H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells

Abstract

BackgroundBivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. However, it is unknown whether another repressive histone modification, histone 4 lysine 20 trimethylation (H4K20me3), co-localizes with activating histone marks in ES cells.ResultsHere, we describe the previously uncharacterized coupling of the repressive H4K20me3 heterochromatin mark with the activating histone modifications H3K4me3 and histone 3 lysine 36 trimethylation (H3K36me3), and transcriptional machinery (RNA polymerase II; RNAPII), in ES cells. These newly described bivalent domains consisting of H3K4me3/H4K20me3 are predominantly located in intergenic regions and near transcriptional start sites of active genes, while H3K36me3/H4K20me3 are located in intergenic regions and within gene body regions of active genes. Global sequential ChIP, also termed reChIP-Seq, confirmed the simultaneous presence of H3K4me3 and H4K20me3 at the same genomic regions in ES cells. Genes containing H3K4me3/H4K20me3 exhibit decreased RNAPII pausing and are poised for deactivation of RNAPII binding during differentiation relative to H3K4me3 marked genes. An evaluation of transcription factor (TF) binding motif enrichment revealed that DNA sequence may play a role in shaping the landscape of these novel bivalent domains. Moreover, H3K4me3/H4K20me3 and H3K36me3/H4K20me3 bound regions are enriched with repetitive LINE and LTR elements.ConclusionsOverall, these findings highlight a previously undescribed subnetwork of ES cell transcriptional circuitry that utilizes dual marking of the repressive H4K20me3 mark with activating histone modifications.

Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells

“…These results suggest that H4K20me3 and H3K4me3 associate with common and distinct sets of transcripts. This finding is consistent with a previous report demonstrating that H4K20me3 and H3K4me3 co-localize at a subset of regions in ES cells (30). Heat maps also show enrichment of transcriptional and epigenetic regulator binding (RNAPII, RNAPII-Ser5P, RNAPII-Ser2P, and KDM5B), histone modification occupancy (H3K36me3, H3K4me3, and H3K4me2), and TF binding (MYC, E2f1, OCT4, ZFX, KLF4, SOX2, NANOG, ESRRB, and STAT3) at H4K20me3 (Fig.…”

“…Although H4K20me3-marked chromatin is thought to be a repressive histone modification, where it is enriched at pericentric hetereochromatin and is involved in repressing transcription of repetitive DNA elements (23,63,64), our data overall suggest that H4K20me3 interacts with many transcripts from loci that are actively transcribed in ES cells. Although H4K20me3 is mainly associated with heterochromatin regions, a recent study demonstrated that a subset of H4K20me3marked regions contain H3K4me3 (30). These previous findings demonstrating that H4K20me3 marks transcriptionally dynamic regions in ES cells is in alignment with results from this study, which show that expression of H4K20me3-associated RNAs is predominantly enriched in undifferentiated ES cells relative to differentiated cells (Fig.…”

“…However, it is unclear whether H4K20me3 directly interacts with RNAs. Moreover, whereas H4K20me3 has recently been shown to co-localize with activating histone modifications, such as H3K4me3, at a subset of regions (30), it is unknown whether H3K4me3 also interacts with RNAs. Therefore, to identify RNAs associated with H4K20me3 and H3K4me3, we surveyed H4K20me3-and H3K4me3-RNA interactions on a global scale in ES cells using a newly developed method, which we have termed CARIP-Seq (see "Experimental procedures") (38), by modifying existing ChIP-Seq (39,40) and RIP (41,42) protocols.…”

“…H4K20me1 is enriched at active genes (27,28), whereas H4K20me3 is predominantly associated with hetereochromatic regions. However, recent findings suggest that H4K20me3 co-localizes with H3K4me3 at a subset of regions (29,30), suggesting that H4K20me3 marks transcriptionally dynamic regions in ES cells. In addition, H3K4me3 is enriched at the transcriptional start sites (TSSs) of active genes (28,(31)(32)(33)(34), where it serves in part as a platform for RNA polymerase II (RNAPII) binding and gene activation (7,35,36).…”

Histone modifications during the life cycle of the brown algaEctocarpus

“…The presence of this mark at intronic transposons was inversely correlated with levels of gene expression but its effect on gene expression may be indirect, for example as a consequence of silencing intronic transposons. The distribution of H4K20me3 suggests a similar role to that observed in animals, where H4K20me3 is enriched at transposons and in heterochromatin [51][52][53] and where it has been shown to repress transposons [53]. Note that H4K20me3 appears to have a different role in land plants as it localises to euchromatin and is associated with transcriptional activation [54].…”