Nucleosome regulatory dynamics in response to TGFβ
PBN-AR
Instytucja
Instytut Podstaw Informatyki Polskiej Akademii Nauk
Informacje podstawowe
Główny język publikacji
angielski
Czasopismo
Nucleic Acids Research
ISSN
0305-1048
EISSN
Wydawca
Oxford University Press
Rok publikacji
2014
Numer zeszytu
11
Strony od-do
6921-6934
Numer tomu
42
Identyfikator DOI
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Autorzy
(liczba autorów: 11)
Pozostali autorzy
+ 10
Streszczenia
Język
angielski
Treść
Nucleosomes play important roles in a cell beyond their basal functionality in chromatin compaction. Their placement affects all steps in transcriptional regulation, from transcription factor (TF) binding to messenger ribonucleic acid (mRNA) synthesis. Careful profiling of their locations and dynamics in response to stimuli is important to further our understanding of transcriptional regulation by the state of chromatin. We measured nucleosome occupancy in human hepatic cells before and after treatment with transforming growth factor beta 1 (TGFβ1), using massively parallel sequencing. With a newly developed method, SuMMIt, for precise positioning of nucleosomes we inferred dynamics of the nucleosomal landscape. Distinct nucleosome positioning has previously been described at transcription start site and flanking TF binding sites. We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci. We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci. Depending on genomic annotation, 44–78% of them were over-represented in binding motifs for TFs. Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.
Inne
System-identifier
PX-56988deb810641ecf9192997
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