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Bivalent domains and heterogeneity. Two scenarios could potentially explain the co-occurrence of H3K4me3 and H3K27me3 observed by ChIP-seq on bivalent promoters. As ChIP-seq cannot establish physical co-occurrence of two marks on the same allele, admixture of cells that either express (green) or do not express (red) the gene in focus could explain the occurrence of both marks as well as the low expression level in the overall population. In contrast, in the case of ''true'' bivalency, virtually all cells in the population carry both marks simultaneously at the promoter in question, leading to low, if any, expression for that gene in all cells.
Source publication
Histone modifications and chromatin-associated protein complexes are crucially involved in the control of gene expression, supervising cell fate decisions and differentiation. Many promoters in embryonic stem (ES) cells harbor a distinctive histone modification signature that combines the activating histone H3 Lys 4 trimethylation (H3K4me3) mark an...
Contexts in source publication
Context 1
... establish bivalency at a given locus. However, these assays are unable to unequivocally establish the coexistence of both marks on the same allele in a given cell. Thus, it has been argued that the observed bivalency simply reflects cellular heterogeneity arising from the averaging of cells that carry either, but not both, marks at a given locus (Fig. 2). However, given that bivalent domains can still be observed-albeit in lower proportion-in unipotent cells such as T cells and MEFs, an admixture of cell populations appears to be an unlikely explanation for the observed coexistence of these marks. Experiments on sorted populations of T cells, ES cells, and embryonic tissue likewise ...
Context 2
... reports suggested that targeting of H2A.Z to bivalent promoters may depend on PRC1/2 complexes and vice versa ( Creyghton et al. 2008). However, recent studies indicate that H2A.Z deposition is independent of the PRCs (Illingworth et al. 2012). Nevertheless, understand- ing H2A.Z recruitment may shed light on how PRCs are targeted to specific loci. ...
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Background:
Bivalent 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 r...
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Here we show that bivalent domains and chromosome architecture for bivalent genes are dynamically regulated during the cell cycle in human pluripotent cells. Central to this is the transient increase in H3K4-trimethylation at developmental genes during G1, thereby creating a "window of opportunity" for cell-fate specification. This mechanism is con...
Bivalent promoters are defined by the presence of both activating (H3K4me3) and repressive (H3K27me3) chromatin marks. In this paper, we first identified high confidence bivalent promoters in murine ES cells integrating data across eight studies using two methods; peak-based and cutoff-based. We showed that peak-based method is more reliable as pro...
Citations
... We model central nervous system development using organoids, and select three histone modifications as proxies for dynamic epigenetic change and validate our findings in a primary developing human brain. We include H3K27me3 as a repressive mark at developmental genes 5 , H3K27ac a mark of active 55 enhancers and promoters 6,7 , and H3K4me3 as a mark of active or bivalent promoters of developmental genes 5,8,9 . In addition, these marks interact with one another and can act in concert or be mutually exclusive 10,11 . ...
... We observed abundant bivalent domains within the neuroepithelium, which are defined 155 by H3K27me3 and H3K4me3 co-enrichment at repressed genes and have been reported to preferentially occur at genes that require rapid activation during development 8, 9,24 (Fig. 2d). A smaller subset of domains remained bivalent as cells transition into the regional branches. ...
Human cell type diversity emerges through a highly regulated series of fate restrictions from pluripotent progenitors. Fate restriction is orchestrated in part through epigenetic modifications at genes and regulatory elements, however it has been difficult to study these mechanisms in humans. Here, we use organoid models of the human central nervous system and establish single-cell profiling of histone modifications (H3K27ac, H3K27me3, H3K4me3) in organoid cells over a time course to reconstruct epigenomic trajectories governing cell identity acquisition from human pluripotency. We capture transitions from pluripotency through neuroepithelium, to retinal and brain region specification, as well as differentiation from progenitors to neuronal and glial terminal states. We find that switching of repressive and activating epigenetic modifications can precede and predict decisions at each stage, providing a temporal census of gene regulatory elements and transcription factors that we characterize in a gene regulatory network underlying human cerebral fate acquisition. We use transcriptome and chromatin accessibility measurements in the same cell from a human developing brain to validate this regulatory mode in a primary tissue. We show that abolishing histone 3 lysine 27 trimethylation (H3K27me3) through inhibition of the polycomb group protein Embryonic Ectoderm Development (EED) at the neuroectoderm stage disrupts fate restriction and leads to aberrant cell fate acquisition, ultimately influencing cell type composition in brain organoids. Altogether, our single-cell genome wide map of histone modifications during human neural organoid development serves as a blueprint ( https://episcape.ethz.ch ) to explore human cell fate decisions in normal physiology and in neurodevelopmental disorders. More broadly, this approach can be used to study human epigenomic trajectory mechanisms in any human organoid system.
Summary
Unguided neural organoids reveal widespread and dynamic switching of epigenetic modifications during development and recapitulate fate restriction from pluripotency to terminally differentiated cells of the human central nervous system.
... KDM6B allows the removal of transcriptionally repressive histone modifications from bivalent loci in the genome. Bivalency can be defined as the presence of both activation (H3K4me3) and repression (H3K27me3) marks allowing time-effective changes in the gene expression, and such phenomenon is vital in embryonic development [22][23][24] . ...
NEUROD1 is a transcription factor that helps maintain a mature phenotype of pancreatic β cells. Disruption of Neurod1 during pancreatic development causes severe neonatal diabetes; however, the exact role of NEUROD1 in the differentiation programs of endocrine cells is unknown. Here, we report a crucial role of the NEUROD1 regulatory network in endocrine lineage commitment and differentiation. Mechanistically, transcriptome and chromatin landscape analyses demonstrate that Neurod1 inactivation triggers a downregulation of endocrine differentiation transcription factors and upregulation of non-endocrine genes within the Neurod1 -deficient endocrine cell population, disturbing endocrine identity acquisition. Neurod1 deficiency altered the H3K27me3 histone modification pattern in promoter regions of differentially expressed genes, which resulted in gene regulatory network changes in the differentiation pathway of endocrine cells, compromising endocrine cell potential, differentiation, and functional properties.
... Together with H3K27 acetylation (H3K27ac), these marks define active enhancers and promoters, respectively [12][13][14][15] . In contrast, H3K4me3 in combination with H3K27me3 establish bivalent chromatin, which is linked to poised promoters 16,17 . Multiple readers have been described, which are thought to convey information encoded in H3K4 methylation, whose effects include chromatin remodeling, RNA polymerase (RNAPII) loading, and H3K4 methylation amplification 18,19 . ...
The trithorax protein ASH2L is essential for organismal and tissue development. As a subunit of COMPASS/KMT2 complexes, ASH2L is necessary for methylation of histone H3 lysine 4 (H3K4). Mono- and trimethylation at this site mark active enhancers and promoters, respectively, although the molecular relevance of H3K4 methylation is only partially understood. Due to the importance of ASH2L in all 6 COMPASS-like complexes and its long half-life, it has been difficult to define direct consequences. To overcome this limitation, we employed a PROTAC system, which allows the rapid degradation of ASH2L and addressing direct effects. Loss of ASH2L resulted in rapid inhibition of proliferation of mouse embryo fibroblasts. Shortly after ASH2L degradation, H3K4me3 decreased with its half-life revealing considerable variability between promoters. Subsequently, H3K4me1 increased at promoters and decreased at some enhancers. H3K27ac and H3K27me3, histone marks closely linked to H3K4 methylation, were affected with considerable delay. In parallel, chromatin compaction increased at promoters. Of note, nascent gene transcription was not affected early but overall RNA expression was deregulated late after ASH2L loss. Together, these findings suggest that downstream effects are ordered but relatively slow, despite the rapid loss of ASH2L and inactivation of KMT2 complexes. It appears that the systems that control gene transcription are well buffered and strong effects are only beginning to unfold after considerable delay.
... Several reports indicated the role of IKAROS in gene priming and poised or bivalent (hereafter, poised) chromatin organization [102][103][104][105][106]. It can also control transcriptional elongation [89] of target genes. ...
... At the promoter of most genes, poised chromatin is characterized by the combination of H3K27me3 and H3K4me3 [104,122]. Initially identified in ESCs [105,106], these poised (bivalent) chromatin marks also define many lineage-specific or signal-inducible genes in tissue-specific stem/progenitor cells. ...
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
... While FACT did not initially seem essential for cell proliferation outside of the context of cancer, more recent work has demonstrated heightened FACT expression and novel requirement in undifferentiated (stem) cells [43][44][45][46][47][48]. Stem cell chromatin is highly regulated by well-characterized features, including an accessible chromatin landscape relative to other cell types and bivalent chromatin, which is epigenetically decorated with both active (e.g., H3K4me3) and repressive (e.g., H3K27me3) modifications [49][50][51][52][53][54][55][56][57]. Embryonic stem (ES) cells specifically regulate their chromatin to prevent differentiation from occurring until appropriate, thereby preserving their pluripotent state. ...
Background
The FACT complex is a conserved histone chaperone with critical roles in transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but otherwise dispensable for most mammalian cell types. FACT deletion or inhibition can block induction of pluripotent stem cells, yet the mechanism through which FACT regulates cell fate decisions remains unclear.
Results
To explore the mechanism for FACT function, we generated AID-tagged murine embryonic cell lines for FACT subunit SPT16 and paired depletion with nascent transcription and chromatin accessibility analyses. We also analyzed SPT16 occupancy using CUT&RUN and found that SPT16 localizes to both promoter and enhancer elements, with a strong overlap in binding with OCT4, SOX2, and NANOG. Over a timecourse of SPT16 depletion, nucleosomes invade new loci, including promoters, regions bound by SPT16, OCT4, SOX2, and NANOG, and TSS-distal DNaseI hypersensitive sites. Simultaneously, transcription of Pou5f1 (encoding OCT4), Sox2, Nanog, and enhancer RNAs produced from these genes’ associated enhancers are downregulated.
Conclusions
We propose that FACT maintains cellular pluripotency through a precise nucleosome-based regulatory mechanism for appropriate expression of both coding and non-coding transcripts associated with pluripotency.
... Evidence from mammals indicates that activity-dependent methylation and demethylation of DNA are key to gene regulation during learning and memory [138][139][140]. The presence of methylated CpG dinucleotides on gene bodies and promoters is widely considered to be an epigenetic mark that acts to suppress transcription, whereas methylcytosine dioxygenase (Tet)mediated demethylation promotes it [141,142]. In in vitro conditioning, the promoter for exon II is rapidly methylated, and the exon III promoter is demethylated shortly after training onset (Fig. 3A). ...
... The chromatin architecture of genes also defines their expression. An open or closed chromatin structure is conferred by post-translational modifications such as methylation and acetylation of histones that control access of DNA binding by regulatory proteins [142,143]. Distinct histone modifications are closely associated Fig. 3 A Timing of promoter II methylation and promoter III demethylation after the onset of conditioning training. Total methylation levels for all CpG sites within promoter II and III are shown. ...
... A and B from Ref. [114]; C from Ref. [160] with observed changes in promoter binding and level of expression. Active gene promoters are generally marked by trimethylation of histone H3 lysine 4 (H3K4me3), while repressed promoters are marked by trimethylation of histone H3 lysine 27 (H3K27me3) [142]. The significance of these histone signatures for learning genes like BDNF is discussed further below. ...
An in vitro model of delay eyeblink classical conditioning was developed to investigate synaptic plasticity mechanisms underlying acquisition of associative learning. This was achieved by replacing real stimuli, such as an airpuff and tone, with patterned stimulation of the cranial nerves using an isolated brainstem preparation from turtle. Here, our primary findings regarding cellular and molecular mechanisms for learning acquisition using this unique approach are reviewed. The neural correlate of the in vitro eyeblink response is a replica of the actual behavior, and features of conditioned responses (CRs) resemble those observed in behavioral studies. Importantly, it was shown that acquisition of CRs did not require the intact cerebellum, but the appropriate timing did. Studies of synaptic mechanisms indicate that conditioning involves two stages of AMPA receptor (AMPAR) trafficking. Initially, GluA1-containing AMPARs are targeted to synapses followed later by replacement by GluA4 subunits that support CR expression. This two-stage process is regulated by specific signal transduction cascades involving PKA and PKC and is guided by distinct protein chaperones. The expression of the brain-derived neurotrophic factor (BDNF) protein is central to AMPAR trafficking and conditioning. BDNF gene expression is regulated by coordinated epigenetic mechanisms involving DNA methylation/demethylation and chromatin modifications that control access of promoters to transcription factors. Finally, a hypothesis is proposed that learning genes like BDNF are poised by dual chromatin features that allow rapid activation or repression in response to environmental stimuli. These in vitro studies have advanced our understanding of the cellular and molecular mechanisms that underlie associative learning.
... In the later course this definition was revised since bivalent domains were not only discovered in mouse and human ES cells but also in mammalian adult stem cells and adult tissues including keratinocytes (Kinkley et al, 2016;Mikkelsen et al, 2007;Barrero et al, 2013). Consequently, bivalency is now commonly seen as a way of expression fine-tuning during cell development and cell fate decisions, respectively, to prevent unscheduled gene activation providing robustness and plasticity but reduced noise during repression (Voigt et al, 2013). One of the central components in establishing and maintaining bivalency are the PcG proteins PRC1 and PRC2 (Harikumar & Meshorer, 2015), which are thought to be recruited by lncRNAs among others (Voigt et al, 2013). ...
... Consequently, bivalency is now commonly seen as a way of expression fine-tuning during cell development and cell fate decisions, respectively, to prevent unscheduled gene activation providing robustness and plasticity but reduced noise during repression (Voigt et al, 2013). One of the central components in establishing and maintaining bivalency are the PcG proteins PRC1 and PRC2 (Harikumar & Meshorer, 2015), which are thought to be recruited by lncRNAs among others (Voigt et al, 2013). In case of the NuRD complex, its role in interrelation with PcG proteins is better explored. ...
Numerous long non-coding RNAs (lncRNAs) were shown to have functional impact on cellular processes such as human epidermal homeostasis. However, the mechanism of action for many lncRNAs remains unclear to date. Here, we report that lncRNA LINC00941 regulates keratinocyte differentiation on an epigenetic level through association with the NuRD complex, one of the major chromatin remodelers in cells. We find that LINC00941 interacts with NuRD-associated MTA2 in human primary keratinocytes. LINC00941 perturbation changes MTA2/NuRD occupancy at bivalent chromatin domains in close proximity to transcriptional regulator genes, including the EGR3 gene coding for a transcription factor regulating epidermal differentiation. Notably, LINC00941 depletion resulted in reduced NuRD occupancy at the EGR3 gene locus, increased EGR3 expression in human primary keratinocytes, as well as increased abundance of EGR3-regulated epidermal differentiation genes in cells and human organotypic epidermal tissue. Our results therefore indicate a role for LINC00941/NuRD in repressing EGR3 expression in non-differentiated keratinocytes, consequentially preventing premature differentiation of human epidermal tissue.
... Ezh2 is known to act as a transcriptional repressor of bivalent genes, characterized by the concomitant presence of both repressive Ezh2dependent H3K27me3 and activating H3K4me3 epigenetic marks at their promoter regions 21,22 . We decided to identify which bivalent genes may be possible direct targets of Ezh2 in macrophages. ...
Epigenetic regulation of histone H3K27 methylation has recently emerged as a key step during alternative immunoregulatory M2-like macrophage polarization; known to impact cardiac repair after Myocardial Infarction (MI). We hypothesized that EZH2, responsible for H3K27 methylation, could act as an epigenetic checkpoint regulator during this process. We demonstrate for the first time an ectopic EZH2, and putative, cytoplasmic inactive localization of the epigenetic enzyme, during monocyte differentiation into M2 macrophages in vitro as well as in immunomodulatory cardiac macrophages in vivo in the post-MI acute inflammatory phase. Moreover, we show that pharmacological EZH2 inhibition, with GSK-343, resolves H3K27 methylation of bivalent gene promoters, thus enhancing their expression to promote human monocyte repair functions. In line with this protective effect, GSK-343 treatment accelerated cardiac inflammatory resolution preventing infarct expansion and subsequent cardiac dysfunction in female mice post-MI in vivo. In conclusion, our study reveals that pharmacological epigenetic modulation of cardiac-infiltrating immune cells may hold promise to limit adverse cardiac remodeling after MI.
... Bivalently marked genes tend to exhibit a low level of transcription that can be activated by the loss of H3K27me3 or repressed by the loss of H3K4me3, a status referred to as transcriptionally "poised" (94). In normal development, chromatin bivalency is enriched at elements regulating the expression of lineage-specific TFs and other developmental factors, enabling dynamic and rapid control of cell state (95,96). A general feature of lineage plasticity is hijacked control of the bivalent chromatin state, resulting in the activation of genes that promote plasticity and repression of genes that block plasticity, which collectively enable dedifferentiation and transdifferentiation processes (Box 1). ...
Unlabelled:
Lineage plasticity, a process whereby cells change their phenotype to take on a different molecular and/or histologic identity, is a key driver of cancer progression and therapy resistance. Although underlying genetic changes within the tumor can enhance lineage plasticity, it is predominantly a dynamic process controlled by transcriptional and epigenetic dysregulation. This review explores the transcriptional and epigenetic regulators of lineage plasticity and their interplay with other features of malignancy, such as dysregulated metabolism, the tumor microenvironment, and immune evasion. We also discuss strategies for the detection and treatment of highly plastic tumors.
Significance:
Lineage plasticity is a hallmark of cancer and a critical facilitator of other oncogenic features such as metastasis, therapy resistance, dysregulated metabolism, and immune evasion. It is essential that the molecular mechanisms of lineage plasticity are elucidated to enable the development of strategies to effectively target this phenomenon. In this review, we describe key transcriptional and epigenetic regulators of cancer cell plasticity, in the process highlighting therapeutic approaches that may be harnessed for patient benefit.
... Further gene function analysis revealed that these four clusters mainly enriched function terms involving cell morphogenesis, neural development and sensory organ development (Fig. 2h, i; Supplementary Fig. 2d, e), which is consistent with the functions of polycomb repressive complex in silencing development-related genes. To address the correlation between restoration rate and gene function in mESCs, we next collected the housekeeping, ES-specific, bivalent and tissue-specific gene lists from publications [31][32][33][34][35][36] and divided H3K27me3 target genes into four categories. Intriguingly, we found that the clusters of "super-fast", "fast" enriched in tissue-specific and bivalent genes, but the "slow" and "bottom-slow" clusters enriched in mostly ES and housekeeping genes ( Fig. 2j; Supplementary Fig. 2f). ...
During cell renewal, epigenetic information needs to be precisely restored to maintain cell identity and genome integrity following DNA replication. The histone mark H3K27me3 is essential for the formation of facultative heterochromatin and the repression of developmental genes in embryonic stem cells. However, how the restoration of H3K27me3 is precisely achieved following DNA replication is still poorly understood. Here we employ ChOR-seq (Chromatin Occupancy after Replication) to monitor the dynamic re-establishment of H3K27me3 on nascent DNA during DNA replication. We find that the restoration rate of H3K27me3 is highly correlated with dense chromatin states. In addition, we reveal that the linker histone H1 facilitates the rapid post-replication restoration of H3K27me3 on repressed genes and the restoration rate of H3K27me3 on nascent DNA is greatly compromised after partial depletion of H1. Finally, our in vitro biochemical experiments demonstrate that H1 facilitates the propagation of H3K27me3 by PRC2 through compacting chromatin. Collectively, our results indicate that H1-mediated chromatin compaction facilitates the propagation and restoration of H3K27me3 after DNA replication.
