshi Shimizu, Roxana S Redis, Maitri Y Shah, Xinna Zhang, Yoshinaga Okugawa, Eun Jung Jung, Aristotelis Tsirigos, Li Huang, Jana Ferdin, Roberta Gafà, Riccardo Spizzo, Milena S Nicoloso, Anurag N Paranjape, Maryam Shariati, Aida Tiron, Jen Jen Yeh, Raul Teruel-Montoya, Lianchun Xiao, Sonia A Melo, David Menter, Zhi-Qin Jiang, Elsa R Flores, Massimo Negrini, Ajay Goel, Menashe Bar-Eli, Sendurai A Mani, Chang Gong Liu, Gabriel Lopez-Berestein, Ioana Berindan-Neagoe, Manel Esteller, Scott Kopetz, Giovanni Lanza, George A Calin
BACKGROUND: Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that modulates the epithelial-to-mesenchymal transition, facilitates cell migration, and increases colorectal cancer invasion. RESULTS: We performed multivariate analyses of data from two independent cohorts of colorectal cancer patients and show that the abundance of N-BLR is associated with tumor stage, invasion potential, and overall patient survival...
May 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28535814/unreeling-the-chromatin-thread-a-genomic-perspective-on-organization-around-the-periphery-of-the-arabidopsis-nucleus
#2
Fredy Barneche, Celia Baroux
The first genome-wide examination of the chromatin landscape at the periphery of the plant cell nucleus reveals substantial enrichment of heterochromatin and Polycomb-based repressive chromatin.
May 23, 2017: Genome Biology
https://www.readbyqxmd.com/read/28535770/emerging-roles-of-chromatin-in-the-maintenance-of-genome-organization-and-function-in-plants
#3
REVIEW
Zaida Vergara, Crisanto Gutierrez
Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish boundaries between chromatin states and nuclear territories. Chromatin organization is crucial for genome replication, transcriptional silencing, and DNA repair and recombination. The replication machinery is relevant for the maintenance of chromatin states, influencing DNA replication origin specification and accessibility...
May 23, 2017: Genome Biology
https://www.readbyqxmd.com/read/28532420/going-beyond-genetics-to-discover-cancer-targets
#4
Gabriel J Sandoval, William C Hahn
Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.
May 22, 2017: Genome Biology
https://www.readbyqxmd.com/read/28521789/a-comparative-evaluation-of-genome-assembly-reconciliation-tools
#5
Hind Alhakami, Hamid Mirebrahim, Stefano Lonardi
BACKGROUND: The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation...
May 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28521766/the-histone-h3-variant-h3-3-regulates-gene-body-dna-methylation-in-arabidopsis-thaliana
#6
Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E Jacobsen, Frédéric Berger
BACKGROUND: Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enrichment profiles over gene bodies are correlated and both have a similar dependence on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. RESULTS: We engineered an H3.3 knockdown in Arabidopsis thaliana and observed transcription reduction that predominantly affects genes responsive to environmental cues...
May 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28511701/easi-crispr-a-robust-method-for-one-step-generation-of-mice-carrying-conditional-and-insertion-alleles-using-long-ssdna-donors-and-crispr-ribonucleoproteins
#7
Rolen M Quadros, Hiromi Miura, Donald W Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M Buckley, Parthasarathy Seshacharyulu, Surinder K Batra, Mark A Behlke, Sarah A Zeiner, Ashley M Jacobi, Yayoi Izu, Wallace B Thoreson, Lisa D Urness, Suzanne L Mansour, Masato Ohtsuka, Channabasavaiah B Gurumurthy
BACKGROUND: Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes. Transgenic mice generated by random genomic insertion approaches pose problems of unreliable expression, and thus there is a need for targeted-insertion models...
May 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/28506277/quantifying-the-mapping-precision-of-genome-wide-association-studies-using-whole-genome-sequencing-data
#8
Yang Wu, Zhili Zheng, Peter M Visscher, Jian Yang
BACKGROUND: Understanding the mapping precision of genome-wide association studies (GWAS), that is the physical distances between the top associated single-nucleotide polymorphisms (SNPs) and the causal variants, is essential to design fine-mapping experiments for complex traits and diseases. RESULTS: Using simulations based on whole-genome sequencing (WGS) data from 3642 unrelated individuals of European descent, we show that the association signals at rare causal variants (minor allele frequency ≤ 0...
May 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28499443/erratum-to-deepcpg-accurate-prediction-of-single-cell-dna-methylation-states-using-deep-learning
#9
Christof Angermueller, Heather J Lee, Wolf Reik, Oliver Stegle
No abstract text is available yet for this article.
May 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28499400/epiteome-simultaneous-detection-of-transposable-element-insertion-sites-and-their-dna-methylation-levels
#10
Josquin Daron, R Keith Slotkin
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads...
May 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28494787/missing-heritability-and-where-to-find-it
#11
Santhosh Girirajan
A report on the 11th Genomics of Rare Disease meeting held at the Wellcome Genome Campus, Hinxton, Cambridge, UK, 5-7 April, 2017.
May 11, 2017: Genome Biology
https://www.readbyqxmd.com/read/28490341/developmental-transitions-integrating-environmental-cues-with-hormonal-signaling-in-the-chromatin-landscape-in-plants
#12
REVIEW
Jun Xiao, Run Jin, Doris Wagner
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems...
May 10, 2017: Genome Biology
https://www.readbyqxmd.com/read/28486944/an-evolutionary-case-for-functional-gene-body-methylation-in-plants-and-animals
#13
Daniel Zilberman
Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation.
May 9, 2017: Genome Biology
https://www.readbyqxmd.com/read/28482897/challenges-and-emerging-directions-in-single-cell-analysis
#14
LETTER
Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guoping Fan, Guoji Guo, Rafael Irizarry, Peter Kharchenko, Junhyong Kim, Stuart Orkin, John Quackenbush, Assieh Saadatpour, Timm Schroeder, Ramesh Shivdasani, Itay Tirosh
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data...
May 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28482857/horizontal-gene-transfer-is-not-a-hallmark-of-the-human-genome
#15
Steven L Salzberg
Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).Please see related Research article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3.
May 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28476144/multi-omics-approaches-to-disease
#16
REVIEW
Yehudit Hasin, Marcus Seldin, Aldons Lusis
High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which gave rise to the field of "integrative genetics". Other omics technologies, such as proteomics and metabolomics, are now often incorporated into the everyday methodology of biological researchers. In this review, we provide an overview of such omics technologies and focus on methods for their integration across multiple omics layers...
May 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28468672/inferring-the-physical-properties-of-yeast-chromatin-through-bayesian-analysis-of-whole-nucleus-simulations
#17
Jean-Michel Arbona, Sébastien Herbert, Emmanuelle Fabre, Christophe Zimmer
BACKGROUND: The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture. However, how assumed chromatin properties affect model predictions was not previously systematically investigated. RESULTS: We used hundreds of dynamic chromosome simulations and Bayesian inference to determine chromatin properties consistent with an extensive dataset that includes hundreds of measurements from imaging in fixed and live cells and two Hi-C studies...
May 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28468635/prc2-represses-transcribed-genes-on-the-imprinted-inactive-x-chromosome-in-mice
#18
Emily Maclary, Michael Hinten, Clair Harris, Shriya Sethuraman, Srimonta Gayen, Sundeep Kalantry
BACKGROUND: Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression broadly, it remains unclear why some but not other PRC2 target genes require PRC2 and H3K27me3 for silencing. RESULTS: Here we define the transcriptional and chromatin features that predict which PRC2 target genes require PRC2/H3K27me3 for silencing by interrogating imprinted mouse X-chromosome inactivation...
May 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28464948/epistatic-and-allelic-interactions-control-expression-of-ribosomal-rna-gene-clusters-in-arabidopsis-thaliana
#19
Fernando A Rabanal, Terezie Mandáková, Luz M Soto-Jiménez, Robert Greenhalgh, David L Parrott, Stefan Lutzmayer, Joshua G Steffen, Viktoria Nizhynska, Richard Mott, Martin A Lysak, Richard M Clark, Magnus Nordborg
BACKGROUND: Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species. RESULTS: By taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions...
May 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28464947/erratum-to-unraveling-the-clonal-hierarchy-of-somatic-genomic-aberrations
#20
Davide Prandi, Sylvan C Baca, Alessandro Romanel, Christopher E Barbieri, Juan-Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis
No abstract text is available yet for this article.
May 2, 2017: Genome Biology
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