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Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin Dewey, Sündüz Keleş, Wyeth W. Wasserman
2011 PLoS Computational Biology  
These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments  ...  approach for mapping transcription-factor binding sites and chromatin modifications.  ...  Qiang Chang for sharing his unpublished 75 mer ChIP-Seq datasets with us. We also thank three anonymous referees for making suggestions that led to an improved version of our manuscript.  ... 
doi:10.1371/journal.pcbi.1002111 pmid:21779159 pmcid:PMC3136429 fatcat:urnfshc36rfpdd7t6u6yt6hlo4

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang, Fran Lewitter
2013 PLoS Computational Biology  
Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data.  ...  Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis.  ...  The Analysis of ChIP-seq Data Sequencing Depth Effective analysis of ChIP-seq data requires sufficient coverage by sequence reads (sequencing depth).  ... 
doi:10.1371/journal.pcbi.1003326 pmid:24244136 pmcid:PMC3828144 fatcat:f7ymrdjm7zgxzdk23n6xqbt2k4

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome

Zijun Zhang, Yi Xing
2017 Nucleic Acids Research  
CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the  ...  We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectationmaximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multimapped reads.  ...  We thank the ENCODE Consortium and the ENCODE production laboratories especially Dr Gene Yeo and Dr Brenton Graveley for generating the eCLIP and RNA-seq data.  ... 
doi:10.1093/nar/gkx646 pmid:28934506 pmcid:PMC5766199 fatcat:l6vzyity55bhpornshhqe5nrku

Hematopoietic transcriptional mechanisms: From locus-specific to genome-wide vantage points

Andrew W. DeVilbiss, Rajendran Sanalkumar, Kirby D. Johnson, Sunduz Keles, Emery H. Bresnick
2014 Experimental Hematology  
However, formidable problems remain, notably ChIP-seq analysis yields hundreds to thousands of chromatin sites occupied by a given transcription factor, and only a fraction of the sites appear to be endowed  ...  Transformative technological advances involving the coupling of next-generation DNA sequencing technology with the chromatin immunoprecipitation assay (ChIP-seq) have enabled genome-wide mapping of factor  ...  A.W.D. is a predoctoral fellow of the American Heart Association.  ... 
doi:10.1016/j.exphem.2014.05.004 pmid:24816274 pmcid:PMC4125519 fatcat:wehtuypxmfcl3m3j3airggf5vq

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

Petra C Schwalie, Michelle C Ward, Carolyn E Cain, Andre J Faure, Yoav Gilad, Duncan T Odom, Paul Flicek
2013 Genome Biology  
One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1.  ...  Because combinatorial transcription factor binding can contribute to the evolutionary stabilization of regulatory regions, we tested whether YY1 and CTCF co-binding could in part account for conservation  ...  Acknowledgements We are grateful to the Cambridge Institute Genomics and Bioinformatics Core facilities and Margus Lukk and Tim F Rayner for computational support.  ... 
doi:10.1186/gb-2013-14-12-r148 pmid:24380390 pmcid:PMC4056453 fatcat:v6glefexnvawpndouh4xlknmuu

Distinct Contribution of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription Factors [article]

Martin Cusack, Hamish W. King, Paolo Spingardi, Benedikt M. Kessler, Robert J. Klose, Skirmantas Kriaucionis
2019 bioRxiv   pre-print
A subset of these elements have elevated binding of the YY1 and GABPA transcription factors and increased expression.  ...  For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase  ...  Altogether, our analysis of ChIP-seq data indicates that both DNA methylation and HDAC activity play distinct roles in limiting occupancy of each of the examined TFs to a fraction of their binding sites  ... 
doi:10.1101/670307 fatcat:uqmrd2isefgixe55mzearcqzxa

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Peter B. Becker
2011 PLoS Biology  
, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.  ...  The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts  ...  Wexler and Julia Zhang at the National Human Genome Research Institute for their support in administering the ENCODE Consortium, additional members of our laboratories and institutions who have contributed  ... 
doi:10.1371/journal.pbio.1001046 pmid:21526222 pmcid:PMC3079585 fatcat:cfshtutffzhfvdqgwnda2sxlym

ELF5 modulates the estrogen receptor cistrome in breast cancer

Catherine L. Piggin, Daniel L. Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha R. Oakes, David Gallego-Ortega, Susan J. Clark (+4 others)
2020 PLoS Genetics  
regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy.  ...  Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight  ...  Acknowledgments The authors acknowledge the support of Ms Gillian Lehrbach, Garvan Tissue Culture Facility Sydney for advice with breast cancer cell tissue culture, Dominic Kaczorowski for DNA sequencing  ... 
doi:10.1371/journal.pgen.1008531 pmid:31895944 pmcid:PMC6959601 fatcat:pg3lau56wnetzpwubb33pwwnca

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism

Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
2019 International Journal of Molecular Sciences  
In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks.  ...  It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory  ...  with these transcription factors and their regulons when followed with ChIP-seq analysis.  ... 
doi:10.3390/ijms21010167 pmid:31881735 pmcid:PMC6981605 fatcat:yv25lasn65cnrpkho2bx5asbgy

Navigating and mining modENCODE data

Nathan Boley, Kenneth H. Wan, Peter J. Bickel, Susan E. Celniker
2014 Methods  
of DNA replication, RNA transcripts and the transcription factor binding sites that control gene expression.  ...  modENCODE was a 5year NHGRI funded project (2007-2012) to map the function of every base in the genomes of worms and flies characterizing positions of modified histones and other chromatin marks, origins  ...  Acknowledgments We thank the members of the modENCODE transcription consortium and especially Ben Brown for helpful discussions.  ... 
doi:10.1016/j.ymeth.2014.03.007 pmid:24636835 pmcid:PMC4857704 fatcat:obs7pn5h4rb4nck3sdsk2rpjwi

Analytical tools and current challenges in the modern era of neuroepigenomics

Ian Maze, Li Shen, Bin Zhang, Benjamin A Garcia, Ningyi Shao, Amanda Mitchell, HaoSheng Sun, Schahram Akbarian, C David Allis, Eric J Nestler
2014 Nature Neuroscience  
, as well as part of aberrant processes implicated in human disease.  ...  Here, we provide a comprehensive overview of currently available tools to analyze neuroepigenomics data, as well as a discussion of pending challenges specific to the field of neuroscience.  ...  Alexey Soshnev for help with illustrations..  ... 
doi:10.1038/nn.3816 pmid:25349914 pmcid:PMC4262187 fatcat:nknocpjbt5bzpatdzuqhtbmirm

Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders

Wanhe Li, Ying Jin, Lisa Prazak, Molly Hammell, Josh Dubnau, Koichi M. Iijima
2012 PLoS ONE  
Third, we discovered that a large fraction of the TEs to which TDP-43 binds become de-repressed in mouse TDP-43 disease models.  ...  By mining a series of deep sequencing datasets of protein-RNA interactions and of gene expression profiles, we uncovered extensive binding of TE transcripts to TDP-43, an RNA-binding protein central to  ...  For the rat data, the read counts were modeled with a Poisson distribution, similarly to two popular ChIP-seq analysis approaches, MACS [33] and PeakSeq [32] .  ... 
doi:10.1371/journal.pone.0044099 pmid:22957047 pmcid:PMC3434193 fatcat:rw4g5ef5ubekbhbzyz2fzy5zm4

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

Vijender Chaitankar, Gökhan Karakülah, Rinki Ratnapriya, Felipe O. Giuste, Matthew J. Brooks, Anand Swaroop
2016 Progress in retinal and eye research  
Some of the NGS analysis required the computational resources of the NIH HPC Biowulf cluster (http:// hpc.nih.gov).  ...  Our work is supported by the Intramural Research Program of the National Eye Institute (grant nos: EY000450, EY000474, EY000546), National Institutes of Health.  ...  ChIP-seq Identification of genomic regions occupied by DNA-binding proteins and elucidation of chromatin state by chromatin Identify genomic regions with a significant overrepresentation of mapped reads  ... 
doi:10.1016/j.preteyeres.2016.06.001 pmid:27297499 pmcid:PMC5112143 fatcat:ticudbtjlff6tgrmq4i5w3eq7y

LANA Binds to Multiple Active Viral and Cellular Promoters and Associates with the H3K4Methyltransferase hSET1 Complex

Jianhong Hu, Yajie Yang, Peter C. Turner, Vaibhav Jain, Lauren M. McIntyre, Rolf Renne, Dirk P. Dittmer
2014 PLoS Pathogens  
We performed a detailed ChIP-seq analysis in cells of lymphoid and endothelial origin and compared H3K4me3, H3K27me3, polII, and LANA occupancy.  ...  Bioinformatic analysis of enriched LANA binding sites in combination with biochemical binding studies revealed three distinct binding patterns.  ...  We would like to thank Alison Morse, University of Florida Genetics Institute for assistance with bioinformatics data analysis. Author Contributions Conceived and designed the experiments: JH RR.  ... 
doi:10.1371/journal.ppat.1004240 pmid:25033463 pmcid:PMC4102568 fatcat:vqy4xsrazbcz3gu56ekia5gtxy

Cancer whole-genome sequencing: present and future

H Nakagawa, C P Wardell, M Furuta, H Taniguchi, A Fujimoto
2015 Oncogene  
Taking account of the extreme diversity of cancer genomes and phenotype, it is also required to analyze much more WGS data and integrate these with multi-omics data, functional data and clinical-pathological  ...  functions of these unexplored genomic regions.  ...  ACKNOWLEDGEMENTS We thank researchers and technical staffs in RIKEN-IMS and Professor Miyano and his fellows in Human Genome Center, Institute of Medical Science, The University of Tokyo for their great  ... 
doi:10.1038/onc.2015.90 pmid:25823020 fatcat:b2mot3e2tzbkjl5g4twehj6ude
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