Table 1 An overview of how epigenetics contributes to transcription dynamics. A highlight of literature on the role of epigenetic chromatin for transcription dynamics and its proposed mechanism

DNA methylation on the promoter

Transcription noise increased

Promotes ON to OFF state transitions

[51]

DNA methylation intrageneic

Transcription noise decreased

May prevent noise-associated histone variant deposition, or transcription from intragenic cryptic promoters

[50,51,52,53,54,55]

H2A.Z promoter deposition

Transcription noise decreased

Promotes productive elongation

[67]

H2A.Z intragenic deposition

Transcription noise increased

Promotes productive elongation from intragenic promoters

[54, 67]

H3.3 turn over

Transcription noise increased

H3.3 may control duration between macroscale transcription bursts

[11, 26, 60]

mH2A induced NRF-1

recruitment

Transcription noise decreased

NRF-1 recruitment maintains ON state by ensuring consistent interactions with the transcriptional machinery macroburst size

[69]

Promoter proximal nucleosome density

Transcription burst frequency reduced, noise increased

Higher nucleosome density prevents deep OFF-ON state transitions, decreasing macroscale burst frequency

[70]

HDAC inhibitors inducing histone acetylation

Burst size increased, possible burst frequency reduced

[25, 60, 72, 73]

dCas9 targeted promoter acetylation

Burst frequency increased

Based on smFISH so likely macroscale burst frequency

[110]

dCas9 targeted enhancer acetylation

Burst size increased

Enhancer acetylation recruits

BRD4 promoting release of paused RNAPII

[75]

H3K79me2 knock out

Transcription burst frequency decreased

Histone methylation changes appear to be related to transcriptional memory

[83]

H3K4 methylation

Transcription burst frequency maintenance

H3K4 methylation persists along gene body after transcription has ceased, acting as memory

[76, 77]

KDM5B (H3K4me demethylation)

Transcription heterogeneity increased

[16]

H3K4me broad domains

Transcription homogeneity

[16]

Histone modifications within gene body

Regulation of transcription burst frequency

H3K4me3, H3K36me3 and H3K79me2 at gene body are associated with an increased burst frequency

[16, 83, 86]

Macro level chromatin structure (TADs, chromosome/chromatin localisation)

Affects transcription mainly beyond the cell cycle

These are stable, less dynamic structures

[93,94,95,96, 98, 111]

Enhancer-promoter loop destabilisation (CTCF depletion)

Transcription noise increased

Enhancer-promoter loops become

more stochastic

[104]

Enhancer-promoter contact stabilisation

Transcription burst frequency increased

Short-lived, highly dynamic enhancer-promoter loops trigger transcription burst

[105, 112]

Enhancer-promoter contact (mediated by Mediator complex)

Burst size increased

Mediator enables rapid succession of RNAPII initiation

[19]

Enhancer regulation

Modulates burst frequency

[108]