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1.
Nat Commun ; 10(1): 2950, 2019 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-31270318

RESUMO

X-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments. SMCHD1 then merges S1/S2s to form the Xi super-structure. Here, we ask how S1/S2 compartments form and reveal that Xist RNA drives their formation via recruitment of Polycomb repressive complex 1 (PRC1). Ablating Smchd1 in post-XCI cells unveils S1/S2 structures. Loss of SMCHD1 leads to trapping Xist in the S1 compartment, impairing RNA spreading into S2. On the other hand, depleting Xist, PRC1, or HNRNPK precludes re-emergence of S1/S2 structures, and loss of S1/S2 compartments paradoxically strengthens the partition between Xi megadomains. Finally, Xi-reactivation in post-XCI cells can be enhanced by depleting both SMCHD1 and DNA methylation. We conclude that Xist, PRC1, and SMCHD1 collaborate in an obligatory, sequential manner to partition, fuse, and direct self-association of Xi compartments required for proper spreading of Xist RNA.


Assuntos
Proteínas Cromossômicas não Histona/metabolismo , Cromossomos de Mamíferos/genética , Complexo Repressor Polycomb 1/metabolismo , RNA Longo não Codificante/metabolismo , Cromossomo X/química , Cromossomo X/genética , Animais , Metilação de DNA/genética , Histonas/metabolismo , Lisina/metabolismo , Camundongos , Modelos Genéticos , Inativação do Cromossomo X/genética
2.
Nat Commun ; 10(1): 3009, 2019 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-31285442

RESUMO

Quantitative genetics theory predicts that X-chromosome dosage compensation (DC) will have a detectable effect on the amount of genetic and therefore phenotypic trait variances at associated loci in males and females. Here, we systematically examine the role of DC in humans in 20 complex traits in a sample of more than 450,000 individuals from the UK Biobank and 1600 gene expression traits from a sample of 2000 individuals as well as across-tissue gene expression from the GTEx resource. We find approximately twice as much X-linked genetic variation across the UK Biobank traits in males (mean h2SNP = 0.63%) compared to females (mean h2SNP = 0.30%), confirming the predicted DC effect. Our DC estimates for complex traits and gene expression are consistent with a small proportion of genes escaping X-inactivation in a trait- and tissue-dependent manner. Finally, we highlight examples of biologically relevant X-linked heterogeneity between the sexes that bias DC estimates if unaccounted for.


Assuntos
Genes Ligados ao Cromossomo X/genética , Loci Gênicos/genética , Variação Genética/genética , Herança Multifatorial/genética , Inativação do Cromossomo X/genética , Conjuntos de Dados como Assunto , Feminino , Estudo de Associação Genômica Ampla , Humanos , Masculino , Modelos Genéticos , Fenótipo , Fatores Sexuais
3.
Res Vet Sci ; 125: 170-175, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31247472

RESUMO

X-chromosome inactivation pattern (XCIP) analysis can be used to assess the clonality of cell populations of various origin by distinguishing the methylated X chromosome from the unmethylated X chromosome. In this study, the utility of XCIP analysis was improved by incorporating the examination of AC dinucleotide repeats in SLIT and NTRK-like family member 4 (SLITRK4) gene into the previously reported CAG repeat examination of androgen receptor (AR) gene in dogs. The rate of heterozygosity when both genes were analysed (125/150, 83.3%) was higher than AR gene examination alone (86/150, 57.3%). Blood samples from heterozygous dogs in either AC-1 or AC-2 of SLITRK4 gene were examined for the corrected inactivation allele ratio (CIAR), resulting in the determination of a reference range of CIAR <3.8 in non-neoplastic cell/tissue samples. Using this analytical method, 49% (21/43) of neoplastic tissue samples from dogs showed a CIAR >3.8, indicating the presence of a clonal population. Through the present study, the availability of canine XCIP analysis was improved by incorporating the examination of the SLITRK4 gene, providing a highly useful laboratory examination system for the detection of the clonality of various cell/tissue samples in dogs.


Assuntos
Proteínas de Membrana/metabolismo , Receptores Androgênicos/metabolismo , Inativação do Cromossomo X , Cromossomo X/fisiologia , Alelos , Animais , Linhagem da Célula , Doenças do Cão/genética , Doenças do Cão/metabolismo , Cães , Feminino , Regulação da Expressão Gênica , Heterozigoto , Masculino , Proteínas de Membrana/genética , Neoplasias/genética , Neoplasias/metabolismo , Receptores Androgênicos/genética
4.
Cell Mol Life Sci ; 76(22): 4525-4538, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31139846

RESUMO

Dosage compensation, which is achieved by X-chromosome inactivation (XCI) in female mammals, ensures balanced X-linked gene expression levels between the sexes. Although eutherian mammals commonly display random XCI in embryonic and adult tissues, imprinted XCI has also been identified in extraembryonic tissues of mouse, rat, and cow. Little is known about XCI in pigs. Here, we sequenced the porcine XIST gene and identified an insertion/deletion mutation between Asian- and Western-origin pig breeds. Allele-specific analysis revealed biallelic XIST expression in porcine ICSI blastocysts. To investigate the XCI pattern in porcine placentas, we performed allele-specific RNA sequencing analysis on individuals from reciprocal crosses between Duroc and Rongchang pigs. Our results were the first to reveal that random XCI occurs in the placentas of pigs. Next, we investigated the H3K27me3 histone pattern in porcine blastocysts, showing that only 17-31.8% cells have attained XCI. The hypomethylation status of an important XIST DMR (differentially methylated region) in gametes and early embryos demonstrated that no methylation is pre-deposited on XIST in pigs. Our findings reveal that the XCI regulation mechanism in pigs is different from that in mice and highlight the importance of further study of the mechanisms regulating XCI during early porcine embryo development.


Assuntos
Impressão Genômica/genética , Placenta/metabolismo , RNA Longo não Codificante/genética , Inativação do Cromossomo X/genética , Alelos , Animais , Blastocisto/metabolismo , Células Cultivadas , Metilação de DNA/genética , Compensação de Dosagem (Genética)/genética , Feminino , Histonas/genética , Camundongos , Gravidez , Suínos
5.
Nat Genet ; 51(6): 1024-1034, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31133748

RESUMO

The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other's TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically upregulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento , RNA Longo não Codificante/genética , Inativação do Cromossomo X , Animais , Diferenciação Celular/genética , Expressão Ectópica do Gene , Células-Tronco Embrionárias/citologia , Células-Tronco Embrionárias/metabolismo , Feminino , Inativação Gênica , Loci Gênicos , Masculino , Camundongos , Modelos Biológicos , Regiões Promotoras Genéticas , Inversão de Sequência , Transcrição Genética
6.
RNA ; 25(8): 1004-1019, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31097619

RESUMO

The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analog of eutherian Xist Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of nonlinear sequence similarity. Xist Repeats B, C, and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.


Assuntos
Marsupiais/genética , RNA Longo não Codificante/química , RNA Longo não Codificante/genética , Animais , Análise por Conglomerados , Humanos , Marsupiais/metabolismo , Proteínas do Grupo Polycomb/metabolismo , Domínios Proteicos , Homologia de Sequência do Ácido Nucleico , Sequências de Repetição em Tandem , Inativação do Cromossomo X
7.
Mol Genet Metab ; 127(1): 31-44, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31097364

RESUMO

Histone demethylases remove transcriptional repressive marks from histones in the nucleus. KDM6A (also known as UTX) is a lysine demethylase which acts on the trimethylated lysine at position 27 in histone 3. The KDM6A gene is located on the X chromosome but escapes X inactivation even though it is not located in the pseudoautosomal region. There is a homologue of KDM6A on the Y chromosome, known as UTY. UTY was thought to have lost its demethylase activity and to represent a non-functional remnant of the ancestral KDM6A gene. However, results with knockout mice suggest that the gene is expressed and the protein performs some function within the cell. Female mice with homozygous deletion of Kdm6a do not survive, but hemizygous males are viable, attributed to the presence of the Uty gene. KDM6A is mutated in the human condition Kabuki syndrome type 2 (OMIM 300867) and in many cases of cancer. The amino acid sequence of KDM6A has been conserved across animal phyla, although it is only found on the X chromosome in eutherian mammals. In this review, we reanalyse existing data from various sources (protein sequence comparison, evolutionary genetics, transcription factor binding and gene expression analysis) to determine the function, expression and evolution of KDM6A and UTY and show that UTY has a functional role similar to KDM6A in metabolism and development.


Assuntos
Histona Desmetilases/genética , Histonas/metabolismo , Antígenos de Histocompatibilidade Menor/genética , Proteínas Nucleares/genética , Sequência de Aminoácidos , Animais , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Histona Desmetilases/metabolismo , Histonas/genética , Humanos , Masculino , Camundongos , Camundongos Knockout , Inativação do Cromossomo X/genética , Cromossomo Y/genética , Cromossomo Y/metabolismo
8.
Mol Cell ; 74(5): 1020-1036.e8, 2019 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-31029541

RESUMO

The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here, we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes, which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.


Assuntos
Cromatina/genética , Genômica , Complexo Repressor Polycomb 1/genética , Inativação do Cromossomo X/genética , Animais , Histonas/genética , Camundongos , Células-Tronco Embrionárias Murinas/metabolismo , Interferência de RNA , Ubiquitinação/genética
9.
BMC Genomics ; 20(1): 201, 2019 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-30871455

RESUMO

BACKGROUND: In mammals, sex chromosomes pose an inherent imbalance of gene expression between sexes. In each female somatic cell, random inactivation of one of the X-chromosomes restores this balance. While most genes from the inactivated X-chromosome are silenced, 15-25% are known to escape X-inactivation (termed escapees). The expression levels of these genes are attributed to sex-dependent phenotypic variability. RESULTS: We used single-cell RNA-Seq to detect escapees in somatic cells. As only one X-chromosome is inactivated in each cell, the origin of expression from the active or inactive chromosome can be determined from the variation of sequenced RNAs. We analyzed primary, healthy fibroblasts (n = 104), and clonal lymphoblasts with sequenced parental genomes (n = 25) by measuring the degree of allelic-specific expression (ASE) from heterozygous sites. We identified 24 and 49 candidate escapees, at varying degree of confidence, from the fibroblast and lymphoblast transcriptomes, respectively. We critically test the validity of escapee annotations by comparing our findings with a large collection of independent studies. We find that most genes (66%) from the unified set were previously reported as escapees. Furthermore, out of the overlooked escapees, 11 are long noncoding RNA (lncRNAs). CONCLUSIONS: X-chromosome inactivation and escaping from it are robust, permanent phenomena that are best studies at a single-cell resolution. The cumulative information from individual cells increases the potential of identifying escapees. Moreover, despite the use of a limited number of cells, clonal cells (i.e., same X- chromosomes are coordinately inhibited) with genomic phasing are valuable for detecting escapees at high confidence. Generalizing the method to uncharacterized genomic loci resulted in lncRNAs escapees which account for 20% of the listed candidates. By confirming genes as escapees and propose others as candidates from two different cell types, we contribute to the cumulative knowledge and reliability of human escapees.


Assuntos
Cromossomos Humanos X , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Célula Única/métodos , Transcriptoma , Inativação do Cromossomo X , Alelos , Mapeamento Cromossômico , Feminino , Fibroblastos/citologia , Fibroblastos/metabolismo , Humanos , Recém-Nascido , Linfócitos/citologia , Linfócitos/metabolismo
10.
Mol Cell ; 74(1): 101-117.e10, 2019 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-30827740

RESUMO

During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/Polycomb spreading, silencing, and changes in chromosome architecture.


Assuntos
Fibroblastos/metabolismo , Deleção de Genes , Inativação Gênica , Células-Tronco Embrionárias Murinas/metabolismo , Complexo Repressor Polycomb 1/genética , Complexo Repressor Polycomb 2/genética , RNA Longo não Codificante/genética , Inativação do Cromossomo X , Cromossomo X/genética , Animais , Linhagem Celular Transformada , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Masculino , Camundongos , Motivos de Nucleotídeos , Complexo Repressor Polycomb 1/metabolismo , Complexo Repressor Polycomb 2/metabolismo , Ligação Proteica , RNA Longo não Codificante/metabolismo , Sequências Repetitivas de Ácido Nucleico , Ribonucleoproteínas/genética , Ribonucleoproteínas/metabolismo , Cromossomo X/metabolismo
11.
Mol Cell ; 73(3): 547-561.e6, 2019 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-30735655

RESUMO

Chromatin organization undergoes drastic reconfiguration during gametogenesis. However, the molecular reprogramming of three-dimensional chromatin structure in this process remains poorly understood for mammals, including primates. Here, we examined three-dimensional chromatin architecture during spermatogenesis in rhesus monkey using low-input Hi-C. Interestingly, we found that topologically associating domains (TADs) undergo dissolution and reestablishment in spermatogenesis. Strikingly, pachytene spermatocytes, where synapsis occurs, are strongly depleted for TADs despite their active transcription state but uniquely show highly refined local compartments that alternate between transcribing and non-transcribing regions (refined-A/B). Importantly, such chromatin organization is conserved in mouse, where it remains largely intact upon transcription inhibition. Instead, it is attenuated in mutant spermatocytes, where the synaptonemal complex failed to be established. Intriguingly, this is accompanied by the restoration of TADs, suggesting that the synaptonemal complex may restrict TADs and promote local compartments. Thus, these data revealed extensive reprogramming of higher-order meiotic chromatin architecture during mammalian gametogenesis.


Assuntos
Reprogramação Celular , Montagem e Desmontagem da Cromatina , Cromatina/metabolismo , Meiose , Espermatogênese , Espermatozoides/metabolismo , Animais , Cromatina/química , Cromatina/genética , Regulação da Expressão Gênica no Desenvolvimento , Células HCT116 , Humanos , Macaca mulatta , Masculino , Camundongos Endogâmicos C57BL , Camundongos Knockout , Conformação de Ácido Nucleico , Estágio Paquíteno , Conformação Proteica , Relação Estrutura-Atividade , Fatores de Tempo , Transcrição Genética , Inativação do Cromossomo X
12.
Nat Commun ; 10(1): 500, 2019 01 30.
Artigo em Inglês | MEDLINE | ID: mdl-30700715

RESUMO

High-resolution molecular programmes delineating the cellular foundations of mammalian embryogenesis have emerged recently. Similar analysis of human embryos is limited to pre-implantation stages, since early post-implantation embryos are largely inaccessible. Notwithstanding, we previously suggested conserved principles of pig and human early development. For further insight on pluripotent states and lineage delineation, we analysed pig embryos at single cell resolution. Here we show progressive segregation of inner cell mass and trophectoderm in early blastocysts, and of epiblast and hypoblast in late blastocysts. We show that following an emergent short naive pluripotent signature in early embryos, there is a protracted appearance of a primed signature in advanced embryonic stages. Dosage compensation with respect to the X-chromosome in females is attained via X-inactivation in late epiblasts. Detailed human-pig comparison is a basis towards comprehending early human development and a foundation for further studies of human pluripotent stem cell differentiation in pig interspecies chimeras.


Assuntos
Análise de Célula Única/métodos , Cromossomo X/metabolismo , Animais , Diferenciação Celular/fisiologia , Feminino , Gastrulação/fisiologia , Regulação da Expressão Gênica no Desenvolvimento , Camadas Germinativas/metabolismo , Humanos , Suínos , Inativação do Cromossomo X/fisiologia
13.
Nucleic Acids Res ; 47(8): 3875-3887, 2019 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-30783652

RESUMO

The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 smaller XIST segments, including repeats A, D and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted in K562 cells using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and RNA fluorescence in situ hybridization experiments. Clones containing en bloc and promoter deletions that consistently displayed no XIST RNAs and a global up-regulation of X-linked genes confirmed that the deletion of XIST reactivates the inactive X chromosome. Systematic analyses of segmental deletions delineated that exon 5 harboring the non-repeat element is important for X-inactivation maintenance, whereas exons 2, 3 and 4 as well as the other repeats in exon 1 are less important, a different situation from that of mouse Xist. This Cas9-assisted dissection of XIST allowed us to understand the unique functional domains within the human XIST RNA.


Assuntos
Sequência de Bases , Cromossomos Humanos X/química , RNA Longo não Codificante/genética , Deleção de Sequência , Inativação do Cromossomo X , Processamento Alternativo , Animais , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/metabolismo , Sistemas CRISPR-Cas , Cromossomos Humanos X/metabolismo , Células Clonais , Éxons , Edição de Genes/métodos , Genoma Humano , Humanos , Células K562 , Camundongos , Regiões Promotoras Genéticas , RNA Guia/genética , RNA Guia/metabolismo , RNA Longo não Codificante/metabolismo , Especificidade da Espécie , Sequenciamento Completo do Genoma
14.
Nat Genet ; 51(2): 285-295, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30643252

RESUMO

During X-chromosome inactivation (XCI), one of the two X-inactivation centers (Xics) upregulates the noncoding RNA Xist to initiate chromosomal silencing in cis. How one Xic is chosen to upregulate Xist remains unclear. Models proposed include localization of one Xic at the nuclear envelope or transient homologous Xic pairing followed by asymmetric transcription factor distribution at Xist's antisense Xite/Tsix locus. Here, we use a TetO/TetR system that can inducibly relocate one or both Xics to the nuclear lamina in differentiating mouse embryonic stem cells. We find that neither nuclear lamina localization nor reduction of Xic homologous pairing influences monoallelic Xist upregulation or choice-making. We also show that transient pairing is associated with biallelic expression, not only at Xist/Tsix but also at other X-linked loci that can escape XCI. Finally, we show that Xic pairing occurs in wavelike patterns, coinciding with genome dynamics and the onset of global regulatory programs during early differentiation.


Assuntos
Núcleo Celular/genética , Inativação do Cromossomo X/genética , Cromossomo X/genética , Animais , Diferenciação Celular/genética , Linhagem Celular , Células-Tronco Embrionárias/fisiologia , Feminino , Regulação da Expressão Gênica/genética , Genes Ligados ao Cromossomo X/genética , Camundongos , RNA Longo não Codificante/genética , Fatores de Transcrição/genética , Regulação para Cima/genética
15.
Nat Commun ; 10(1): 30, 2019 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-30604745

RESUMO

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Here we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contributes to this unique chromosome architecture. Specifically, allelic mapping of the transcriptome and epigenome in SmcHD1 mutant cells reveals the appearance of sub-megabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me3. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells, additionally adopt features of active X chromosome higher-order chromosome architecture, including A/B compartments and partial restoration of TAD boundaries. Xi chromosome architecture changes also occurred following SmcHD1 knockout in a somatic cell model, but in this case, independent of Xi gene derepression. We conclude that SmcHD1 is a key factor in defining the unique chromosome architecture of Xi.


Assuntos
Proteínas Cromossômicas não Histona/genética , Metilação de DNA/genética , Ativação Transcricional/genética , Inativação do Cromossomo X , Alelos , Animais , Sistemas CRISPR-Cas , Linhagem Celular , Proteínas Cromossômicas não Histona/metabolismo , Ilhas de CpG , Éxons/genética , Feminino , Fibroblastos , Técnicas de Inativação de Genes , Histonas/genética , Histonas/metabolismo , Masculino , Camundongos , Mutação Puntual , Proteínas do Grupo Polycomb/metabolismo
16.
BMC Bioinformatics ; 20(1): 11, 2019 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-30616589

RESUMO

BACKGROUND: Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked diseases. However, no statistical method is available in the literature to measure the degree of the skewness of XCI for case-control design. Therefore, it is necessary to develop methods for such a task. RESULTS: In this article, we first proposed a statistical measure for the degree of XCI skewing by using a case-control design, which is a ratio of two logistic regression coefficients after a simple reparameterization. Based on the point estimate of the ratio, we further developed three types of confidence intervals (the likelihood ratio, Fieller's and delta methods) to evaluate its variation. Simulation results demonstrated that the likelihood ratio method and the Fieller's method have more accurate coverage probability and more balanced tail errors than the delta method. We also applied these proposed methods to analyze the Graves' disease data for their practical use and found that rs3827440 probably undergoes a skewed XCI pattern with 68.7% of cells in heterozygous females having the risk allele T active, while the other 31.3% of cells keeping the normal allele C active. CONCLUSIONS: For practical application, we suggest using the Fieller's method in large samples due to the non-iterative computation procedure and using the LR method otherwise for its robustness despite its slightly heavy computational burden.


Assuntos
Cromossomos Humanos X/genética , Genes Ligados ao Cromossomo X , Heterozigoto , Modelos Estatísticos , Inativação do Cromossomo X , Alelos , Estudos de Casos e Controles , Feminino , Humanos
17.
Cell ; 176(1-2): 182-197.e23, 2019 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-30595450

RESUMO

During development, the precise relationships between transcription and chromatin modifications often remain unclear. We use the X chromosome inactivation (XCI) paradigm to explore the implication of chromatin changes in gene silencing. Using female mouse embryonic stem cells, we initiate XCI by inducing Xist and then monitor the temporal changes in transcription and chromatin by allele-specific profiling. This reveals histone deacetylation and H2AK119 ubiquitination as the earliest chromatin alterations during XCI. We show that HDAC3 is pre-bound on the X chromosome and that, upon Xist coating, its activity is required for efficient gene silencing. We also reveal that first PRC1-associated H2AK119Ub and then PRC2-associated H3K27me3 accumulate initially at large intergenic domains that can then spread into genes only in the context of histone deacetylation and gene silencing. Our results reveal the hierarchy of chromatin events during the initiation of XCI and identify key roles for chromatin in the early steps of transcriptional silencing.


Assuntos
Cromatina/metabolismo , Inativação do Cromossomo X/genética , Inativação do Cromossomo X/fisiologia , Acetilação , Animais , Cromatina/genética , Células-Tronco Embrionárias , Epigenômica/métodos , Feminino , Inativação Gênica , Histona Desacetilases/metabolismo , Histonas/metabolismo , Camundongos , Proteínas do Grupo Polycomb/metabolismo , Processamento de Proteína Pós-Traducional , RNA Longo não Codificante/metabolismo , Transcrição Genética , Ubiquitinação , Cromossomo X/metabolismo
18.
Genet Epidemiol ; 43(4): 427-439, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30657195

RESUMO

Analysis of the X chromosome has been largely neglected in genetic studies mainly because of complex underlying biological mechanisms. On the other hand, the study of human microbiome data (typically over-dispersed counts with an excess of zeros) has generated great interest recently because of advancements in next-generation sequencing technologies. We propose a novel approach to infer the association between host genetic variants in the X-chromosome and microbiome data. The method accounts for random X-chromosome inactivation (XCI), skewed (or nonrandom) XCI (XCI-S), and escape of XCI (XCI-E). The inference is performed through a finite mixture model (FMM), in which an indicator variable denoting the "true" biological mechanism is treated as missing data. An expectation-maximization algorithm on zero-inflated and two-part models is implemented to estimate genetic effects. We investigate the performance of the FMM along with strategies that assume XCI and XCI-E mechanisms for all subjects compared with alternative approaches. Briefly, an XCI mechanism codes males' genotypes as homozygous females, whereas under XCI-E, males are treated as heterozygous females. By comprehensive simulations, we evaluate tests of the hypothesis under a computationally efficient score statistic. In summary, the FMM renders reduced bias and commensurate power compared to XCI, XCI-E, and alternative strategies while maintaining adequate Type 1 error control. The proposed method has far-reaching applications. In particular, we illustrate its usage on a large-scale human microbiome study, the Genetic, Environmental and Microbial (GEM) project, to test for the genetic association on the X chromosome.


Assuntos
Cromossomos Humanos X , Microbiota/genética , Cromossomos Humanos X/genética , Estudos de Coortes , Doença de Crohn/epidemiologia , Doença de Crohn/genética , Doença de Crohn/microbiologia , Análise de Dados , Família , Feminino , Análise de Elementos Finitos , Interação Gene-Ambiente , Estudos de Associação Genética/estatística & dados numéricos , Genótipo , Heterozigoto , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Modelos Genéticos , Inativação do Cromossomo X
19.
Hum Genomics ; 13(1): 2, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30621780

RESUMO

The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference. Females are functional mosaics for X-linked genes due to X chromosome inactivation and this, combined with other X chromosome inactivation mechanisms such as genes that escape silencing and skewed inactivation, could contribute to an immunological advantage for females in many infections. In this review, we discuss the involvement of the X chromosome and X inactivation in immunity and address its role in sexual dimorphism of infectious diseases using tuberculosis susceptibility as an example, in which male sex bias is clear, yet not fully explored.


Assuntos
Cromossomos Humanos X/genética , Predisposição Genética para Doença , Infecção/genética , Feminino , Humanos , Masculino , Tuberculose/genética , Inativação do Cromossomo X
20.
Hum Mol Genet ; 28(8): 1331-1342, 2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30576442

RESUMO

X chromosome inactivation (XCI) is a key epigenetic gene expression regulatory process, which may play a role in women's cancer. In particular tissues, some genes are known to escape XCI, yet patterns of XCI in ovarian cancer (OC) and their clinical associations are largely unknown. To examine XCI in OC, we integrated germline genotype with tumor copy number, gene expression and DNA methylation information from 99 OC patients. Approximately 10% of genes showed different XCI status (either escaping or being subject to XCI) compared with the studies of other tissues. Many of these genes are known oncogenes or tumor suppressors (e.g. DDX3X, TRAPPC2 and TCEANC). We also observed strong association between cis promoter DNA methylation and allele-specific expression imbalance (P = 2.0 × 10-10). Cluster analyses of the integrated data identified two molecular subgroups of OC patients representing those with regulated (N = 47) and dysregulated (N = 52) XCI. This XCI cluster membership was associated with expression of X inactive specific transcript (P = 0.002), a known driver of XCI, as well as age, grade, stage, tumor histology and extent of residual disease following surgical debulking. Patients with dysregulated XCI (N = 52) had shorter time to recurrence (HR = 2.34, P = 0.001) and overall survival time (HR = 1.87, P = 0.02) than those with regulated XCI, although results were attenuated after covariate adjustment. Similar findings were observed when restricted to high-grade serous tumors. We found evidence of a unique OC XCI profile, suggesting that XCI may play an important role in OC biology. Additional studies to examine somatic changes with paired tumor-normal tissue are needed.


Assuntos
Carcinoma Epitelial do Ovário/genética , Genes Ligados ao Cromossomo X/genética , Inativação do Cromossomo X/fisiologia , Idoso , Alelos , Carcinoma Epitelial do Ovário/metabolismo , Cromossomos Humanos X/genética , Análise por Conglomerados , Metilação de DNA/genética , Epigênese Genética/genética , Feminino , Regulação da Expressão Gênica/genética , Frequência do Gene/genética , Estudos de Associação Genética/métodos , Genótipo , Humanos , Pessoa de Meia-Idade , Neoplasias Ovarianas/genética , Regiões Promotoras Genéticas/genética , RNA Longo não Codificante , Fatores de Transcrição/genética , Inativação do Cromossomo X/genética
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