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https://www.readbyqxmd.com/read/28368037/high-resolution-rna-allelotyping-along-the-inactive-x-chromosome-evidence-of-rna-polymerase-iii-in-regulating-chromatin-configuration
#1
Ru Hong, Bingqing Lin, Xinyi Lu, Lan-Tian Lai, Xin Chen, Amartya Sanyal, Huck-Hui Ng, Kun Zhang, Li-Feng Zhang
We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromosome inactivation (XCI) in early embryos, is conditionally deleted from Xi in somatic cells (Xi(∆Xist)). We also monitored the behaviors of X-linked non-coding transcripts before and after XCI. In each mutant cell line, gene reactivation occurs to ~6% genes along Xi(∆Xist) in a recognizable pattern...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28257137/novel-players-in-x-inactivation-insights-into-xist-mediated-gene-silencing-and-chromosome-conformation
#2
REVIEW
Simão T da Rocha, Edith Heard
The nuclear long noncoding RNA (lncRNA) Xist ensures X-chromosome inactivation (XCI) in female placental mammals. Although Xist is one of the most intensively studied lncRNAs, the mechanisms associated with its capacity to trigger chromosome-wide gene silencing, the formation of facultative heterochromatin and an unusual 3D conformation of the inactive X chromosome (Xi) have remained elusive. Now researchers have identified novel functional partners of Xist in a series of breakthrough studies, using unbiased techniques to isolate Xist-bound proteins, as well as forward genetic screens...
March 3, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28236732/x-chromosome-inactivation-silencing-topology-and-reactivation
#3
REVIEW
Teresa Robert Finestra, Joost Gribnau
To ensure X-linked gene dosage compensation between females (XX) and males (XY), one X chromosome undergoes X chromosome inactivation (XCI) in female cells. This process is tightly regulated throughout development by many different factors, with Xist as a key regulator, encoding a long non-coding RNA, involved in establishment of several layers of repressive epigenetic modifications. Several recent studies on XCI focusing on identification and characterization of Xist RNA-protein interactors, revealed new factors involved in gene silencing, genome topology and nuclear membrane attachment, amongst others...
February 21, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28143937/screen-for-reactivation-of-mecp2-on-the-inactive-x-chromosome-identifies-the-bmp-tgf-%C3%AE-superfamily-as-a-regulator-of-xist-expression
#4
Smitha Sripathy, Vid Leko, Robin L Adrianse, Taylor Loe, Eric J Foss, Emily Dalrymple, Uyen Lao, Tonibelle Gatbonton-Schwager, Kelly T Carter, Bernhard Payer, Patrick J Paddison, William M Grady, Jeannie T Lee, Marisa S Bartolomei, Antonio Bedalov
Rett syndrome (RS) is a debilitating neurological disorder affecting mostly girls with heterozygous mutations in the gene encoding the methyl-CpG-binding protein MeCP2 on the X chromosome. Because restoration of MeCP2 expression in a mouse model reverses neurologic deficits in adult animals, reactivation of the wild-type copy of MeCP2 on the inactive X chromosome (Xi) presents a therapeutic opportunity in RS. To identify genes involved in MeCP2 silencing, we screened a library of 60,000 shRNAs using a cell line with a MeCP2 reporter on the Xi and found 30 genes clustered in seven functional groups...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28118853/allele-specific-analysis-of-cell-fusion-mediated-pluripotent-reprograming-reveals-distinct-and-predictive-susceptibilities-of-human-x-linked-genes-to-reactivation
#5
Irene Cantone, Gopuraja Dharmalingam, Yi-Wah Chan, Anne-Celine Kohler, Boris Lenhard, Matthias Merkenschlager, Amanda G Fisher
BACKGROUND: Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the inactive X chromosome (Xi) and the determinants of locus susceptibility are, however, poorly understood. Here we use cell fusion-mediated pluripotent reprograming to study human Xi reactivation and allele-specific single nucleotide polymorphisms (SNPs) to identify reactivated loci...
January 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/27989770/human-naive-pluripotent-stem-cells-model-x-chromosome-dampening-and-x-inactivation
#6
Anna Sahakyan, Rachel Kim, Constantinos Chronis, Shan Sabri, Giancarlo Bonora, Thorold W Theunissen, Edward Kuoy, Justin Langerman, Amander T Clark, Rudolf Jaenisch, Kathrin Plath
Naive human embryonic stem cells (hESCs) can be derived from primed hESCs or directly from blastocysts, but their X chromosome state has remained unresolved. Here, we show that the inactive X chromosome (Xi) of primed hESCs was reactivated in naive culture conditions. Like cells of the blastocyst, the resulting naive cells contained two active X chromosomes with XIST expression and chromosome-wide transcriptional dampening and initiated XIST-mediated X inactivation upon differentiation. Both establishment of and exit from the naive state (differentiation) happened via an XIST-negative XaXa intermediate...
January 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/27989715/human-embryonic-stem-cells-do-not-change-their-x-inactivation-status-during-differentiation
#7
Sanjeet Patel, Giancarlo Bonora, Anna Sahakyan, Rachel Kim, Constantinos Chronis, Justin Langerman, Sorel Fitz-Gibbon, Liudmilla Rubbi, Rhys J P Skelton, Reza Ardehali, Matteo Pellegrini, William E Lowry, Amander T Clark, Kathrin Plath
Applications of embryonic stem cells (ESCs) require faithful chromatin changes during differentiation, but the fate of the X chromosome state in differentiating ESCs is unclear. Female human ESC lines either carry two active X chromosomes (XaXa), an Xa and inactive X chromosome with or without XIST RNA coating (Xi(XIST+)Xa;XiXa), or an Xa and an eroded Xi (XeXa) where the Xi no longer expresses XIST RNA and has partially reactivated. Here, we established XiXa, XeXa, and XaXa ESC lines and followed their X chromosome state during differentiation...
January 3, 2017: Cell Reports
https://www.readbyqxmd.com/read/27507283/ordered-chromatin-changes-and-human-x-chromosome-reactivation-by-cell-fusion-mediated-pluripotent-reprogramming
#8
Irene Cantone, Hakan Bagci, Dirk Dormann, Gopuraja Dharmalingam, Tatyana Nesterova, Neil Brockdorff, Claire Rougeulle, Celine Vallot, Edith Heard, Ronan Chaligne, Matthias Merkenschlager, Amanda G Fisher
Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we use cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. We show that a rapid and widespread loss of Xi-associated H3K27me3 and XIST occurs in fused cells and precedes the bi-allelic expression of selected Xi-genes by many heterokaryons (30-50%)...
August 10, 2016: Nature Communications
https://www.readbyqxmd.com/read/27437574/structural-organization-of-the-inactive-x-chromosome-in-the-mouse
#9
Luca Giorgetti, Bryan R Lajoie, Ava C Carter, Mikael Attia, Ye Zhan, Jin Xu, Chong Jian Chen, Noam Kaplan, Howard Y Chang, Edith Heard, Job Dekker
X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed...
July 28, 2016: Nature
https://www.readbyqxmd.com/read/27001848/unusual-maintenance-of-x-chromosome-inactivation-predisposes-female-lymphocytes-for-increased-expression-from-the-inactive-x
#10
Jianle Wang, Camille M Syrett, Marianne C Kramer, Arindam Basu, Michael L Atchison, Montserrat C Anguera
Females have a greater immunological advantage than men, yet they are more prone to autoimmune disorders. The basis for this sex bias lies in the X chromosome, which contains many immunity-related genes. Female mammals use X chromosome inactivation (XCI) to generate a transcriptionally silent inactive X chromosome (Xi) enriched with heterochromatic modifications and XIST/Xist RNA, which equalizes gene expression between the sexes. Here, we examine the maintenance of XCI in lymphocytes from females in mice and humans...
April 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26951653/impaired-imprinted-x-chromosome-inactivation-is-responsible-for-the-skewed-sex-ratio-following-in-vitro-fertilization
#11
Kun Tan, Lei An, Kai Miao, Likun Ren, Zhuocheng Hou, Li Tao, Zhenni Zhang, Xiaodong Wang, Wei Xia, Jinghao Liu, Zhuqing Wang, Guangyin Xi, Shuai Gao, Linlin Sui, De-Sheng Zhu, Shumin Wang, Zhonghong Wu, Ingolf Bach, Dong-Bao Chen, Jianhui Tian
Dynamic epigenetic reprogramming occurs during normal embryonic development at the preimplantation stage. Erroneous epigenetic modifications due to environmental perturbations such as manipulation and culture of embryos during in vitro fertilization (IVF) are linked to various short- or long-term consequences. Among these, the skewed sex ratio, an indicator of reproductive hazards, was reported in bovine and porcine embryos and even human IVF newborns. However, since the first case of sex skewing reported in 1991, the underlying mechanisms remain unclear...
March 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26360551/cancer-testis-antigen-expression-in-serous-endometrial-cancer-with-loss-of-x-chromosome-inactivation
#12
Jun Kang, Hee Jin Lee, Sun-Young Jun, Eun Su Park, Lee-So Maeng
BACKGROUND: Cancer-testis antigens (CTAs) are potential targets for cancer immunotherapy. Many CTAs are located on the X chromosome and are epigenetically regulated. Loss of X chromosome inactivation (XCI) is observed in breast and ovarian cancers and is thought to be related to the overexpression of CTAs. We investigated the relation between expression of CTAs and loss of XCI in endometrial cancer. MATERIALS AND METHODS: We used data generated by The Cancer Genome Atlas Genome Data Analysis Centers and data for Xist knockout mice available at the Gene Expression Omnibus...
2015: PloS One
https://www.readbyqxmd.com/read/26260844/dynamic-interplay-and-function-of-multiple-noncoding-genes-governing-x-chromosome-inactivation
#13
REVIEW
Minghui Yue, John Lalith Charles Richard, Yuya Ogawa
There is increasing evidence for the emergence of long noncoding RNAs (lncRNAs) as important components, especially in the regulation of gene expression. In the event of X chromosome inactivation, robust epigenetic marks are established in a long noncoding Xist RNA-dependent manner, giving rise to a distinct epigenetic landscape on the inactive X chromosome (Xi). The X inactivation center (Xic) is essential for induction of X chromosome inactivation and harbors two topologically associated domains (TADs) to regulate monoallelic Xist expression: one at the noncoding Xist gene and its upstream region, and the other at the antisense Tsix and its upstream region...
January 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/26244333/xist-exon-7-contributes-to-the-stable-localization-of-xist-rna-on-the-inactive-x-chromosome
#14
Norishige Yamada, Yuko Hasegawa, Minghui Yue, Tomofumi Hamada, Shinichi Nakagawa, Yuya Ogawa
To equalize X-linked gene dosage between the sexes in mammalian females, Xist RNA inactivates one of the two X-chromosomes. Here, we report the crucial function of Xist exon 7 in X-inactivation. Xist exon 7 is the second-largest exon with a well-conserved repeat E in eutherian mammals, but its role is often overlooked in X-inactivation. Although female ES cells with a targeted truncation of the Xist exon 7 showed no significant differences in their Xist expression levels and RNA stability from control cells expressing wild-type Xist, compromised localization of Xist RNA and incomplete silencing of X-linked genes on the inactive X-chromosome (Xi) were observed in the exon 7-truncated mutant cells...
August 2015: PLoS Genetics
https://www.readbyqxmd.com/read/26195790/the-xist-rna-prc2-complex-at-20-nm-resolution-reveals-a-low-xist-stoichiometry-and-suggests-a-hit-and-run-mechanism-in-mouse-cells
#15
Hongjae Sunwoo, John Y Wu, Jeannie T Lee
X-chromosome inactivation (XCI) is initiated by the long noncoding RNA Xist, which coats the inactive X (Xi) and targets Polycomb repressive complex 2 (PRC2) in cis. Epigenomic analyses have provided significant insight into Xist binding patterns and chromatin organization of the Xi. However, such epigenomic analyses are limited by averaging of population-wide dynamics and do not inform behavior of single cells. Here we view Xist RNA and the Xi at 20-nm resolution using STochastic Optical Reconstruction Microscopy (STORM) in mouse cells...
August 4, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26089354/chromosomes-a-comprehensive-xist-interactome-reveals-cohesin-repulsion-and-an-rna-directed-chromosome-conformation
#16
Anand Minajigi, John E Froberg, Chunyao Wei, Hongjae Sunwoo, Barry Kesner, David Colognori, Derek Lessing, Bernhard Payer, Myriam Boukhali, Wilhelm Haas, Jeannie T Lee
The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform "identification of direct RNA interacting proteins" (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors-including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers, and modifiers-that synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing...
July 17, 2015: Science
https://www.readbyqxmd.com/read/26039248/chromosome-x-genomic-and-epigenomic-aberrations-and-clinical-implications-in-breast-cancer-by-base-resolution-profiling
#17
Zhifu Sun, Naresh Prodduturi, Susan Y Sun, E Aubrey Thompson, Jean-Pierre A Kocher
AIM: Abnormal inactivation or loss of inactivated X chromosome (Xi) is implicated in women's cancer. However, the underlying mechanisms and clinical relevance are little known. MATERIALS & METHODS: High-throughput sequencing was conducted on breast cancer cell lines for copy number, RNA expression and 5'-methylcytosine in ChrX. The results were examined in primary breast tumors. RESULTS & CONCLUSION: Breast cancer cells demonstrated reduced or total loss of hemimethylation...
October 2015: Epigenomics
https://www.readbyqxmd.com/read/25982976/understanding-the-complex-circuitry-of-lncrnas-at-the-x-inactivation-center-and-its-implications-in-disease-conditions
#18
REVIEW
John Lalith Charles Richard, Yuya Ogawa
Balanced gene expression is a high priority in order to maintain optimal functioning since alterations and variations could result in acute consequences. X chromosome inactivation (X-inactivation) is one such strategy utilized by mammalian species to silence the extra X chromosome in females to uphold a similar level of expression between the two sexes. A functionally versatile class of molecules called long noncoding RNA (lncRNA) has emerged as key regulators of gene expression and plays important roles during development...
2016: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/25921272/erosion-of-x-chromosome-inactivation-in-human-pluripotent-cells-initiates-with-xact-coating-and-depends-on-a-specific-heterochromatin-landscape
#19
Céline Vallot, Jean-François Ouimette, Mélanie Makhlouf, Olivier Féraud, Julien Pontis, Julien Côme, Cécile Martinat, Annelise Bennaceur-Griscelli, Marc Lalande, Claire Rougeulle
Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells...
May 7, 2015: Cell Stem Cell
https://www.readbyqxmd.com/read/25578780/knockdown-of-long-non-coding-rna-xist-exerts-tumor-suppressive-functions-in-human-glioblastoma-stem-cells-by-up-regulating-mir-152
#20
Yilong Yao, Jun Ma, Yixue Xue, Ping Wang, Zhen Li, Jing Liu, Liangyu Chen, Zhuo Xi, Hao Teng, Zhenhua Wang, Zhiqing Li, Yunhui Liu
Glioblastoma (GBM) is the most common and aggressive primary brain tumor. Great interest persists in useful therapeutic targets in GBM. Aberrant expression of long non-coding RNAs (lncRNAs) has been functionally associated with many cancers. Here, we elucidated the function and the possible molecular mechanisms of lncRNA XIST in human glioblastoma stem cells (GSCs). Our results proved that XIST expression was up-regulated in glioma tissues and GSCs. Functionally, knockdown of XIST exerted tumor-suppressive functions by reducing cell proliferation, migration and invasion as well as inducing apoptosis...
April 1, 2015: Cancer Letters
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