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1.
EMBO Rep ; 25(5): 2258-2277, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38654121

RESUMEN

X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions in cis to silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. The chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing. In this study, we examine mouse embryonic stem cell lines with an inducible Xist allele (iXist-ChrX mESCs) and integrate allele-specific data of gene silencing and decreasing inactive X (Xi) chromatin accessibility over time courses of Xist induction with cellular differentiation. Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results suggest that YY1 acts as a barrier to Xist-mediated silencing until the late stages of the XCI process.


Asunto(s)
Silenciador del Gen , ARN Largo no Codificante , Inactivación del Cromosoma X , Factor de Transcripción YY1 , Animales , Femenino , Masculino , Ratones , Alelos , Diferenciación Celular/genética , Línea Celular , Cromatina/metabolismo , Cromatina/genética , Células Madre Embrionarias de Ratones/metabolismo , Regiones Promotoras Genéticas , Unión Proteica , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Cromosoma X/genética , Cromosoma X/metabolismo , Inactivación del Cromosoma X/genética , Factor de Transcripción YY1/metabolismo , Factor de Transcripción YY1/genética
2.
Mol Cell ; 68(5): 955-969.e10, 2017 Dec 07.
Artículo en Inglés | MEDLINE | ID: mdl-29220657

RESUMEN

The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element. Deletion of XR-PID abolishes Xist-dependent Polycomb recruitment, in turn abrogating Xist-mediated gene silencing and reversing Xist-induced chromatin inaccessibility. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking XR-PID is sufficient for Xist-dependent Polycomb recruitment. Our findings define a key pathway for Polycomb recruitment by Xist RNA, providing important insights into mechanisms of chromatin modification by non-coding RNA.


Asunto(s)
Células Madre Embrionarias/metabolismo , Complejo Represivo Polycomb 1/metabolismo , Proteínas del Grupo Polycomb/metabolismo , ARN Largo no Codificante/metabolismo , Ribonucleoproteínas/metabolismo , Inactivación del Cromosoma X , Cromosoma X/metabolismo , Animales , Sitios de Unión , Línea Celular , Ribonucleoproteína Heterogénea-Nuclear Grupo K , Histonas/metabolismo , Lisina/metabolismo , Ratones , Complejo Represivo Polycomb 1/genética , Proteínas del Grupo Polycomb/genética , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Interferencia de ARN , ARN Largo no Codificante/genética , Ribonucleoproteínas/genética , Transcripción Genética , Transfección , Ubiquitinación , Cromosoma X/genética
3.
Genes Dev ; 31(9): 876-888, 2017 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-28546514

RESUMEN

The nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) promotes DNA replication in association with cyclins and has been linked to adult and pediatric cancers. Here we show that CIZ1 is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. CIZ1 is recruited to Xi in response to expression of X inactive-specific transcript (Xist) RNA during the earliest stages of X inactivation in embryonic stem cells and is dependent on the C-terminal nuclear matrix anchor domain of CIZ1 and the E repeats of Xist CIZ1-null mice, although viable, display fully penetrant female-specific lymphoproliferative disorder. Interestingly, in mouse embryonic fibroblast cells derived from CIZ1-null embryos, Xist RNA localization is disrupted, being highly dispersed through the nucleoplasm rather than focal. Focal localization is reinstated following re-expression of CIZ1. Focal localization of Xist RNA is also disrupted in activated B and T cells isolated from CIZ1-null animals, suggesting a possible explanation for female-specific lymphoproliferative disorder. Together, these findings suggest that CIZ1 has an essential role in anchoring Xist to the nuclear matrix in specific somatic lineages.


Asunto(s)
Regulación de la Expresión Génica , Trastornos Linfoproliferativos/patología , Proteínas Nucleares/fisiología , ARN Largo no Codificante/metabolismo , Inactivación del Cromosoma X , Cromosoma X/metabolismo , Animales , Diferenciación Celular , Células Cultivadas , Embrión de Mamíferos/metabolismo , Embrión de Mamíferos/patología , Células Madre Embrionarias/metabolismo , Células Madre Embrionarias/patología , Femenino , Fibroblastos/metabolismo , Fibroblastos/patología , Humanos , Trastornos Linfoproliferativos/genética , Trastornos Linfoproliferativos/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos CBA , Ratones Noqueados , ARN Largo no Codificante/genética , Caracteres Sexuales , Cromosoma X/genética
4.
Mol Cell ; 62(6): 848-861, 2016 06 16.
Artículo en Inglés | MEDLINE | ID: mdl-27237052

RESUMEN

Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos.


Asunto(s)
Reprogramación Celular , Metilación de ADN , Células Madre Embrionarias/metabolismo , Epigénesis Genética , Regulación del Desarrollo de la Expresión Génica , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/metabolismo , Animales , Proteínas Potenciadoras de Unión a CCAAT , Células Cultivadas , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Dioxigenasas , Histonas/metabolismo , Ratones , Modelos Genéticos , Mutación , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Proteínas Proto-Oncogénicas/genética , Proteínas Proto-Oncogénicas/metabolismo , Factores de Tiempo , Transfección , Ubiquitina-Proteína Ligasas
6.
Proc Natl Acad Sci U S A ; 111(6): 2235-40, 2014 Feb 11.
Artículo en Inglés | MEDLINE | ID: mdl-24469834

RESUMEN

In female mammals, one of the two X chromosomes is transcriptionally silenced to equalize X-linked gene dosage relative to XY males, a process termed X chromosome inactivation. Mechanistically, this is thought to occur via directed recruitment of chromatin modifying factors by the master regulator, X-inactive specific transcript (Xist) RNA, which localizes in cis along the entire length of the chromosome. A well-studied example is the recruitment of polycomb repressive complex 2 (PRC2), for which there is evidence of a direct interaction involving the PRC2 proteins Enhancer of zeste 2 (Ezh2) and Supressor of zeste 12 (Suz12) and the A-repeat region located at the 5' end of Xist RNA. In this study, we have analyzed Xist-mediated recruitment of PRC2 using two approaches, microarray-based epigenomic mapping and superresolution 3D structured illumination microscopy. Making use of an ES cell line carrying an inducible Xist transgene located on mouse chromosome 17, we show that 24 h after synchronous induction of Xist expression, acquired PRC2 binding sites map predominantly to gene-rich regions, notably within gene bodies. Paradoxically, these new sites of PRC2 deposition do not correlate with Xist-mediated gene silencing. The 3D structured illumination microscopy was performed to assess the relative localization of PRC2 proteins and Xist RNA. Unexpectedly, we observed significant spatial separation and absence of colocalization both in the inducible Xist transgene ES cell line and in normal XX somatic cells. Our observations argue against direct interaction between Xist RNA and PRC2 proteins and, as such, prompt a reappraisal of the mechanism for PRC2 recruitment in X chromosome inactivation.


Asunto(s)
Proteínas del Grupo Polycomb/aislamiento & purificación , ARN Largo no Codificante/aislamiento & purificación , ARN/genética , Animales , Línea Celular , Silenciador del Gen , Ratones , Microscopía Electrónica , Análisis de Secuencia por Matrices de Oligonucleótidos , ARN Largo no Codificante/genética , Transcripción Genética
7.
Development ; 138(8): 1541-50, 2011 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-21389056

RESUMEN

In XX female mammals a single X chromosome is inactivated early in embryonic development, a process that is required to equalise X-linked gene dosage relative to XY males. X inactivation is regulated by a cis-acting master switch, the Xist locus, the product of which is a large non-coding RNA that coats the chromosome from which it is transcribed, triggering recruitment of chromatin modifying factors that establish and maintain gene silencing chromosome wide. Chromosome coating and Xist RNA-mediated silencing remain poorly understood, both at the level of RNA sequence determinants and interacting factors. Here, we describe analysis of a novel targeted mutation, Xist(INV), designed to test the function of a conserved region located in exon 1 of Xist RNA during X inactivation in mouse. We show that Xist(INV) is a strong hypomorphic allele that is appropriately regulated but compromised in its ability to silence X-linked loci in cis. Inheritance of Xist(INV) on the paternal X chromosome results in embryonic lethality due to failure of imprinted X inactivation in extra-embryonic lineages. Female embryos inheriting Xist(INV) on the maternal X chromosome undergo extreme secondary non-random X inactivation, eliminating the majority of cells that express the Xist(INV) allele. Analysis of cells that express Xist(INV) RNA demonstrates reduced association of the mutant RNA to the X chromosome, suggesting that conserved sequences in the inverted region are important for Xist RNA localisation.


Asunto(s)
Exones/genética , Genes Ligados a X/genética , ARN no Traducido/genética , Inactivación del Cromosoma X/genética , Animales , Northern Blotting , Células Cultivadas , Femenino , Fibroblastos/metabolismo , Técnica del Anticuerpo Fluorescente , Hibridación Fluorescente in Situ , Masculino , Ratones , ARN Largo no Codificante , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
8.
Chromosoma ; 120(2): 177-83, 2011 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-21110203

RESUMEN

In somatic cells of female marsupial and eutherian mammals, X chromosome inactivation (XCI) occurs. XCI results in the transcriptional silencing of one of the two X chromosomes and is accompanied by specific covalent histone modifications attributable to the inactive chromatin state. Because data about repressed chromatin of the inactive X chromosome (Xi) in marsupials are sparse, we examined in more detail the distribution of active and inactive chromatin markers on metaphase X chromosomes of an American marsupial, Monodelphis domestica. Consistent with data reported previously both for eutherian and marsupial mammals, we found that the Xi of M. domestica lacks active histone markers-H3K4 dimethylation and H3K9 acetylation. We did not observe on metaphase spreads enrichment of the Xi with H3K27 trimethylation which is involved in XCI in eutherians and was detected on the Xi in the interphase nuclei of mature female M. domestica in an earlier study. Moreover, we found that the Xi of M. domestica was specifically marked with H3K9 trimethylation, which is known to be a component of the Xi chromatin in eutherians and is involved in both marsupials and eutherians in meiotic sex chromosome inactivation which has been proposed as an ancestral mechanism of XCI.


Asunto(s)
Histonas/metabolismo , Lisina/metabolismo , Metafase , Monodelphis/genética , Monodelphis/metabolismo , Inactivación del Cromosoma X , Cromosoma X/genética , Animales , Línea Celular , Cromatina/genética , Cromatina/metabolismo , Femenino , Histonas/química , Histonas/genética , Masculino , Metilación , Cromosoma X/metabolismo
9.
Cell Rep ; 39(7): 110830, 2022 05 17.
Artículo en Inglés | MEDLINE | ID: mdl-35584662

RESUMEN

X chromosome inactivation (XCI) is mediated by the non-coding RNA Xist, which directs chromatin modification and gene silencing in cis. The RNA binding protein SPEN and associated corepressors have a central role in Xist-mediated gene silencing. Other silencing factors, notably the Polycomb system, have been reported to function downstream of SPEN. In recent work, we found that SPEN has an additional role in correct localization of Xist RNA in cis, indicating that its contribution to chromatin-mediated gene silencing needs to be reappraised. Making use of a SPEN separation-of-function mutation, we show that SPEN and Polycomb pathways, in fact, function in parallel to establish gene silencing. We also find that differentiation-dependent recruitment of the chromosomal protein SmcHD1 is required for silencing many X-linked genes. Our results provide important insights into the mechanism of X inactivation and the coordination of chromatin-based gene regulation with cellular differentiation and development.


Asunto(s)
Proteínas de Drosophila , ARN Largo no Codificante , Cromatina , Proteínas de Drosophila/metabolismo , Proteínas del Grupo Polycomb/genética , Proteínas del Grupo Polycomb/metabolismo , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Cromosoma X , Inactivación del Cromosoma X/genética
10.
J Exp Med ; 201(9): 1367-73, 2005 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-15867090

RESUMEN

The ribonuclease III enzyme Dicer is essential for the processing of micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) from double-stranded RNA precursors. miRNAs and siRNAs regulate chromatin structure, gene transcription, mRNA stability, and translation in a wide range of organisms. To provide a model system to explore the role of Dicer-generated RNAs in the differentiation of mammalian cells in vivo, we have generated a conditional Dicer allele. Deletion of Dicer at an early stage of T cell development compromised the survival of alphabeta lineage cells, whereas the numbers of gammadelta-expressing thymocytes were not affected. In developing thymocytes, Dicer was not required for the maintenance of transcriptional silencing at pericentromeric satellite sequences (constitutive heterochromatin), the maintenance of DNA methylation and X chromosome inactivation in female cells (facultative heterochromatin), and the stable shutdown of a developmentally regulated gene (developmentally regulated gene silencing). Most remarkably, given that one third of mammalian mRNAs are putative miRNA targets, Dicer seems to be dispensable for CD4/8 lineage commitment, a process in which epigenetic regulation of lineage choice has been well documented. Thus, although Dicer seems to be critical for the development of the early embryo, it may have limited impact on the implementation of some lineage-specific gene expression programs.


Asunto(s)
Apoptosis/fisiología , Diferenciación Celular/fisiología , Regulación del Desarrollo de la Expresión Génica , Ribonucleasa III/genética , Linfocitos T/fisiología , Animales , Apoptosis/genética , Southern Blotting , Diferenciación Celular/genética , Células Cultivadas , Islas de CpG/fisiología , Metilación de ADN , Heterocromatina/metabolismo , Hibridación Fluorescente in Situ , Ratones , Ratones Transgénicos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
11.
Chromosoma ; 119(5): 541-52, 2010 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-20473512

RESUMEN

During early development in female mammals, most genes on one of the two X-chromosomes undergo transcriptional silencing. In the extraembryonic lineages of some eutherian species, imprinted X-inactivation of the paternal X-chromosome occurs. In the cells of the embryo proper, the choice of the future inactive X-chromosome is random. We mapped several genes on the X-chromosomes of five common vole species and compared their expression and methylation patterns in somatic and extraembryonic tissues, where random and imprinted X-inactivation occurs, respectively. In extraembryonic tissues, more genes were expressed on the inactive X-chromosome than in somatic tissues. We also found that the methylation status of the X-linked genes was always in accordance with their expression pattern in somatic, but not in extraembryonic tissues. The data provide new evidence that imprinted X-inactivation is less complete and/or stable than the random form and DNA methylation contributes less to its maintenance.


Asunto(s)
Arvicolinae/genética , Metilación de ADN , Expresión Génica , Impresión Genómica , Inactivación del Cromosoma X , Animales , Mapeo Cromosómico , Femenino , Genes Ligados a X , Humanos , Hibridación Fluorescente in Situ , Masculino , Muridae , ARN Largo no Codificante , ARN no Traducido/genética , Proteínas Represoras , Cromosoma X/genética , Cromosoma X/metabolismo
12.
Dev Cell ; 7(5): 663-76, 2004 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-15525528

RESUMEN

In many higher organisms, 5%-15% of histone H2A is ubiquitylated at lysine 119 (uH2A). The function of this modification and the factors involved in its establishment, however, are unknown. Here we demonstrate that uH2A occurs on the inactive X chromosome in female mammals and that this correlates with recruitment of Polycomb group (PcG) proteins belonging to Polycomb repressor complex 1 (PRC1). Based on our observations, we tested the role of the PRC1 protein Ring1B and its closely related homolog Ring1A in H2A ubiquitylation. Analysis of Ring1B null embryonic stem (ES) cells revealed extensive depletion of global uH2A levels. On the inactive X chromosome, uH2A was maintained in Ring1A or Ring1B null cells, but not in double knockout cells, demonstrating an overlapping function for these proteins in development. These observations link H2A ubiquitylation, X inactivation, and PRC1 PcG function, suggesting an unanticipated and novel mechanism for chromatin-mediated heritable gene silencing.


Asunto(s)
Proteínas Portadoras/metabolismo , Compensación de Dosificación (Genética) , Silenciador del Gen , Histonas/metabolismo , Ubiquitina/metabolismo , Proteínas de Unión al GTP rab/metabolismo , Animales , Anticuerpos Monoclonales/metabolismo , Blastocisto/metabolismo , Western Blotting , Proteínas Portadoras/clasificación , Proteínas Portadoras/genética , Línea Celular , Cruzamientos Genéticos , Embrión de Mamíferos/citología , Femenino , Fibroblastos/metabolismo , Eliminación de Gen , Marcación de Gen , Histonas/aislamiento & purificación , Péptidos y Proteínas de Señalización Intracelular , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos CBA , Mapeo Restrictivo , Células Madre/metabolismo , Proteínas de Unión al GTP rab/clasificación , Proteínas de Unión al GTP rab/genética
13.
Dev Cell ; 4(4): 481-95, 2003 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-12689588

RESUMEN

Previous studies have implicated the Eed-Enx1 Polycomb group complex in the maintenance of imprinted X inactivation in the trophectoderm lineage in mouse. Here we show that recruitment of Eed-Enx1 to the inactive X chromosome (Xi) also occurs in random X inactivation in the embryo proper. Localization of Eed-Enx1 complexes to Xi occurs very early, at the onset of Xist expression, but then disappears as differentiation and development progress. This transient localization correlates with the presence of high levels of the complex in totipotent cells and during early differentiation stages. Functional analysis demonstrates that Eed-Enx1 is required to establish methylation of histone H3 at lysine 9 and/or lysine 27 on Xi and that this, in turn, is required to stabilize the Xi chromatin structure.


Asunto(s)
Compensación de Dosificación (Genética) , Embrión de Mamíferos/embriología , N-Metiltransferasa de Histona-Lisina , Metiltransferasas/metabolismo , Proteínas Represoras/metabolismo , Células Madre Totipotentes/metabolismo , Cromosoma X/genética , Secuencia de Aminoácidos/genética , Animales , Diferenciación Celular/genética , Células Cultivadas , Cromatina/genética , Cromatina/metabolismo , Metilación de ADN , Femenino , Feto , Regulación del Desarrollo de la Expresión Génica/genética , Histona Metiltransferasas , Histonas/genética , Histonas/metabolismo , Lisina/genética , Lisina/metabolismo , Masculino , Metiltransferasas/genética , Ratones , Ratones Endogámicos C57BL , Complejo Represivo Polycomb 2 , Proteínas del Grupo Polycomb , Proteína Metiltransferasas , ARN Largo no Codificante , ARN no Traducido/genética , ARN no Traducido/metabolismo , Proteínas Represoras/genética , Células Madre Totipotentes/citología
14.
Nat Commun ; 10(1): 30, 2019 01 03.
Artículo en Inglés | MEDLINE | ID: mdl-30604745

RESUMEN

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.


Asunto(s)
Proteínas Cromosómicas no Histona/genética , Metilación de ADN/genética , Activación Transcripcional/genética , Inactivación del Cromosoma X , Alelos , Animales , Sistemas CRISPR-Cas , Línea Celular , Proteínas Cromosómicas no Histona/metabolismo , Islas de CpG , Exones/genética , Femenino , Fibroblastos , Técnicas de Inactivación de Genes , Histonas/genética , Histonas/metabolismo , Masculino , Ratones , Mutación Puntual , Proteínas del Grupo Polycomb/metabolismo
15.
Nat Commun ; 10(1): 3129, 2019 07 16.
Artículo en Inglés | MEDLINE | ID: mdl-31311937

RESUMEN

Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing.


Asunto(s)
ARN Largo no Codificante/metabolismo , Proteínas de Unión al ARN/metabolismo , Inactivación del Cromosoma X , Cromosoma X/genética , Animales , Línea Celular , Proteínas de Unión al ADN , Técnicas de Inactivación de Genes , Silenciador del Gen , Histonas/genética , Ratones , Células Madre Embrionarias de Ratones , Proteínas del Grupo Polycomb/metabolismo , Proteínas de Unión al ARN/genética
16.
BMC Bioinformatics ; 9: 501, 2008 Nov 27.
Artículo en Inglés | MEDLINE | ID: mdl-19038045

RESUMEN

BACKGROUND: There is accumulating evidence that the milieu of repeat elements and other non-genic sequence features at a given chromosomal locus, here defined as the genome environment, can play an important role in regulating chromosomal processes such as transcription, replication and recombination. The availability of whole-genome sequences has allowed us to annotate the genome environment of any locus in detail. The development of genome wide experimental analyses of gene expression, chromatin modification and chromatin proteins means that it is now possible to identify potential links between chromosomal processes and the underlying genome environment. There is a need for novel bioinformatic tools that facilitate these studies. RESULTS: We developed the Genome Environment Browser (GEB) in order to visualise the integration of experimental data from large scale high throughput analyses with repeat sequence features that define the local genome environment. The browser has incorporated dynamic scales adjustable in real-time, which enables scanning of large regions of the genome as well as detailed investigation of local regions on the same page without the need to load new pages. The interface also accommodates a 2-dimensional display of repetitive features which vary substantially in size, such as LINE-1 repeats. Specific queries for preliminary quantitative analysis of genome features can also be formulated, results of which can be exported for further analysis. CONCLUSION: The Genome Environment Browser is a versatile program which can be easily adapted for displaying all types of genome data with known genomic coordinates. It is currently available at http://web.bioinformatics.ic.ac.uk/geb/.


Asunto(s)
Biología Computacional/métodos , Genómica/métodos , Secuencias Repetitivas de Ácidos Nucleicos/genética , Programas Informáticos , Interfaz Usuario-Computador
17.
BMC Genomics ; 9: 162, 2008 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-18402712

RESUMEN

BACKGROUND: Oct4 is a POU-domain transcriptional factor which is essential for maintaining pluripotency in several mammalian species. The mouse, human, and bovine Oct4 orthologs display a high conservation of nucleotide sequence and genomic organization. RESULTS: Here we report an isolation of a common vole (Microtus rossiaemeridionalis) Oct4 ortholog. Organization and exon-intron structure of vole Oct4 gene are similar to the gene organization in other mammalian species. It consists of five exons and a regulatory region including the minimal promoter, proximal and distal enhancers. Promoter and regulatory regions of the vole Oct4 gene also display a high similarity to the corresponding regions of Oct4 in other mammalian species, and are active during the transient transfection within luciferase reporter constructs into mouse P19 embryonic carcinoma cells and TG-2a embryonic stem cells. The vole Oct4 gene expression is detectable starting from the morula stage and until day 17 of embryonic development. CONCLUSION: Genomic organization of this gene and its intron-exon structure in vole are identical to those in all previously studied species: it comprises five exons and the regulatory region containing several conserved elements. The activity of the Oct4 gene in vole, as well as in mouse, is confined only to pluripotent cells.


Asunto(s)
Arvicolinae/genética , Factor 3 de Transcripción de Unión a Octámeros/genética , Animales , Arvicolinae/embriología , Secuencia de Bases , Bovinos , Línea Celular , Secuencia Conservada , ADN/genética , Perros , Desarrollo Embrionario/genética , Exones , Regulación del Desarrollo de la Expresión Génica , Genes Reporteros , Humanos , Intrones , Ratones , Datos de Secuencia Molecular , Pan troglodytes/genética , Regiones Promotoras Genéticas , Ratas , Secuencias Reguladoras de Ácidos Nucleicos , Homología de Secuencia de Ácido Nucleico , Especificidad de la Especie
18.
Science ; 356(6342): 1081-1084, 2017 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-28596365

RESUMEN

Recruitment of the Polycomb repressive complexes PRC1 and PRC2 by Xist RNA is an important paradigm for chromatin regulation by long noncoding RNAs. Here, we show that the noncanonical Polycomb group RING finger 3/5 (PCGF3/5)-PRC1 complex initiates recruitment of both PRC1 and PRC2 in response to Xist RNA expression. PCGF3/5-PRC1-mediated ubiquitylation of histone H2A signals recruitment of other noncanonical PRC1 complexes and of PRC2, the latter leading to deposition of histone H3 lysine 27 methylation chromosome-wide. Pcgf3/5 gene knockout results in female-specific embryo lethality and abrogates Xist-mediated gene repression, highlighting a key role for Polycomb in Xist-dependent chromosome silencing. Our findings overturn existing models for Polycomb recruitment by Xist RNA and establish precedence for H2AK119u1 in initiating Polycomb domain formation in a physiological context.


Asunto(s)
Células Madre Embrionarias/metabolismo , Complejo Represivo Polycomb 1/metabolismo , Proteínas del Grupo Polycomb/metabolismo , Inactivación del Cromosoma X , Animales , Femenino , Ratones , Proteínas del Grupo Polycomb/genética , ARN Largo no Codificante/metabolismo
20.
Stem Cell Reports ; 6(5): 635-642, 2016 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-27150236

RESUMEN

Numerous developmentally regulated genes in mouse embryonic stem cells (ESCs) are marked by both active (H3K4me3)- and polycomb group (PcG)-mediated repressive (H3K27me3) histone modifications. This bivalent state is thought to be important for transcriptional poising, but the mechanisms that regulate bivalent genes and the bivalent state remain incompletely understood. Examining the contribution of microRNAs (miRNAs) to the regulation of bivalent genes, we found that the miRNA biogenesis enzyme DICER was required for the binding of the PRC2 core components EZH2 and SUZ12, and for the presence of the PRC2-mediated histone modification H3K27me3 at many bivalent genes. Genes that lost bivalency were preferentially upregulated at the mRNA and protein levels. Finally, reconstituting Dicer-deficient ESCs with ESC miRNAs restored bivalent gene repression and PRC2 binding at formerly bivalent genes. Therefore, miRNAs regulate bivalent genes and the bivalent state itself.


Asunto(s)
ARN Helicasas DEAD-box/genética , Proteína Potenciadora del Homólogo Zeste 2/genética , MicroARNs/genética , Células Madre Embrionarias de Ratones/metabolismo , Complejo Represivo Polycomb 2/genética , Ribonucleasa III/genética , Animales , Diferenciación Celular/genética , Regulación del Desarrollo de la Expresión Génica , Código de Histonas/genética , N-Metiltransferasa de Histona-Lisina/genética , Ratones , Regiones Promotoras Genéticas , Activación Transcripcional/genética
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