Regulation of HOXA2 gene expression by the ATP‐dependent chromatin remodeling enzyme CHD8
TL;DR: This data indicates that CHD8 physically interacts with RbBP5, ASH2L, ASh2L and WDR5 by anti tag coimmunoprecipitation by anti tagged particles.
Abstract: Chromodomain, helicase, DNA-binding protein 8 (CHD8) is an ATP-dependent chromatin remodeling enzyme that has been demonstrated to exist within a large protein complex which includes WDR5, Ash2L, and RbBP5, members of the Mixed Lineage Leukemia (MLL) histone modifying complexes. Here we show that CHD8 relocalizes to the promoter of the MLL regulated gene HOXA2 upon gene activation. Depletion of CHD8 enhances HOXA2 expression under activating conditions. Furthermore, depletion of CHD8 results in a loss of the WDR5/Ash2L/RbBP5 subcomplex, and consequently H3K4 trimethylation, at the HOXA2 promoter. These studies suggest that CHD8 alters HOXA2 gene expression and regulates the recruitment of chromatin modifying enzymes.
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TL;DR: A comprehensive review of the epigenetic processes in the testes, correlation of epigenetic aberrations with male infertility, impact of environmental factors on the epigenome and male fertility, and significance of epigenetics changes/aberrations in assisted reproduction are provided.
Abstract: Epigenetic modifications characterized by DNA methylation, histone modifications, and chromatin remodeling are important regulators in a number of biological processes, including spermatogenesis. Several genes in the testes are regulated through epigenetic mechanisms, indicating a direct influence of epigenetic mechanisms on the process of spermatogenesis. In the present article, we have provided a comprehensive review of the epigenetic processes in the testes, correlation of epigenetic aberrations with male infertility, impact of environmental factors on the epigenome and male fertility, and significance of epigenetic changes/aberrations in assisted reproduction. The literature review suggested a significant impact of epigenetic aberrations (epimutations) on spermatogenesis, and this could lead to male infertility. Epimutations (often hypermethylation) in several genes, namely MTHFR, PAX8, NTF3, SFN, HRAS, JHM2DA, IGF2, H19, RASGRF1, GTL2, PLAG1, D1RAS3, MEST, KCNQ1, LIT1, and SNRPN, have been reported in association with poor semen parameters or male infertility. Environmental toxins/drugs may affect fertility via epigenetic modifications. For example, 5-aza-2'-deoxycytidine, an anticancer agent, causes a decrease in global DNA methylation that leads to altered sperm morphology, decreased sperm motility, decreased fertilization capacity, and decreased embryo survival. Similarly, Endocrine disruptors, such as methoxychlor (an estrogenic pesticide) and vinclozolin (an anti-androgenic fungicide) have been found by experiments on animals to affect epigenetic modifications that may cause spermatogenic defects in subsequent generations. Assisted reproduction procedures that have been considered rather safe, are now being implicated in inducing epigenetic changes that could affect fertility in subsequent generations. Techniques such as intracytoplasmic sperm injection (ICSI) and round spermatid injection (ROSI) may increase the incidence of imprinting disorders and adversely affect embryonic development by using immature spermatozoa that may not have established proper imprints or global methylation. Epigenetic changes, in contrast to genetic aberrations, may be less deleterious because they are potentially reversible. Further research could identify certain drugs capable of reversing epigenetic changes.
263 citations
Cites background from "Regulation of HOXA2 gene expression..."
...The SWI/SNF and ISWI families are ubiquitous, as well as act in a non-specific fashion on various loci [23]....
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...SWI/SNF, ISWI Chromatin remodeling [22,23]...
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TL;DR: Transmission pattern analyses reveal that LOF variants are more likely to be transmitted to affected individuals than controls, and especially true for private LOF variant in genes intolerant to functional genetic variation, which highlights the contribution of LOF mutations to the genetic architecture of schizophrenia.
Abstract: Loss-of-function (LOF) (i.e., nonsense, splice site, and frameshift) variants that lead to disruption of gene function are likely to contribute to the etiology of neuropsychiatric disorders. Here, we perform a systematic investigation of the role of both de novo and inherited LOF variants in schizophrenia using exome sequencing data from 231 case and 34 control trios. We identify two de novo LOF variants in the SETD1A gene, which encodes a subunit of histone methyltransferase, a finding unlikely to have occurred by chance, and provide evidence for a more general role of chromatin regulators in schizophrenia risk. Transmission pattern analyses reveal that LOF variants are more likely to be transmitted to affected individuals than controls. This is especially true for private LOF variants in genes intolerant to functional genetic variation. These findings highlight the contribution of LOF mutations to the genetic architecture of schizophrenia and provide important insights into disease pathogenesis.
163 citations
Cites background from "Regulation of HOXA2 gene expression..."
...…which recurrent de novo LOF mutations have been identified in ASD patients (O’Roak et al., Neuron 82, 773–780, May 21, 2014 ª2014 Elsevier Inc. 777 2012a, 2012b), directly interacts with common subunits of Set/ COMPASS and plays a role in the regulation of H3K4 trimethylation (Yates et al., 2010)....
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...2012a, 2012b), directly interacts with common subunits of Set/ COMPASS and plays a role in the regulation of H3K4 trimethylation (Yates et al., 2010)....
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TL;DR: It is shown that CHD8 promotes the association of β-catenin and histone H1, with formation of the trimeric complex on chromatin being required for inhibition ofβ- catenin-dependent transactivation.
Abstract: Members of the chromodomain helicase DNA-binding (CHD) family of proteins are thought to regulate gene expression. Among mammalian CHD proteins, CHD8 was originally isolated as a negative regulator of the Wnt-β-catenin signaling pathway that binds directly to β-catenin and suppresses its transactivation activity. The mechanism by which CHD8 inhibits β-catenin-dependent transcription has been unclear, however. Here we show that CHD8 promotes the association of β-catenin and histone H1, with formation of the trimeric complex on chromatin being required for inhibition of β-catenin-dependent transactivation. A CHD8 mutant that lacks the histone H1 binding domain did not show such inhibitory activity, indicating that histone H1 recruitment is essential for the inhibitory effect of CHD8. Furthermore, either depletion of histone H1 or expression of a dominant negative mutant of this protein resulted in enhancement of the response to Wnt signaling. These observations reveal a new mode of regulation of the Wnt signaling pathway by CHD8, which counteracts β-catenin function through recruitment of histone H1 to Wnt target genes. Given that CHD8 is expressed predominantly during embryogenesis, it may thus contribute to setting a threshold for responsiveness to Wnt signaling that operates in a development-dependent manner.
124 citations
Cites background from "Regulation of HOXA2 gene expression..."
...CHD8 has also been implicated as a positive or negative transcriptional regulator of various genes (19, 32, 33, 45, 46)....
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TL;DR: Emerging evidence suggests that exposure to environmental stresses in older generations may predispose subsequent generations to disease in a manner that involves the transgenerational inheritance of epigenetic information.
Abstract: Epigenetic control of gene expression programs is essential for normal organismal development and cellular function. Abrogation of epigenetic regulation is seen in many human diseases, including cancer and neuropsychiatric disorders, where it can affect disease etiology and progression. Abnormal epigenetic profiles can serve as biomarkers of disease states and predictors of disease outcomes. Therefore, epigenetics is a key area of clinical investigation in diagnosis, prognosis, and treatment. In this review, we give an overarching view of epigenetic mechanisms of human disease. Genetic mutations in genes that encode chromatin regulators can cause monogenic disease or are incriminated in polygenic, multifactorial diseases. Environmental stresses can also impact directly on chromatin regulation, and these changes can increase the risk of, or directly cause, disease. Finally, emerging evidence suggests that exposure to environmental stresses in older generations may predispose subsequent generations to disease in a manner that involves the transgenerational inheritance of epigenetic information.
117 citations
TL;DR: A novel interaction site is identified on the core complex protein WD repeat protein-5 (WDR5), and the complementary site on its partner retinoblastoma-binding protein- 5 (RbBP5) is mapped, characterized by x-ray crystallography and shown how it is fundamental to the assembly of the complex and to the regulation of methyltransferase activity.
Abstract: Histone modification is well established as a fundamental mechanism driving the regulation of transcription, replication, and DNA repair through the control of chromatin structure. Likewise, it is apparent that incorrect targeting of histone modifications contributes to misregulated gene expression and hence to developmental disorders and diseases of genomic instability such as cancer. The KMT2 family of SET domain methyltransferases, typified by mixed lineage leukemia protein-1 (MLL1), is responsible for histone H3 lysine 4 methylation, a marker of active genes. To ensure that this modification is correctly targeted, a multiprotein complex associates with the methyltransferase and directs activity. We have identified a novel interaction site on the core complex protein WD repeat protein-5 (WDR5), and we mapped the complementary site on its partner retinoblastoma-binding protein-5 (RbBP5). We have characterized this interaction by x-ray crystallography and show how it is fundamental to the assembly of the complex and to the regulation of methyltransferase activity. We show which region of RbBP5 contributes directly to mixed lineage leukemia activation, and we combine our structural and biochemical data to produce a model to show how WDR5 and RbBP5 act cooperatively to stimulate activity.
102 citations
References
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TL;DR: Current ideas on the protein and DNA components of this transcriptional memory system are reviewed and how they interact dynamically with each other to orchestrate cellular memory for several hundred genes are reviewed.
Abstract: During the development of multicellular organisms, cells become different from one another by changing their genetic program in response to transient stimuli. Long after the stimulus is gone, "cellular memory" mechanisms enable cells to remember their chosen fate over many cell divisions. The Polycomb and Trithorax groups of proteins, respectively, work to maintain repressed or active transcription states of developmentally important genes through many rounds of cell division. Here we review current ideas on the protein and DNA components of this transcriptional memory system and how they interact dynamically with each other to orchestrate cellular memory for several hundred genes.
1,050 citations
TL;DR: The results are the first demonstration that a WD40-repeat protein acts as a module for recognition of a specific histone modification and suggest a mechanism for reading and writing an epigenetic mark for gene activation.
Abstract: Histone H3 lysine 4 (K4) methylation has been linked to the transcriptional activation in a variety of eukaryotic species. Here we show that a common component of MLL1, MLL2, and hSet1 H3 K4 methyltransferase complexes, the WD40-repeat protein WDR5, directly associates with histone H3 di- and trimethylated at K4 and with H3-K4-dimethylated nucleosomes. WDR5 is required for binding of the methyltransferase complex to the K4-dimethylated H3 tail as well as for global H3 K4 trimethylation and HOX gene activation in human cells. WDR5 is essential for vertebrate development, in that WDR5-depleted X. laevis tadpoles exhibit a variety of developmental defects and abnormal spatial Hox gene expression. Our results are the first demonstration that a WD40-repeat protein acts as a module for recognition of a specific histone modification and suggest a mechanism for reading and writing an epigenetic mark for gene activation.
820 citations
"Regulation of HOXA2 gene expression..." refers background in this paper
...Because WAR is also involved in establishing methylation patterns at target genes [8,9,12,13], we next asked whether CHD8 is involved in the recruitment of WAR to the promoters of target genes....
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...Previous studies have demonstrated that WAR is recruited to the HOX locus and is an important regulator of HOX gene expression [8,9,12,13]....
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TL;DR: Observations constitute the first instance of extensive somatic differentiation of a clonal human EC cell line in vitro when exposed to retinoic acid.
Abstract: The human embryonal carcinoma cell lines NT2 /D1 and NT2 /B9, clonally derived from Tera-2, differentiate extensively in vitro when exposed to retinoic acid. This differentiation is marked by the appearance of several morphologically distinct cell types and by changes in cell surface phenotype, particularly by the disappearance of stage-specific embryonic antigen-3 (SSEA-3), which is characteristically expressed by human EC cells. Among the differentiated cells are neurons, which form clusters interconnected by extended networks of axon bundles, and which express tetanus toxin receptors and neurofilament proteins. These observations constitute the first instance of extensive somatic differentiation of a clonal human EC cell line in vitro.
804 citations
"Regulation of HOXA2 gene expression..." refers methods in this paper
...The NT2/D1 embryonal carcinoma cell line was chosen as treatment of these cells with ATRA induces the expression of many genes, including the HOX genes [16], and ultimately induces cellular differentiation into neuronal-like lineages [17]....
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TL;DR: This study reports the first biochemical reconstitution of a functional four-component mixed-lineage leukemia protein-1 (MLL1) core complex and demonstrates that WDR5 mediates interactions of the MLL1 catalytic unit both with the common structural platform and with the histone substrate.
Abstract: Histone H3 Lys4 (H3K4) methylation is a prevalent mark associated with transcription activation. A common feature of several H3K4 methyltransferase complexes is the presence of three structural components (RbBP5, Ash2L and WDR5) and a catalytic subunit containing a SET domain. Here we report the first biochemical reconstitution of a functional four-component mixed-lineage leukemia protein-1 (MLL1) core complex. This reconstitution, combined with in vivo assays, allows direct analysis of the contribution of each component to MLL1 enzymatic activity and their roles in transcriptional regulation. Moreover, taking clues from a crystal structure analysis, we demonstrate that WDR5 mediates interactions of the MLL1 catalytic unit both with the common structural platform and with the histone substrate. Mechanistic insights gained from this study can be generalized to the whole family of SET1-like histone methyltransferases in mammals.
722 citations
"Regulation of HOXA2 gene expression..." refers background in this paper
...As WDR5, Ash2L, and RbBP5 (WAR) form a subcomplex in the absence of MLL [12,13], we asked whether CHD8 could also associate with WDR5 in the context of the subcomplex....
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...Hox expression is controlled by the opposing actions of the Polycomb group of repressors and the Trithorax/Mixed Lineage Leukemia (MLL) group of activators [2]....
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...MLL1 is a histone H3 lysine 4 (H3K4) methyltransferase and is a member of the MLL/hSet1 family of enzymes....
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...journal homepage: www.FEBSLetters .org Regulation of HOXA2 gene expression by the ATP-dependent chromatin remodeling enzyme CHD8 Joel A. Yates, Tushar Menon 1, Brandi A. Thompson 1,2, Daniel A. Bochar * The Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA a r t i c l e i n f o a b s t r a c t Article history: Received 12 November 2009 Revised 23 December 2009 Accepted 7 January 2010 Available online 17 January 2010 Edited by Ivan Sadowski Keywords: Chromodomain, helicase, DNA-binding protein 8 (CHD8) HOX gene regulation ATP-dependent chromatin remodeling WDR5 0014-5793/$36.00 2010 Federation of European Bio doi:10.1016/j.febslet.2010.01.022 Abbreviations: ATRA, all-trans retinoic acid; CHD, c binding; ChIP, chromatin immunoprecipitation; DME Medium; MLL, Mixed Lineage Leukemia; NT2/D1, NTE PCR; RT, reverse transcription; shRNA, short hairpi RbBP5 * Corresponding author....
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...2 Present address: Laboratory of Cellular and De National Institutes of Health, Bethesda, MD 20892, USA Chromodomain, helicase, DNA-binding protein 8 (CHD8) is an ATP-dependent chromatin remodeling enzyme that has been demonstrated to exist within a large protein complex which includes WDR5, Ash2L, and RbBP5, members of the Mixed Lineage Leukemia (MLL) histone modifying complexes....
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TL;DR: The biochemical purification of MLL is reported and it is demonstrated that it associates with a cohort of proteins shared with the yeast and human SET1 histone methyltransferase complexes, including a homolog of Ash2, another Trx-G group protein, and a potential mechanism for regulating its antagonistic transcriptional properties.
Abstract: MLL (for mixed-lineage leukemia) is a proto-oncogene that is mutated in a variety of human leukemias. Its product, a homolog of Drosophila melanogaster trithorax, displays intrinsic histone methyltransferase activity and functions genetically to maintain embryonic Hox gene expression. Here we report the biochemical purification of MLL and demonstrate that it associates with a cohort of proteins shared with the yeast and human SET1 histone methyltransferase complexes, including a homolog of Ash2, another Trx-G group protein. Two other members of the novel MLL complex identified here are host cell factor 1 (HCF-1), a transcriptional coregulator, and the related HCF-2, both of which specifically interact with a conserved binding motif in the MLLN (p300) subunit of MLL and provide a potential mechanism for regulating its antagonistic transcriptional properties. Menin, a product of the MEN1 tumor suppressor gene, is also a component of the 1-MDa MLL complex. Abrogation of menin expression phenocopies loss of MLL and reveals a critical role for menin in the maintenance of Hox gene expression. Oncogenic mutant forms of MLL retain an ability to interact with menin but not other identified complex components. These studies link the menin tumor suppressor protein with the MLL histone methyltransferase machinery, with implications for Hox gene expression in development and leukemia pathogenesis.
671 citations