Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response

Oncotarget
Brittany S SextonJonathan H Dennis

Abstract

Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture c...Continue Reading

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May 15, 2013·PloS One·Steven E WeickselCharles G Sagerström
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May 7, 2021·Nature Communications·Lauren ColeDavid J Tremethick

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Datasets Mentioned

BETA
GM18508

Methods Mentioned

BETA
MNase-seq
PCR
immunoprecipitation
Illumina sequencing

Software Mentioned

bedtools
R
Casava
RAGE
cutadept
samtools
R environement
bowtie2

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