Chromatin accessibility: a window into the genome
Maria Tsompana,Michael J. Buck +1 more
TL;DR: The limitations and advantages of current genome-wide chromatin accessibility assays are discussed with especial attention on experimental precautions and sequence data analysis and the perspective on future improvements necessary for moving the field of chromatin profiling forward is concluded.
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Abstract: Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.
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Citations
Chromatin accessibility profiling reveals that human fibroblasts respond to mechanical stimulation in a cell-specific manner.
Niall J Logan,Krystyna L Broda,Nikolaos Pantelireis,Claire A Higgins +3 more
TL;DR: The results suggest that these 2 stimuli (OMSW) elicit cell-specific responses by modifying chromatin accessibility of osteogenic-related gene promoters, and suggest that these 2 stimuli (OMSW) elicit cell-specific responses by modifying chromatin accessibility of osteogenic-related gene promoters.
Genomic insights into chromatin reprogramming to totipotency in embryos
TL;DR: Changes in DNA methylation, chromatin accessibility, and topological architecture occurring during the reprogramming to totipotency in the early embryo are discussed.
Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription
Umut Berkay Altintas,Ji-Heui Seo,Claudia Giambartolomei,Dogancan Ozturan,Brad J. Fortunato,Geoffrey M. Nelson,S. R. Goldman,Karen Adelman,Faraz Hach,M. Freedman,Nathan A. Lack +10 more
TL;DR: It is shown that binding of AR does not result in a substantial rewiring of chromatin loops, but instead increases the contact frequency of pre-existing loops to target promoters, and the results show that gene expression strongly correlates to the changes in contact frequency.
Upregulation and cell specificity of C4 genes are derived from ancestral C3 gene regulatory networks
Pallavi Singh,Sean R. Stevenson,Ivan Reyna-Llorens,Gregory Reeves,Tina B. Schreier,Julian M. Hibberd +5 more
TL;DR: Overall, it is concluded that during evolution of the complex C4 trait, C4 cycle genes gain cis-elements that operate in the C3 leaf such that they become integrated into existing gene regulatory networks associated with cell specificity and photosynthesis.
Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks.
Jonathan D. Diedrich,Qian Dong,Daniel C. Ferguson,Brennan P. Bergeron,Robert J Autry,Robert J Autry,Maoxiang Qian,Wenjian Yang,Colton Smith,James B Papizan,Jon P. Connelly,Kohei Hagiwara,Kristine R. Crews,Shondra M. Pruett-Miller,Ching-Hon Pui,Jun J. Yang,Mary V. Relling,William E. Evans,Daniel Savic,Daniel Savic +19 more
TL;DR: In this article, the authors mapped accessible chromatin in 24 primary ALL cell biospecimens comprising three common molecular subtypes (DUX4/ERG, ETV6-RUNX1 and hyperdiploid) from patients treated at St. Jude Children's Research Hospital.
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•Journal Article
An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
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