Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription
PBN-AR
Instytucja
Instytut Podstaw Informatyki Polskiej Akademii Nauk
Informacje podstawowe
Główny język publikacji
en
Czasopismo
BMC GENOMICS
ISSN
1471-2164
EISSN
Wydawca
BIOMED CENTRAL LTD
DOI
URL
Rok publikacji
2015
Numer zeszytu
Strony od-do
1-13
Numer tomu
16:300
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Autorzy
(liczba autorów: 3)
Pozostali autorzy
+ 2
Słowa kluczowe
angielski
Antisense transcription
CTCF
RAD21
Cohesin
CAGE
Epigenetics
Transcription factor
Histone modification
Open access
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Język
angielski
Treść
Background Several post-translational histone modifications are mainly found in gene promoters and are associated with the promoter activity. It has been hypothesized that histone modifications regulate the transcription, as opposed to the traditional view with transcription factors as the key regulators. Promoters of most active genes do not only initiate transcription of the coding sequence, but also a substantial amount of transcription of the antisense strand upstream of the transcription start site (TSS). This promoter feature has generally not been considered in previous studies of histone modifications and transcription factor binding. Results We annotated protein-coding genes as bi- or unidirectional depending on their mode of transcription and compared histone modifications and transcription factor occurrences between them. We found that H3K4me3, H3K9ac, and H3K27ac were significantly more enriched upstream of the TSS in bidirectional genes compared with the unidirectional ones. In contrast, the downstream histone modification signals were similar, suggesting that the upstream histone modifications might be a consequence of transcription rather than a cause. Notably, we found well-positioned CTCF and RAD21 peaks approximately 60-80 bp upstream of the TSS in the unidirectional genes. The peak heights were related to the amount of antisense transcription and we hypothesized that CTCF and cohesin act as a barrier against antisense transcription. Conclusions Our results provide insights into the distribution of histone modifications at promoters and suggest a novel role of CTCF and cohesin as regulators of transcriptional direction.
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System-identifier
ICIL2020136
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