Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2

Chromatin remodeling is essential for controlling the expression of genes during development. The histone-modifying enzyme G9a/KMT1C can act both as a coactivator and a corepressor of transcription. Here, we show that the dual function of G9a as a coactivator vs. a corepressor entails its association within two distinct protein complexes, one containing the coactivator Mediator and one containing the corepressor Jarid1a/KDM5A. Functionally, G9a is important in stabilizing the Mediator complex for gene activation, whereas its repressive function entails a coordinate action with the histone H3 lysine 4 (H3K4) demethylase Jarid1a for the maintenance of gene repression. The essential nature of cross-talk between the histone methyltransferase G9a and the demethylase Jarid1a is demonstrated on the embryonic E y -globin gene, where the concurrent introduction of repressive histone marks (dimethylated H3K9 and dimethylated H3K27) and removal of activating histone mark (trimethylated H3K4) is required for maintenance of gene silencing. Taken together with our previous demonstration of cross-talk between UTX and MLL2 to mediate activation of the adult β maj -globin gene, these data suggest a model where “active” and “repressive” cross-talk between histone-modifying enzymes coexist on the same multigene locus and play a crucial role in the precise control of developmentally regulated gene expression.

Section: Resultsmentioning

confidence: 80%

Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A

Chaturvedi

Somasundaram

Singh

et al. 2012

“…Decreased H3K4 methylation has been detected during differentiation at the promoters of MFN2, BRD8/KIF20A, FGF4, OTX2, HOXA1, HOXA5, and HOXA7 genes bound by KDM5A (9,11,14,17). The question of whether the regulation of a cell cycle gene involves removal of H3K4 trimethylation by KDM5A has not been studied.…”

Section: Resultsmentioning

confidence: 99%

“…In particular, HOXA9 is expressed more than 100-fold higher in stem and progenitor cells than in differentiated cell populations (23). One study showed that the PRC2 complex recruits KDM5A to a large number of genes, which is required for repression of PRC2 target genes during ES cell differentiation (17). However, we and another group were unable to see a significant overlap between ChIP-seq KDM5A peaks and the PRC2 location in U937 cells and mouse ES cells (24), indicating that this is not a major mechanism for repression of KDM5A bound genes.…”

Section: Discussionmentioning

confidence: 99%

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation

Beshiri

Holmes

Richter

et al. 2012

Epigenetic regulation underlies the robust changes in gene expression that occur during development. How precisely epigenetic enzymes contribute to development and differentiation processes is largely unclear. Here we show that one of the enzymes that removes the activating epigenetic mark of trimethylated lysine 4 on histone H3, lysine (K)-specific demethylase 5A (KDM5A), reinforces the effects of the retinoblastoma (RB) family of transcriptional repressors on differentiation. Global location analysis showed that KDM5A cooccupies a substantial portion of target genes with the E2F4 transcription factor. During ES cell differentiation, knockout of KDM5A resulted in derepression of multiple genomic loci that are targets of KDM5A, denoting a direct regulatory function. In terminally differentiated cells, common KDM5A and E2F4 gene targets were bound by the pRB-related protein p130, a DREAM complex component. KDM5A was recruited to the transcription start site regions independently of E2F4; however, it cooperated with E2F4 to promote a state of deepened repression at cell cycle genes during differentiation. These findings reveal a critical role of H3K4 demethylation by KDM5A in the transcriptional silencing of genes that are suppressed by RB family members in differentiated cells.chromatin | histone demethylase | whole-genome sequencing | histone methylation R egulation of gene expression is accomplished by transcription factors, histone-modifying enzymes, and chromatin remodeling machinery. The combined action of these three has been implicated in a number of biological processes, including cell cycle control, development, reprogramming, differentiation, and aging. Deregulation of chromatin-modifying enzymes has been strongly linked to the development of cancer. For example, two enzymes that regulate methylation at the histone H3 lysine 4 (H3K4) residue, mixed lineage leukemia-1 (MLL1) and lysine (K)-specific demethylase 5A (KDM5A), have been identified in translocations associated with human leukemia. H3K4 histone methylation states exhibit a highly distinct distribution pattern in the genome. Specifically, H3K4 trimethylation (H3K4me3) is strongly associated with transcriptional activation, with the highest levels observed near transcriptional start sites (TSS). In vitro studies suggest that the four KDM5 enzymes (KDM5A, KDM5B, KDM5C, and KDM5D) are able to remove methylation at lysine 4 of histone H3, and in vivo KDM5A and KDM5B may be recruited to common gene regions (1). This finding leads to multiple questions: (i) Do KDM5 proteins play a role in gene regulation by transcription factors? (ii) Are KDM5 enzymes nonredundant H3K4 demethylases?During differentiation, cells exhibit two novel properties: repression of cell cycle genes associated with permanent cell cycle exit and activation of cell type-specific genes. Histone modifications are thought to be important epigenetic events intimately linked to initiation and maintenance of transcriptional changes for both of these processes. Cell cycle exit is associat...

“…It adds weight to the expectation that we will also find physical coupling of the opposite combination of activities, histone deactivation and repression, which are effectively coordinated in many systems (3,4,6,45). Identification of the H3K36me3 demethylase at FLC will allow its physical association with PRC2 to be investigated.…”

Section: Elf6 and Jumonji Domain-containing Protein 13 Are Partiallymentioning

confidence: 99%

“…Transcriptional states are induced by internal developmental signals or triggered by environmental conditions and are then epigenetically maintained through many cell divisions. Considerable evidence suggests that opposing histone modifications mark different transcriptional states (1)(2)(3)(4)(5)(6). However, there is still great debate as to how histone-based transcriptional states are initially established and maintained through development (7,8).…”

mentioning

confidence: 99%

Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC

Yang

Howard

Dean

2016

Establishment and maintenance of gene expression states is central to development and differentiation. Transcriptional and epigenetic mechanisms interconnect in poorly understood ways to determine these states. We explore these mechanisms through dissection of the regulation of Arabidopsis thaliana FLOWERING LOCUS C (FLC). FLC can be present in a transcriptionally active state marked by H3K36me3 or a silent state marked by H3K27me3. Here, we investigate the trans factors modifying these opposing histone states and find a physical coupling in vivo between the H3K36 methyltransferase, SDG8, and the H3K27me3 demethylase, ELF6. Previous modeling has predicted this coupling would exist as it facilitates bistability of opposing histone states. We also find association of SDG8 with the transcription machinery, namely RNA polymerase II and the PAF1 complex. Delivery of the active histone modifications is therefore likely to be through transcription at the locus. SDG8 and ELF6 were found to influence the localization of each other on FLC chromatin, showing the functional importance of the interaction. In addition, both influenced accumulation of the associated H3K27me3 and H3K36me3 histone modifications at FLC. We propose the physical coupling of activation and derepression activities coordinates transcriptional activity and prevents ectopic silencing.epigenetic regulation | histone modifications | histone methyltransferase | histone demethylase | FLOWERING LOCUS C C hromatin-based transcriptional activity is particularly important in multicellular organisms, where cells differentiate into very different developmental states. Transcriptional states are induced by internal developmental signals or triggered by environmental conditions and are then epigenetically maintained through many cell divisions. Considerable evidence suggests that opposing histone modifications mark different transcriptional states (1-6). However, there is still great debate as to how histone-based transcriptional states are initially established and maintained through development (7,8). We used Arabidopsis FLOWERING LOCUS C (FLC) as a model gene to explore histone-based transcriptional regulation and epigenetic memory. Local chromatin states are critical for quantitatively controlling FLC expression (9). Active FLC expression requires functional FRIGIDA (FRI) and a set of histone modifying Trithorax homologs, Complex Proteins Associated with Set1 (COMPASS), RNA polymerase II Associated Factor 1 complex (PAF1C), and SET DOMAIN GROUP 8 (SDG8), the major H3K36 methyltransferase (10-17). Repression of FLC requires either the autonomous pathway, which coordinately influences transcriptional initiation and elongation with associated chromatin modulation, or vernalization, the cold-induced Polycomb silencing (18-21). Both of these involve accumulation of high levels of H3K27me3 at FLC (20-22). A series of FLC antisense transcripts (COOLAIR) contribute to these repression pathways (18,(23)(24)(25)(26) Opposing H3K36me3 and H3K27me3 states are particularly ...