Evidence map›Paper›PMID 27634286›Full record

ArticleBMC medical genomics2016

Genome-wide positioning of bivalent mononucleosomes.

Subhojit Sen, Kirsten F Block, Alice Pasini, Stephen B Baylin, Hariharan Easwaran

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC medical genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
1.7field-weighted citation impact, top 15% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed, 26 citations in OpenAlex.

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  14. The Regulatory Capacity of Bivalent Genes-A Theoretical Approach.International journal of molecular sciences · 2017
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 2 institutions in 3 countries.

Subhojit SenCRB1, Room 530, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.
Kirsten F BlockCRB1, Room 530, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA.
Alice PasiniDivision of Respiratory Medicine and Nottingham Respiratory Biomedical Research Unit, University of Nottingham, City Hospital, Nottingham, NG5 1BP, UK.
Stephen B BaylinCRB1, Room 530, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA. sbaylin@jhmi.edu.
Hariharan EaswaranCRB1, Room 530, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, 21287, MD, USA. heaswar2@jhmi.edu.ORCID 0000-0002-5517-2972
Johns Hopkins University · USUniversity of Nottingham · GB

Funding

METHYLATION OF THE CALCITONIN GENE IN HUMAN TUMORSR01CA043318 · NCI · JOHNS HOPKINS UNIVERSITY · PI BAYLIN, STEPHEN B. · 1986 to 2013
$6.0M
NCI NIH HHS R01 CA043318
6 · The paper itself

Abstract

backgroundBivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes.

resultsHere, we developed an efficacious sequential ChIP technique for examining global positioning of individual bivalent nucleosomes. Using next generation sequencing approaches we show that although individual H3K4me3 and H3K27me3 marks overlap in broad zones, bivalent nucleosomes are focally enriched in the vicinity of the transcription start site (TSS). These seem to occupy the H2A.Z nucleosome positions previously described as salt-labile nucleosomes, and are correlated with low gene expression. Although the enrichment profiles of bivalent nucleosomes show a clear dependency on CpG island content, they demonstrate a stark anti-correlation with methylation status.

conclusionsWe show that regional overlap of H3K4me3 and H3K27me3 chromatin tend to be upstream to the TSS, while bivalent nucleosomes with both marks are mainly promoter proximal near the TSS of CpG island-containing genes with poised/low expression. We discuss the implications of the focal enrichment of bivalent nucleosomes around the TSS on the poised chromatin state of promoters in stem cells.

Indexed as

GenomicsCell Line, TumorCpG IslandsEpigenesis, GeneticHistonesHumansLysineMethylationNucleosomesPromoter Regions, GeneticTranscription Initiation SiteHistonesLysineNucleosomesBivalencyBivalent mononucleosomesChromatinDNA methylationH3K27me3H3K4me3

Identifiers

PMID27634286
PMCPMC5025636
OpenAlexW2519449049

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.