Srivastava-2017-Histone H2A Monoubiquitination.pdf

Histone H2A monoubiquitination in neurodevelopmental disordersAnshika Srivastava1,Brian McGrath2,and Stephanie L.Bielas1,2,*1Department of Human Genetics,University of Michigan Medical School,Ann Arbor,Michigan,U.S.A2Cell and Molecular Biology Program,University of Michigan Medical School,Ann Arbor,Michigan,U.S.AAbstractCovalent histone modifications play an essential role in gene regulation and cellular specification required for multicellular organism development.Mono-ubiquitination of histone H2A(H2AUb1)is a reversible transcriptionally repressive mark.Exchange of histone H2A mono-ubiquitination and deubiquitination reflects the succession of transcriptional profiles during development required to produce cellular diversity from pluripotent cells.Germline pathogenic variants in components of the H2AUb1 regulatory axis are being identified as the genetic basis of congenital neurodevelopmental disorders.Here,we review the human genetics findings coalescing on molecular mechanisms that alter the genome-wide distribution of this histone modification required for development.KeywordsHistone mono-ubiquitination;Polycomb repression;neurogenetics;neurodevelopment disordersChromatin modifications in brain developmentDevelopmental decisions during lineage commitment are precisely coordinated at the genome level by gene expression programs that jointly activate or repress transcription 1.Brain development requires the concurrent differentiation of neuronal cell types that must be organized into a complex organ 2,3.This process involves specification of pluripotent cells to ectoderm and neural precursors prior to terminal differentiation.Thus,brain development depends on precise temporal control of gene expression patterns,and disruption of transcriptional networks in brain development underlies neurodevelopmental disorders.It is not known how groups of genes are co-regulated during fate specification of*Corresponding Author:Stephanie L.Bielas,Department of Human Genetics,University of Michigan Medical School,3703 Medical Science II,1137 Catherine St.SPC 5618,Ann Arbor,MI 48109-5618,U.S.A.Phone:001.734.647.8890;Fax:011.734.763.3784;sbielasumich.edu.Publishers Disclaimer:This is a PDF file of an unedited manuscript that has been accepted for publication.As a service to our customers we are providing this early version of the manuscript.The manuscript will undergo copyediting,typesetting,and review of the resulting proof before it is published in its final citable form.Please note that during the production process errors may be discovered which could affect the content,and all legal disclaimers that apply to the journal pertain.HHS Public AccessAuthor manuscriptTrends Genet.Author manuscript;available in PMC 2018 August 01.Published in final edited form as:Trends Genet.2017 August;33(8):566578.doi:10.1016/j.tig.2017.06.002.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptneural lineages.Modification of histone marks is fundamentally important in specifying different cell types during embryonic development and pathogenic variants in genes that encode a broad-set of molecules that mediate chromatin modifications,including mono-ubiquitination of histone H2A lysine 119(H2AUb1),are emerging as a prominent contribution to the genetic and molecular etiology of neurodevelopmental disorders 46.DNA,wound around nucleosomes,is organized as chromatin fibers.Each nucleosome octamer is composed of two of each evolutionarily conserved histones H2A,H2B,H3 and H4 7,8.The N-terminal tail of histones undergo numerous post-translational modifications(PTMs),including acetylation,ubiquitination,phosphorylation,or methylation of specific amino acid residues.Histone PTMs influence chromatin compaction,transcriptional regulation and interaction with protein complexes.Histone PTMs also correlate with active,repressive,and poised gene expression states.The genome-wide histone PTM landscape requires active maintenance to accommodate changing transcriptional profiles that allow for differentiation of diverse cell types and tissues from pluripotent stem cells during development 9.Ubiquitin is a small molecule,which when covalently bound to substrates serves many biological functions.While poly-ubiquitination targets proteins for degradation via the 26S proteasome,monoubiquitination of histone H2A acts as a repressive chromatin modification.H2AUb1 has historically been associated with the E3 ubiquitin ligase activity of Polycomb repressive complex 1(PRC1)and Polycomb transcriptional repression(Box 1),yet a variety of molecules that ubiquitinate or deubiquitinate H2A comprised of components of the H2AUb1 regulatory axis 1013.The components that decorate H2A with ubiquitin include canonical PRC1,variant PRC1,and TRIM37.Among the deubiquitinating components are the Polycomb repressive deubiquitinating complexes(PR-DUB)and USP16 14,15(Figure 1,Key Figure).Dynamic exchange of this histone modification reflect the succession of transcriptional profile changes required to produce the cellular diversity from pluripotent cells during development.Box 1Polycomb Chromatin ModifiersPolycomb group(PcG)proteins function as chromatin-based transcriptional repressors and are essential for gene regulation during development.The functions of PcG complexes include modifying the genomic histone PTM landscape and establishing 3D chromatin topology and condensed chromatin at developmentally regulated loci 81.First identified in Drosophila as important regulators of body plan specification,orthologous PcG systems were subsequently identified in vertebrates and also shown to be essential for developmental gene regulation 8284.Three PcG complexes,polycomb repressive complex 1(PRC1),complex 2(PRC2)and polycomb repressive deubiquitination complex(PR-DUB)have been identified and have various histone modifying activities(Figure.1B)64,85.PRC2 catalyzes trimethylation and dimethylation of histone H3 lysine 27(H3K27me3/2)86.H3K27me3 plays a crucial role in the establishment of facultative heterochromatin throughout development.PRC1 catalyzes the mono-ubiquitination of H2A,while PR-DUB hydrolyzes ubiquitin from Srivastava et al.Page 2Trends Genet.Author manuscript;available in PMC 2018 August 01.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor ManuscriptH2AUb1.The opposing functions of PRC1 and PR-DUB complex on histone H2AUb1 accentuates the important role for genome-wide H2AUb1 modification exchange in cell specification and development.In the hierarchical model,CBX recognizes the PRC2 H3K27me3 mark then recruits PRC1 to bivalent loci.However,when H3K27me3 levels were reduced in Eed knockout mESC,required for PRC2 stability,the levels and localization of H2AUb1 remained relatively unchanged implicating PRC2 independent H2A ubiquitination activity 76.Furthermore,a series of experiments have demonstrated H2Aub1 recruiting PRC2 to genomic loci 8789.The mechanisms by which these PTM activities of PcG complexes are coordinated and recruited for transcriptional repression varies between organisms,across development and by tissue and is an important area of research elegantly addressed in recent reviews 11,83,85,90.A number of recent in vitro and in vivo studies have determined that the chromatin compaction functions of PRC1 and PRC2 can occur independent of their histone PTM activity 9193.Developmental repression of genomic loci by PRC1 is achieved by tethering compacted chromatin in nuclear foci that are modified during differentiation and development.Formation of these chromatin structures require chromatin tethering functions of canonical PRC1 complexes,but not H2AUb1 or variant PRC1 complexes.Large scale sequencing studies and widespread use of clinical exome sequencing are identifying inherited and de novo germline variants enriched in the H2AUb1 regulatory axis as important molecular pathology of syndromic neurodevelopmental disorders with features of autism and intellectual disability.Pathogenic human variants observed in Autism susceptibility candidate 2(AUTS2),Polyhomeotic-like 1(PHC1),Additional sex combs like family members(ASXl1,2,3),Tripartite motif-containing protein 37(TRIM37),BCL6 corepressor(BCOR)and Ubiquitin-specific protease 16(USP16)are components of the histone H2A ubiquitination regulatory axis.In this review,we will summarize the confluence of human neurogenetic findings around this important area of histone modification critical for brain development(Table 1).Mono-ubiquitinated histone H2AReversible H2AUb1 has diverse roles in a complex transcriptional milieu comprised of multiple chromatin modifications,DNA methylation,and chromatin remodeling molecules.H2AUb1 is enriched at bivalent promoters,characterized by the presence of both the activating H3K4me3 and repressive H3K27me3 histone PTMs 1621.Within ESCs,bivalent promoters are signature of developmentally important genes that establish cell identity 17,22,23.H2AUb1 serves to prevent elongation of RNA polymerase machinery at bivalent loci,while RNA polymerase initiation remains unhindered 24,25.This poised state allows for dynamic transition between a transcriptionally active or repressed state required for normal development.Ubiquitinating and deubiquitinating components of the H2AUb1 regulatory axis reflect a similar genome-wide binding pattern implicating developmental modulation of this modification as an important regulatory mechanism 21,26,27.Resolution of bivalent promoters at developmentally regulated genes towards active or fully repressed involves the concerted activity of various chromatin-modifying complexes 28,29.The emerging mechanisms suggest they can interact.The compounding effect Srivastava et al.Page 3Trends Genet.Author manuscript;available in PMC 2018 August 01.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptamong histone modifications due to alteration of a single histone modification can complicate interpreting the resulting molecular and transcriptional impacts.The majority of mammalian gene promoters are encompassed by CpG islands,that correspond to contiguous non-methylated segments of the genome with a higher than average level of CpG dinucleotides 30.DNA methylation of CpG islands acts as a stable and heritable repressive epigenetic mark essential for development and generating a diversity of cell fates from multipotent progenitor cells.H2AUb1 plays an important role in epigenetic establishment of mature cell fates by protecting CpG islands against DNA methylation required for constitutive repression of the corresponding genes 31,32.It still remains mechanistically unclear how developmental redistribution of H2AUb1 contributes to this diversity of transcriptional functions.Nevertheless,it underscores the diversity of clinical features and syndromic nature of inherited neurodevelopmental disorders that impact the H2AUb1 regulatory axis.Polycomb H2A ubiquitinationPRC1 is an important source of H2A E3 ubiquitin ligase activity that has been the focus of substantial research.PRC1 is a multimeric complex with evolutionarily conserved function in transcriptional repression and non-enzymatic chromatin compaction.Polycomb group(PcG)proteins were originally described in Drosophila based on their regulation of Hox gene expression,that when dysregulated results in homeotic transformations,including additional sex combs,a structure present on the legs of male flies.Genetic screens of Drosophila mutants that exhibit this phenotype were important for identifying the composition of PcG complexes and mechanisms of transcriptional repression.PRC1 and PRC2 were the founding complexes that choreograph H2A monoubiquitination and H3 lysine 27 trimethylation(H3K27Me3)respectively required for transcriptional regulation(Box 1).Work in invertebrates and vertebrates are uncovering differences in the mechanisms of PcG transcriptional repression and the composition of PRC1 between these organisms.In Drosophila,the dynamic functions of PRC1 and PRC2 are coordinated in a sequential manner at polycomb repressive elements(PREs)to mediate transcriptional repression and chromatin compaction,with PRC2 initiating this molecular cascade.In vertebrates PREs are not the functional genomic element that provides the platform for PcG repression and coordination of PRC1 and PRC2 activities exhibits more diversity.Likewise,the compositions of PRC1 complexes are more heterogeneous in vertebrates(Box 2),yet the E3 ubiquitin ligase and chromatin compaction activities are conserved.Interestingly,evidence that these two PRC1 activities are functionally distinct has precipitated a series of studies designed to isolate their functional impacts on development.Box 2PRC1-Canonical vs.VariantCanonical and variant PRC1 complexes are defined by the presence of the E3 ubiquitin ligase RING1A or RING1B,but differ in protein assembly of the larger multimeric Srivastava et al.Page 4Trends Genet.Author manuscript;available in PMC 2018 August 01.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptcomplex.In depth discussion of PRC1 components and complexities have been reviewed elsewhere 10,11.Briefly,canonical PRC1 is comprised of RING1,PHC1,and CBX family members as well as PCGF2 or PCGF4(Figure 3).Each family of core proteins consists of a number of paralogs,RING1 has two,PHC1 three and CBX five,increasing the diversity of potential canonical PRC1 complexes.Variant PRC1 can contain a combination of these proteins and several accessory binding partners including BCOR,KDM2B,E2F6,RYBP,and AUTS2 that uniquely specify variant PRC1 complexes(Figure I).Canonical and variant PRC1 are distinguished and labeled by which of the PCGF are incorporated 12,94.Expression of family members and PRC1 composition vary across cell types and developmental time points 72,73.CBX7 is the only homolog present in the PRC1 complexes within ESCs.However,upon differentiation CBX7 expression is reduced while CBX2 and CBX4 are increased demonstrating cell type specificity 73.Several distinct PRC1 complexes can coexist within the same cell type but bind to and regulate distinct genomic loci 57,76.In ESCs,RYBP and CBX form mutually exclusive PRC1 complexes,which bind to coincident and unique targets 11,12,73.CBX-PRC1 only targets are enriched for developmental and lineage specific genes,whereas RYBP-Prc1 localized to metabolic and M-phase associated genes 73.Variant PRC1 accessory proteins can also provide unique functionality to the PRC1 complexes.For example,the H3K36me2 demethylase,KDM2,interacts with the variant BCOR complex and recruits the complex to CPG islands 32,77,78.Beyond ubiquitination,PRC1 complexes repress gene activity by chromatin compaction 20,33,92.Canonical PRC1 complexes can generate self-contained interaction domains at target sites,which can be lost upon differentiation 92.Chromosomal compaction by PRC1 in this manner is independent of H2AUb1 and variant PRC1 proteins 33,92.It will be inter