Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Feb 2;8:14.
doi: 10.1186/s13148-016-0179-4. eCollection 2016.

H3K4 Tri-Methylation Breadth at Transcription Start Sites Impacts the Transcriptome of Systemic Lupus Erythematosus

Affiliations
Free PMC article

H3K4 Tri-Methylation Breadth at Transcription Start Sites Impacts the Transcriptome of Systemic Lupus Erythematosus

Zhe Zhang et al. Clin Epigenetics. .
Free PMC article

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

Keywords: Epigenome; H3K4me3; Integrative analysis; Pattern recognition; Systemic lupus erythematosus.

Figures

Fig. 1
Fig. 1
H3K4me3 at TSS. a The average H3K4me3 around TSS reduces by 50 % at ~400–500 bp upstream and ~600–700 bp downstream. This plot was based on the normalized average sequencing depth of six control samples. b Four distinctive patterns of TSS H3K4me3 were defined: narrow peak, upstream extended downstream extended, and broad symmetric. The same control samples were used for this plot. c Complementary pattern of other histone modifications to the downstream extended pattern of H3K4me3. Data of the other histone modifications in CD14+ monocyte were provided by the ENCODE project
Fig. 2
Fig. 2
Transcription and H3K4me3 pattern. Control samples were used to examine the relationship between gene transcription and H3K4me3 patterns. a Genes with the downstream extended H3K4me3 pattern had higher level of transcription. b Genes with the downstream extended H3K4me3 pattern had higher between sample variance of transcription. The dependence of between-sample variance on transcription level was removed using the Loess local fitting method, as genes having higher transcription tend to have higher variance too. Error bars represent standard errors, and p values were calculated by comparing each pattern to unclassified group using Wilcoxon rank-sum test
Fig. 3
Fig. 3
Differential transcription in SLE and H3K4me3 pattern. Genes with certain H3K4m43 patterns at their TSS were significantly less or more likely to have increased transcription in SLE. Fisher’s exact test was applied to each H3K4me3 pattern and genes with significantly decreased and increased transcription in SLE to calculate odds ratios and error bars
Fig. 4
Fig. 4
The effect of H3K4me3 change on differential transcription in SLE. a Each plot shows the average change of transcription in SLE in response to 1 % of H3K4me3 increase or decrease at three neighboring regions. b Such association was re-evaluated after removing the dependence of H3K4me3 at these regions on each other. Red diamonds represent the TSS, green triangles represent the upstream region, and the blue circles represent the downstream region. Error bars represent standard errors
Fig. 5
Fig. 5
H3K4me3 patterns of increased gene transcription in SLE. a The distributions of H3K4me3 changes at genes with increased transcription were different among three nearby regions after their dependence on each other was removed. Each bar defines the number of genes and the x-axis displays the magnitude of H3K4me3 change. b The TSS H3K4me3 of genes with increased transcription in SLE had the most increase at ~700 bp. The dotted lines represent TSS and the peak summit. c Relative change of H3K4me3 at upstream and downstream of TSS is often shadowed by higher level of H3K4me3 at TSS when sequencing depth of control and patient samples was plotted separately (upper panel), and becomes more prominent when the relative depth difference is plotted (lower panel). TDP2 encodes a protein associated with major regulators of immune response, such as CD40, TNF, and TRAFs. Its transcription was significantly increased by 96 % in SLE (p = 0.004). We encourage readers to use our online tool (see “Methods” section) to make similar plots of their genes of interest
Fig. 6
Fig. 6
TFBS enrichment of H3K4me3 patterns. a The enrichment of TFBSs was different between TSSs with different H3K4me3 patterns. The enrichment was spread across a broader region at TSSs with non-narrow H3K4me3 peaks, suggesting that TF binding plays a role in maintaining H3K4me3 breadth. Matches to 2414 known protein-binding motifs were searched within the −1 to 1 kb region around TSSs. We found that 340 motifs were enriched by at least 20 % at TSS with H3K4me3. The average enrichment of these motifs was plotted separately for each H3K4me3 pattern. b The UP00408 motif of GABPA was highly enriched at TSSs with narrow H3K4me3 peaks
Fig. 7
Fig. 7
Validation in other inflammatory models. a Genes with significantly increased or decreased transcription in inflammatory bowel disease (IBD) were obtained from our unpublished RNA-seq data. The average H3K4me3 changes in our unmatched SLE samples were calculated at three different regions, showing that the only significant change was the increase of downstream H3K4me3 at TSS of genes with increased transcription. b The same analysis was applied to a published data set (GSE10500) comparing the transcriptome of rheumatoid arthritis (RA) patients and controls in macrophage. c This analysis used matching RNA-seq and H3K4me3 data obtained from primary monocytes treated with LPS or cell culture medium as control (GSE58310). Average H3K4me3 changes of gene sets with increased or decreased transcription by LPS were calculated for the same three regions. Error bars indicate that average H3K4me3 was changed significantly towards the same direction as the change of transcription. d The same analysis was applied to matching ChIP-seq H3K4me3 and microarray transcriptome data generated from TNF-treated endothelium (GSE54000). All plots normalized H3K4me3 data to make the average change of all genes equal to zero at each region

Similar articles

See all similar articles

Cited by 11 articles

See all "Cited by" articles

References

    1. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, et al. Active genes are tri-methylated at K4 of histone H3. Nature. 2002;419(6905):407–11. doi: 10.1038/nature01080. - DOI - PubMed
    1. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823–37. doi: 10.1016/j.cell.2007.05.009. - DOI - PubMed
    1. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell. 2007;130(1):77–88. doi: 10.1016/j.cell.2007.05.042. - DOI - PMC - PubMed
    1. Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell. 2012;151(5):994–1004. doi: 10.1016/j.cell.2012.09.045. - DOI - PMC - PubMed
    1. Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, et al. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell. 2014;158(3):673–88. doi: 10.1016/j.cell.2014.06.027. - DOI - PMC - PubMed

Publication types

Feedback