Data · dataset · 2014
Altered promoter nucleosome positioning is an early event in gene silencing
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Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions.
Description
How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DNA methylation, and gene expression in the early stages of gene silencing.
Genome-wide gene expression correlated with highly positioned nucleosomes upstream and downstream of a nucleosome-depleted transcription start site (TSS). Hypermethylated promoters displayed increased nucleosome occupancy, specifically at the TSS. We investigated 2 genes, CDH1 and CDKN2B , which were silenced in adenomas but lacked promoter hypermethylation.
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Instead, silencing correlated with loss of nucleosomes from the -2 position upstream of the TSS relative to normal mucosa. In contrast, permanent CDH1 silencing in carcinoma cells was characterized by promoter hypermethylation and dense nucleosome occupancy. Our findings suggest that silenced genes transition through an intermediary stage involving altered promoter nucleosome positioning, before permanent silencing by hypermethylation and dense nucleosome occupancy.
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Where it is published
- Repository landing page tandf.figshare.com/articles/dataset/Altered_promoter_nucleosome_positioning_is_an… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.1255029.v1 ↗
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Documentation and papers
- Creative Commons Attribution 4.0 International creativecommons.org/licenses/by/4.0/legalcode ↗
license · from DataCite
- IsSupplementTo 10.4161/15592294.2014.970077 doi.org/10.4161/15592294.2014.970077 ↗
publication · from DataCite
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.1255029.v1 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.1255029.v1 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Biological sciences · Clinical medicine
- From keywords
- Chemistry · Life Sciences · Medicine & Health
- Inferred from text
- Cancer 75%
Related
Provenance · 1 source records, 14 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.1255029.v1 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].fos:biological-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:clinical-medicine | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · DataCite | vocabulary-mapper@1.0.0 | keywords['Chemistry'] |
| concepts[field].local:field:life-sciences | mapping · DataCite | vocabulary-mapper@1.0.0 | keywords['Biological Sciences'] |
| concepts[field].local:field:medicine-health | mapping · DataCite | vocabulary-mapper@1.0.0 | keywords['Medicine'] |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |