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H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus

Overview of attention for article published in Clinical Epigenetics, February 2016
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  • Above-average Attention Score compared to outputs of the same age and source (61st percentile)

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10 tweeters

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25 Dimensions

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52 Mendeley
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Title
H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus
Published in
Clinical Epigenetics, February 2016
DOI 10.1186/s13148-016-0179-4
Pubmed ID
Authors

Zhe Zhang, Lihua Shi, Noor Dawany, Judith Kelsen, Michelle A. Petri, Kathleen E. Sullivan

Abstract

The autoimmune disease systemic lupus erythematosus (SLE) has a modified epigenome with modified tri-methylation of histone H3 lysine 4 (H3K4me3) at specific loci across the genome. H3K4me3 is a canonical chromatin mark of active transcription. Recent studies have suggested that H3K4me3 breadth has an important regulatory role in cell identity. This project examined H3K4me3 breadth at transcription start sites (TSS) in primary monocytes and its association with differential gene transcription in SLE. Integrative analysis was applied to chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data generated from primary monocytes as well as genomic data available in public repositories. Four distinctive H3K4me3 patterns of ChIP-seq peaks were identified at 8399 TSSs. Narrow peaks were highly enriched with genes related to housekeeping functions. The broader peaks with extended H3K4me3 immediately upstream and/or downstream of TSS were associated with immune response genes. Many TSSs had downstream H3K4me3 extended to ~650 bp, where the transition of H3K4me3 to H3K36me3, a transcriptional elongation mark, is often found. The H3K4me3 pattern was strongly associated with transcription in SLE. Genes with narrow peaks were less likely (OR = 0.14, p = 2 × 10(-4)) while genes with extended downstream H3K4me3 were more likely (OR = 2.37, p = 1 × 10(-11)) to be overexpressed in SLE. Of the genes significantly overexpressed in SLE, 78.8 % had increased downstream H3K4me3 while only 47.1 % had increased upstream H3K4me3. Gene transcription sensitively and consistently responded to H3K4me3 change downstream of TSSs. Every 1 % increase of H3K4me3 in this region leads to ~1.5 % average increase of transcription. We identified the immediate TSS downstream nucleosome as a crucial regulator responsible for transcription changes in SLE. This study applied a unique method to study the effect of H3K4me3 breadth on diseases and revealed new insights about epigenetic modifications in SLE, which could lead to novel treatments.

Twitter Demographics

The data shown below were collected from the profiles of 10 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 52 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 52 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 27%
Researcher 7 13%
Student > Master 6 12%
Student > Doctoral Student 4 8%
Student > Postgraduate 3 6%
Other 8 15%
Unknown 10 19%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 15 29%
Agricultural and Biological Sciences 14 27%
Medicine and Dentistry 6 12%
Nursing and Health Professions 2 4%
Computer Science 1 2%
Other 2 4%
Unknown 12 23%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 February 2016.
All research outputs
#4,357,067
of 16,639,069 outputs
Outputs from Clinical Epigenetics
#272
of 893 outputs
Outputs of similar age
#85,232
of 347,404 outputs
Outputs of similar age from Clinical Epigenetics
#5
of 13 outputs
Altmetric has tracked 16,639,069 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 893 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.1. This one has gotten more attention than average, scoring higher than 69% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 347,404 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 75% of its contemporaries.
We're also able to compare this research output to 13 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 61% of its contemporaries.