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Culver-Cochran AE, Chadwick BP. Loss of WSTF results in spontaneous fluctuations of heterochromatin formation and resolution, combined with substantial changes to gene expression. BMC Genomics 2013; 14:740. [PMID: 24168170 PMCID: PMC3870985 DOI: 10.1186/1471-2164-14-740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS). RESULTS To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus, appearing as large DAPI-dense staining blocks, defined by histone H3 lysine-9 trimethylation and association of the proteins heterochromatin protein 1 and structural maintenance of chromosomes flexible hinge domain containing 1. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. CONCLUSIONS Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states, a property that is likely compromised by WSTF haploinsufficiency in WBS patients.
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Affiliation(s)
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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2
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The WSTF-ISWI chromatin remodeling complex transiently associates with the human inactive X chromosome during late S-phase prior to BRCA1 and γ-H2AX. PLoS One 2012; 7:e50023. [PMID: 23166813 PMCID: PMC3498190 DOI: 10.1371/journal.pone.0050023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/16/2012] [Indexed: 01/08/2023] Open
Abstract
Replicating the genome prior to each somatic cell division not only requires precise duplication of the genetic information, but also accurately reestablishing the epigenetic signatures that instruct how the genetic material is to be interpreted in the daughter cells. The mammalian inactive X chromosome (Xi), which is faithfully inherited in a silent state in each daughter cell, provides an excellent model of epigenetic regulation. While much is known about the early stages of X chromosome inactivation, much less is understood with regards to retaining the Xi chromatin through somatic cell division. Here we report that the WSTF-ISWI chromatin remodeling complex (WICH) associates with the Xi during late S-phase as the Xi DNA is replicated. Elevated levels of WICH at the Xi is restricted to late S-phase and appears before BRCA1 and γ-H2A.X. The sequential appearance of WICH and BRCA1/γ-H2A.X implicate each as performing important but distinct roles in the maturation and maintenance of heterochromatin at the Xi.
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3
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X-linked expressed single nucleotide polymorphisms and dosage compensation. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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4
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Serov OL, Matveeva NM, Khabarova AA. Reprogramming mediated by cell fusion technology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 291:155-90. [PMID: 22017976 DOI: 10.1016/b978-0-12-386035-4.00005-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This review is focused on recent advances in fusion-based reprogramming of cells of different pluripotent statuses or lineage origins. Recent findings are discussed from standpoints of both the developmental potency of hybrid cells generated by fusion of pluripotent embryonic stem (ES) cells, embryonal carcinoma (EC) cells, and somatic cells and epigenetic mechanisms and other aspects involved in the reprogramming process. Complete reprogramming occurs at least 5-7 days after fusion and includes at least two steps. (i) initiation at the heterokaryon stage and choice of the direction of reprogramming using an "all-or-none principle" to establish the dominance of one parental genome and (ii) "fixation" of the newly acquired expression profile by epigenetic mechanisms. The first step is realized without cell division, whereas the second requires cell proliferation. Reprogramming in hybrid cells is rapid and complete. Thus, cell fusion is a powerful tool for reprogramming.
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Affiliation(s)
- Oleg L Serov
- Institute of Cytology and Genetics, Academy of Sciences of Russia, Siberian Branch, Novosibirsk, Russia
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5
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Abstract
X chromosome inactivation (XCI) is a process in mammals that ensures equal transcript levels between males and females by genetic inactivation of one of the two X chromosomes in females. Central to XCI is the long non-coding RNA Xist, which is highly and specifically expressed from the inactive X chromosome. Xist covers the X chromosome in cis and triggers genetic silencing, but its working mechanism remains elusive. Here, we review current knowledge about Xist regulation, structure, function and conservation and speculate on possible mechanisms by which its action is restricted in cis. We also discuss dosage compensation mechanisms other than XCI and how knowledge from invertebrate species may help to provide a better understanding of the mechanisms of mammalian XCI.
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Affiliation(s)
- Daphne B. Pontier
- Department of Reproduction and Development, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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6
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Barakat TS, Jonkers I, Monkhorst K, Gribnau J. X-changing information on X inactivation. Exp Cell Res 2010; 316:679-87. [PMID: 20083102 DOI: 10.1016/j.yexcr.2010.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 01/04/2010] [Accepted: 01/10/2010] [Indexed: 10/20/2022]
Abstract
In female somatic cells of mammalian species one X chromosome is inactivated to ensure dosage equality of X-encoded genes between females and males, during development and adulthood. X chromosome inactivation (XCI) involves various epigenetic mechanisms, including RNA mediated gene silencing in cis, DNA methylation, and changes in chromatin modifications and composition. XCI therefore provides an attractive paradigm to study epigenetic gene regulation in a more general context. The XCI process starts with counting of the number of X chromosomes present in a nucleus, and initiation of XCI follows if this number exceeds one per diploid genome. Recently, X-encoded RNF12 has been identified as a dose-dependent activator of XCI. In addition, other factors, including the pluripotency factors OCT4, SOX2 and Nanog, have been implicated to play a role in suppression of initiation of XCI. In this review, we highlight and explain these new and old findings in the context of a stochastic model for X chromosome counting and XCI initiation.
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, Room Ee 09-71, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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7
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Barakat TS, Gribnau J. X chromosome inactivation and embryonic stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:132-54. [PMID: 21222204 DOI: 10.1007/978-1-4419-7037-4_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
X chromosome inactivation (XCI) is a process required to equalize the dosage of X-encoded genes between female and male cells. XCI is initiated very early during female embryonic development or upon differentiation of female embryonic stem (ES) cells and results in inactivation of one X chromosome in every female somatic cell. The regulation of XCI involves factors that also play a crucial role in ES cell maintenance and differentiation and the XCI process therefore provides a beautiful paradigm to study ES cell biology. In this chapter we describe the important cis and trans acting regulators of XCI and introduce the models that have been postulated to explain initiation of XCI in female cells only. We also discuss the proteins involved in the establishment of the inactive X chromosome and describe the different chromatin modifications associated with the inactivation process. Finally, we describe the potential of mouse and human ES and induced pluripotent stem (iPS) cells as model systems to study the XCI process.
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, University Medical Center, Room Ee 09-71, Erasmus MC, 3015 GE, Rotterdam, Netherlands
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8
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Monkhorst K, Jonkers I, Rentmeester E, Grosveld F, Gribnau J. X inactivation counting and choice is a stochastic process: evidence for involvement of an X-linked activator. Cell 2008; 132:410-21. [PMID: 18267073 DOI: 10.1016/j.cell.2007.12.036] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 10/16/2007] [Accepted: 12/21/2007] [Indexed: 11/28/2022]
Abstract
Female mammalian cells achieve dosage compensation of X-encoded genes by X chromosome inactivation (XCI). This process is thought to involve X chromosome counting and choice. To explore how this process is initiated, we analyzed XCI in tetraploid XXXX, XXXY, and XXYY embryonic stem cells and found that every X chromosome within a single nucleus has an independent probability to initiate XCI. This finding suggests a stochastic mechanism directing XCI counting and choice. The probability is directly proportional to the X chromosome:ploidy ratio, indicating the presence of an X-encoded activator of XCI, that itself is inactivated by the XCI process. Deletion of a region including Xist, Tsix, and Xite still results in XCI on the remaining wild-type X chromosome in female cells. This result supports a stochastic model in which each X chromosome in a nucleus initiates XCI independently and positions an X-encoded trans-acting XCI-activator outside the deleted region.
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Affiliation(s)
- Kim Monkhorst
- Department of Cell Biology, Erasmus Medical Center, P.O. Box 2040, Rotterdam 3000 CA, The Netherlands; Department of Reproduction and Development, Erasmus Medical Center, P.O. Box 2040, Rotterdam 3000 CA, The Netherlands
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9
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Vasilkova AA, Kizilova HA, Puzakov MV, Shilov AG, Zhelezova AI, Golubitsa AN, Battulin NR, Vedernikov VE, Menzorov AG, Matveeva NM, Serov OL. Dominant manifestation of pluripotency in embryonic stem cell hybrids with various numbers of somatic chromosomes. Mol Reprod Dev 2007; 74:941-51. [PMID: 17219428 DOI: 10.1002/mrd.20623] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Developmental potential was assessed in 8 intra-specific and 20 inter-specific hybrid clones obtained by fusion of embryonic stem (ES) cells with either splenocytes or fetal fibroblasts. Number of chromosomes derived from ES cells in these hybrid clones was stable while contribution of somatic partner varied from single chromosomes to complete complement. This allowed us to compare pluripotency of the hybrid cells with various numbers of somatic chromosomes. Three criteria were used for the assessment: (i) expression of Oct-4 and Nanog genes; (ii) analyses of teratomas generated by subcutaneous injections of the tested cells into immunodeficient mice; (iii) contribution of the hybrid cells in chimeras generated by injection of the tested cells into C57BL blastocysts. All tested hybrid clones showed expression of Oct-4 and Nanog at level comparable to ES cells. Histological and immunofluorescent analyses demonstrated that most teratomas formed from the hybrid cells with different number of somatic chromosomes contained derivatives of three embryonic layers. Tested hybrid clones make similar contribution in various tissues of chimeras in spite of significant differences in the number of somatic chromosomes they contained. The data indicate that pluripotency is manifested as a dominant trait in the ES hybrid cells and does not depend substantially on the number of somatic chromosomes. The latter suggests that the developmental potential derived from ES cells is maintained in ES-somatic cell hybrids by cis-manner and is rather resistant to trans-acting factors emitted from the somatic one.
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Affiliation(s)
- Anna A Vasilkova
- Institute of Cytology and Genetics, Academy of Sciences of Russia, Siberian Branch, Novosibirsk, Russia
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10
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Hartshorn C, Rice JE, Wangh LJ. Developmentally-regulated changes of Xist RNA levels in single preimplantation mouse embryos, as revealed by quantitative real-time PCR. Mol Reprod Dev 2002; 61:425-36. [PMID: 11891913 DOI: 10.1002/mrd.10037] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Xist RNA localizes to the inactive X chromosome in cells of late cleavage stage female mouse embryos (Sheardown et al., 1997: Cell 91:99-107). Fluorescence in situ hybridization (FISH), however, does not quantify the number of Xist transcripts per nucleus. We have used real-time reverse transcription-polymerase chain reaction (RT-PCR) to measure Xist RNA levels in single preimplantation embryos and to establish developmental profiles in both female and male samples. The gender of each embryo was readily established based on Xist RNA levels, by counting Xist gene copies per cell, and by independent detection of the presence/absence of Sry, a Y chromosome-specific gene. Xist expression in males was found to be very low at all stages, as suggested by FISH. In contrast, female embryos contained measurable levels of Xist mRNA starting at the late 2-cell stage and rapidly accumulated Xist transcripts until morula stage. Xist RNA accumulation per embryo then reached a plateau, while cell division continued. We propose that during early cleavage high enough levels of Xist mRNA are transcribed to generate a pool of unbound molecules. This pool would serve to temporarily maintain X chromosome inactivation without additional transcription while the trophectoderm and inner cell mass (ICM) differentiate. The ICM would then loose the paternally imprinted pattern of X inactivation originally present in all embryonic cells.
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Affiliation(s)
- Cristina Hartshorn
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
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11
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Serov O, Matveeva N, Kuznetsov S, Kaftanovskaya E, Mittmann J. Embryonic hybrid cells: a powerful tool for studying pluripotency and reprogramming of the differentiated cell chromosomes. AN ACAD BRAS CIENC 2001; 73:561-8. [PMID: 11743603 DOI: 10.1590/s0001-37652001000400009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The properties of embryonic hybrid cells obtained by fusion of embryonic stem (ES) or teratocarcinoma (TC) cells with differentiated cells are reviewed. Usually, ES-somatic or TC-somatic hybrids retain pluripotent capacity at high levels quite comparable or nearly identical with those of the pluripotent partner. When cultured in vitro, ES-somatic- and TC-somatic hybrid cell clones, as a rule, lose the chromosomes derived from the somatic partner; however, in some clones the autosomes from the ES cell partner were also eliminated, i.e. the parental chromosomes segregated bilaterally in the ES-somatic cell hybrids. This opens up ways for searching correlation between the pluripotent status of the hybrid cells and chromosome segregation patterns and therefore for identifying the particular chromosomes involved in the maintenance of pluripotency. Use of selective medium allows to isolate in vitro the clones of ES-somatic hybrid cells in which "the pluripotent" chromosome can be replaced by "the somatic" counterpart carrying the selectable gene. Unlike the TC-somatic cell hybrids, the ES-somatic hybrids with a near-diploid complement of chromosomes are able to contribute to various tissues of chimeric animals after injection into the blastocoel cavity. Analysis of the chimeric animals showed that the "somatic" chromosome undergoes reprogramming during development. The prospects for the identification of the chromosomes that are involved in the maintenance of pluripotency and its cis- and trans-regulation in the hybrid cell genome are discussed.
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Affiliation(s)
- O Serov
- Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, 21949-900, Brazil.
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12
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Abstract
The inactive X chromosome differs from the active X in a number of ways; some of these, such as allocyclic replication and altered histone acetylation, are associated with all types of epigenetic silencing, whereas others, such as DNA methylation, are of more restricted use. These features are acquired progressively by the inactive X after onset of initiation. Initiation of X-inactivation is controlled by the X-inactivation center (Xic) and influenced by the X chromosome controlling element (Xce), which causes primary nonrandom X-inactivation. Other examples of nonrandom X-inactivation are also presented in this review. The definition of a major role for Xist, a noncoding RNA, in X-inactivation has enabled investigation of the mechanism leading to establishment of the heterochromatinized X-chromosome and also of the interactions between X-inactivation and imprinting as well as between X-inactivation and developmental processes in the early embryo.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, URA CNRS 1968, Institut Pasteur, Paris, France.
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Takagi N. Mouse embryonal carcinoma cell-somatic cell hybrids as experimental tools for the study of cell differentiation and X chromosome activity. CANCER GENETICS AND CYTOGENETICS 1997; 93:48-55. [PMID: 9062580 DOI: 10.1016/s0165-4608(96)00274-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Remarkable properties of murine embryonal carcinoma cells, stem cells of teratocarcinomas, manifest themselves when they are fused with differentiated somatic cells. Among others the capacity to reprogram genomes from these somatic cells and restore genetic pluripotency is most striking.
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Affiliation(s)
- N Takagi
- Division of Bioscience, Hokkaido University, Sapporo, Japan
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15
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Molecular genetics of X-chromosome inactivation. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1067-5701(96)80006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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