Apr 29, 2020

Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics

BioRxiv : the Preprint Server for Biology
P.-O. EsteveSriharsa Pradhan

Abstract

Chromatin accessibility is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S and G2/M) - specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations. Genome-wide alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells progressed from G1 to G2M, with distinct differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylases promoted accessible chromatin within gene bodies, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for the MYC oncogene pathway correlated with down regulation of pertinent genes. Surprisingly, repetitive RNA loci expression remained unaltered following histone acetylation-mediated increased accessibility. Therefore, we su...Continue Reading

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Mentioned in this Paper

Size
Genetic Disorders Screening
Genome
Impacted Tooth
Genetic Pedigree
Genomics
Cell Growth
Hereditary Diseases
Core
Inbreeding

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