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X chromosome inactivation

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https://www.readbyqxmd.com/read/29900581/statistics-for-x-chromosome-associations
#1
Umut Özbek, Hui-Min Lin, Yan Lin, Daniel E Weeks, Wei Chen, John R Shaffer, Shaun M Purcell, Eleanor Feingold
In a genome-wide association study (GWAS), association between genotype and phenotype at autosomal loci is generally tested by regression models. However, X-chromosome data are often excluded from published analyses of autosomes because of the difference between males and females in number of X chromosomes. Failure to analyze X-chromosome data at all is obviously less than ideal, and can lead to missed discoveries. Even when X-chromosome data are included, they are often analyzed with suboptimal statistics...
June 13, 2018: Genetic Epidemiology
https://www.readbyqxmd.com/read/29892053/a-systematic-review-and-meta-analysis-of-271-pcdh19-variant-individuals-identifies-psychiatric-comorbidities-and-association-of-seizure-onset-and-disease-severity
#2
REVIEW
Kristy L Kolc, Lynette G Sadleir, Ingrid E Scheffer, Atma Ivancevic, Rachel Roberts, Duyen H Pham, Jozef Gecz
Epilepsy and Mental Retardation Limited to Females (EFMR) is an infantile onset disorder characterized by clusters of seizures. EFMR is due to mutations in the X-chromosome gene PCDH19, and is underpinned by cellular mosaicism due to X-chromosome inactivation in females or somatic mutation in males. This review characterizes the neuropsychiatric profile of this disorder and examines the association of clinical and molecular factors with neuropsychiatric outcomes. Data were extracted from 38 peer-reviewed original articles including 271 individual cases...
June 11, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29887375/smchd1-merges-chromosome-compartments-and-assists-formation-of-super-structures-on-the-inactive-x
#3
Chen-Yu Wang, Teddy Jégu, Hsueh-Ping Chu, Hyun Jung Oh, Jeannie T Lee
Mammalian chromosomes are partitioned into A/B compartments and topologically associated domains (TADs). The inactive X (Xi) chromosome, however, adopts a distinct conformation without evident compartments or TADs. Here, through exploration of an architectural protein, structural-maintenance-of-chromosomes hinge domain containing 1 (SMCHD1), we probe how the Xi is reconfigured during X chromosome inactivation. A/B compartments are first fused into "S1" and "S2" compartments, coinciding with Xist spreading into gene-rich domains...
May 28, 2018: Cell
https://www.readbyqxmd.com/read/29878089/eldecalcitol-causes-fgf23-resistance-for-pi-reabsorption-and-improves-rachitic-bone-phenotypes-in-the-male-hyp-mouse
#4
Ichiro Kaneko, Hiroko Segawa, Kayo Ikuta, Ai Hanasaki, Toru Fujii, Sawako Tatsumi, Shinsuke Kido, Tomoka Hasegawa, Norio Amizuka, Hitoshi Saito, Ken-Ichi Miyamoto
X-linked hypophosphatemia (XLH), the most common form of inheritable rickets, is caused by inactivation of PHEX (phosphate-regulating gene with homologies to endopeptidases on the X chromosome), and leads to fibroblast growth factor 23 (FGF23)-dependent renal phosphate (Pi) wasting. In the present study, we investigated whether maintaining Pi homeostasis with a novel potent vitamin D3 analog, eldecalcitol (1α,25-dihydroxy-2β-(3-hydroxypropyloxy)vitamin D3; ED71), could improve hypophosphatemic rickets in a murine model of XLH, the Hyp mouse...
June 5, 2018: Endocrinology
https://www.readbyqxmd.com/read/29872011/a-cross-eyed-geneticist-s-view-i-making-sense-of-the-lamin-b-receptor-a-chimeric-protein
#5
Durgadas P Kasbekar
The vertebrate inner nuclear membrane protein, lamin B receptor, has an N-terminal ~200 residue nucleoplasmic domain (NTD), and a ~420 residue C-terminal domain (CTD) that anchors the NTD to the INM. Chen et al (2016) showed the NTD interacts with Xist long noncoding RNA to effect X chromosome inactivation in female mammals. Tsai et al (2016) showed the CTD has sterol reductase activity that is essential for viability. And Nikolakaki et al (2017) proposed a model to interconnect these disparate functions of this chimeric protein...
June 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29861859/epigenetic-reprogramming-by-na%C3%A3-ve-conditions-establishes-an-irreversible-state-of-partial-x-chromosome-reactivation-in-female-stem-cells
#6
Alexandra V Panova, Alexandra N Bogomazova, Maria A Lagarkova, Sergey L Kiselev
Female human pluripotent stem cells (PSCs) have variable X-chromosome inactivation (XCI) status. One of the X chromosomes may either be inactive (Xi) or display some active state markers. Long-term cultivation of PSCs may lead to an erosion of XCI and partial X reactivation. Such heterogeneity and instability of XCI status might hamper the application of human female PSCs for therapy or disease modeling. We attempted to address XCI heterogeneity by reprogramming human embryonic stem cells (hESCs) to the naïve state...
May 18, 2018: Oncotarget
https://www.readbyqxmd.com/read/29848858/-new-approach-to-the-investigation-of-dohad-using-x-inactivation-gene-expression-system
#7
Takayuki Kumamoto, Shigeru Oshio
X-chromosome inactivation (XCI) occurs during the gestation period to compensate for the dosage of X-linked genes in female mammals. Xist RNA is a long noncoding RNA with a global epigenetic function and is indispensable for XCI from the initiation to establishment and maintenance phases. The X chromosome contains over 1,000 genes that are essential for proper development, especially that of the brain, immune system, metabolism and reproductive functions. We found that exposure to bisphenol A or folate deficiency during the fetal period changes the expressions of Xist, Tsix (the antisense repressor of Xist), and many X chromosome linked genes widely in newborn mice...
2018: Nihon Eiseigaku Zasshi. Japanese Journal of Hygiene
https://www.readbyqxmd.com/read/29844229/reproductive-long-intergenic-non-coding-rnas-exhibit-male-gamete-specificity-and-polycomb-repressive-complex-2-mediated-repression
#8
Cameron Johnson, Liza Conrad, Ravi Patel, Sarah Anderson, Andy Pereira, Venkatesan Sundaresan, Chen Xin Li
Long non-coding RNAs (lncRNAs) have been extensively characterized in animals and are involved in several processes, including homeobox gene expression and X-chromosome inactivation. In comparison, there has been much less detailed characterization of plant lncRNAs, and the number of distinct lncRNAs encoded in plant genomes and their regulation by developmental and epigenetic mechanisms remain largely unknown. Here we analyzed transcriptome data from Asian rice (Oryza sativa) and identified 6309 long intergenic non-coding RNAs (lincRNAs), focusing on their expression in reproductive tissues and organs...
May 29, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29804891/exit-from-naive-pluripotency-induces-a-transient-x-chromosome-inactivation-like-state-in-males
#9
Elsa J Sousa, Hannah T Stuart, Lawrence E Bates, Mohammadmersad Ghorbani, Jennifer Nichols, Sabine Dietmann, José C R Silva
A hallmark of naive pluripotency is the presence of two active X chromosomes in females. It is not clear whether prevention of X chromosome inactivation (XCI) is mediated by gene networks that preserve the naive state. Here, we show that robust naive pluripotent stem cell (nPSC) self-renewal represses expression of Xist, the master regulator of XCI. We found that nPSCs accumulate Xist on the male X chromosome and on both female X chromosomes as they become NANOG negative at the onset of differentiation. This is accompanied by the appearance of a repressive chromatin signature and partial X-linked gene silencing, suggesting a transient and rapid XCI-like state in male nPSCs...
May 16, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29800566/genome-wide-rnai-screen-identify-melanoma-associated-antigen-mageb3-involved-in-x-chromosome-inactivation
#10
Wei Li, Ru Hong, Lan-Tian Lai, Qiman Dong, Peiling Ni, Rosi Chelliah, Mehnaz Huq, Siti Nadirah Binte Ismail, Udita Chandola, Zhiwei Ang, Bingqing Lin, Xin Chen, Lingyi Chen, Li-Feng Zhang
Xist (inactivated X chromosome specific transcript) is a prototype long non-coding RNA (lncRNA) in charge of epigenetic silencing of one X chromosome in each female cell in mammals. In a genetic screen, we identify Mageb3, and its homologs Mageb1 and Mageb2 as genes functionally required for Xist-mediated gene silencing. Mageb1-3 are previously uncharacterized genes belonging to the MAGE (melanoma-associated antigen) gene family. Mageb1-3 are expressed in undifferentiated ES cells and early stages of in vitro differentiation, a critical time window of X chromosome inactivation...
May 22, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29784772/a-heterochromatin-domain-forms-gradually-at-a-new-telomere-and-is-dynamic-at-stable-telomeres
#11
Jinyu Wang, Jessica R Eisenstatt, Julien Audry, Kristen Cornelius, Matthew Shaughnessy, Kathleen L Berkner, Kurt W Runge
Heterochromatin domains play important roles in chromosome biology, organismal development and aging, including centromere function, mammalian female X-chromosome inactivation and senescence-associated heterochromatin foci. In the fission yeast Schizosaccharomyces pombe and metazoans, heterochromatin contains histone H3 that is dimethylated at lysine 9. While factors required for heterochromatin have been identified, the dynamics of heterochromatin formation are poorly understood. Telomeres convert adjacent chromatin into heterochromatin...
May 21, 2018: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29773953/mir-34a-mediated-regulation-of-xist-in-female-cells-under-inflammation
#12
Botros B Shenoda, Yuzhen Tian, Guillermo M Alexander, Enrique Aradillas-Lopez, Robert J Schwartzman, Seena K Ajit
Background: Evidence is overwhelming for sex differences in pain, with women representing the majority of the chronic pain patient population. There is a need to explore novel avenues to elucidate this sex bias in the development of chronic inflammatory pain conditions. Complex regional pain syndrome (CRPS) is a chronic neuropathic pain disorder, and the incidence of CRPS is greater in women than in men by ~4:1. Since neurogenic inflammation is a key feature of CRPS, dysregulation of inflammatory responses can be a factor in predisposing women to chronic pain...
2018: Journal of Pain Research
https://www.readbyqxmd.com/read/29769284/dynamic-copy-number-evolution-of-x-and-y-linked-ampliconic-genes-in-human-populations
#13
Elise A Lucotte, Laurits Skov, Jacob Malte Jensen, Moisès Coll Macià, Kasper Munch, Mikkel H Schierup
Ampliconic genes are multicopy, in majority found on sex-chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29763708/pcdh19-regulation-of-neural-progenitor-cell-differentiation-suggests-asynchrony-of-neurogenesis-as-a-mechanism-contributing-to-pcdh19-girls-clustering-epilepsy
#14
Claire C Homan, Stephen Pederson, Thu-Hien To, Chuan Tan, Sandra Piltz, Mark Corbett, Ernst Wolvetang, Paul Thomas, Lachlan A Jolly, Jozef Gecz
PCDH19-Girls Clustering Epilepsy (PCDH19-GCE) is a childhood epileptic encephalopathy characterised by a spectrum of neurodevelopmental problems. PCDH19-GCE is caused by heterozygous loss-of-function mutations in the X-chromosome gene, Protocadherin 19 (PCDH19) encoding a cell-cell adhesion molecule. Intriguingly, hemizygous males are generally unaffected. As PCDH19 is subjected to random X-inactivation, heterozygous females are comprised of a mosaic of cells expressing either the normal or mutant allele, which is thought to drive pathology...
May 12, 2018: Neurobiology of Disease
https://www.readbyqxmd.com/read/29756331/mammalian-x-chromosome-dosage-compensation-perspectives-from-the-germ-line
#15
REVIEW
Mahesh N Sangrithi, James M A Turner
Sex chromosomes are advantageous to mammals, allowing them to adopt a genetic rather than environmental sex determination system. However, sex chromosome evolution also carries a burden, because it results in an imbalance in gene dosage between females (XX) and males (XY). This imbalance is resolved by X dosage compensation, which comprises both X chromosome inactivation and X chromosome upregulation. X dosage compensation has been well characterized in the soma, but not in the germ line. Germ cells face a special challenge, because genome wide reprogramming erases epigenetic marks responsible for maintaining the X dosage compensated state...
May 14, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29747568/classical-fragile-x-phenotype-in-a-female-infant-disclosed-by-comprehensive-genomic-studies
#16
Paula Jorge, Elsa Garcia, Ana Gonçalves, Isabel Marques, Nuno Maia, Bárbara Rodrigues, Helena Santos, Jacinta Fonseca, Gabriela Soares, Cecília Correia, Margarida Reis-Lima, Vincenzo Cirigliano, Rosário Santos
BACKGROUND: We describe a female infant with Fragile-X syndrome, with a fully expanded FMR1 allele and preferential inactivation of the homologous X-chromosome carrying a de novo deletion. This unusual and rare case demonstrates the importance of a detailed genomic approach, the absence of which could be misguiding, and calls for reflection on the current clinical and diagnostic workup for developmental disabilities. CASE PRESENTATION: We present a female infant, referred for genetic testing due to psychomotor developmental delay without specific dysmorphic features or relevant family history...
May 10, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29733970/thyroxine-binding-globulin-deficiency-due-to-a-novel-serpina7-mutation-clinical-characterization-analysis-of-x-chromosome-inactivation-pattern-and-protein-structural-modeling
#17
Cristiane Jeyce Gomes Lima, Andressa Aby Faraj Linhares Maciel, Matheus de Oliveira Andrade, Vinicius Santos da Cunha, Juliana Forte Mazzeu, Lucas Bleicher, Francisco de Assis Rocha Neves, Adriana Lofrano-Porto
OBJECTIVE: Thyroxine-binding globulin (TBG) is the major human thyroid hormone transport protein, encoded by the SERPINA7 gene (Xq22.2). We aim to investigate the molecular basis of partial TBG deficiency (TBG-PD) in a female, by evaluating the X-chromosome inactivation pattern as well as the mutant protein structural modeling. DESIGN AND METHODS: Sequencing of the coding region of the SERPINA7 gene was performed in a female with a TBG-PD phenotype and her first-degree relatives...
May 4, 2018: Gene
https://www.readbyqxmd.com/read/29729430/functional-genetics-of-early-human-development
#18
REVIEW
Nicolás M Ortega, Nerges Winblad, Alvaro Plaza Reyes, Fredrik Lanner
Understanding the genetic underpinning of early human development is of great interest not only for basic developmental and stem cell biology but also for regenerative medicine, infertility treatments, and better understanding the causes of congenital disease. Our current knowledge has mainly been generated with the use of laboratory animals, especially the mouse. While human and mouse early development present morphological resemblance, we know that the timing of the events as well as the cellular and genetic mechanisms that control fundamental processes are distinct between the species...
May 2, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29728705/pathogenic-variants-in-e3-ubiquitin-ligase-rlim-rnf12-lead-to-a-syndromic-x-linked-intellectual-disability-and-behavior-disorder
#19
Suzanna G M Frints, Aysegul Ozanturk, Germán Rodríguez Criado, Ute Grasshoff, Bas de Hoon, Michael Field, Sylvie Manouvrier-Hanu, Scott E Hickey, Molka Kammoun, Karen W Gripp, Claudia Bauer, Christopher Schroeder, Annick Toutain, Theresa Mihalic Mosher, Benjamin J Kelly, Peter White, Andreas Dufke, Eveline Rentmeester, Sungjin Moon, Daniel C Koboldt, Kees E P van Roozendaal, Hao Hu, Stefan A Haas, Hans-Hilger Ropers, Lucinda Murray, Eric Haan, Marie Shaw, Renee Carroll, Kathryn Friend, Jan Liebelt, Lynne Hobson, Marjan De Rademaeker, Joep Geraedts, Jean-Pierre Fryns, Joris Vermeesch, Martine Raynaud, Olaf Riess, Joost Gribnau, Nicholas Katsanis, Koen Devriendt, Peter Bauer, Jozef Gecz, Christelle Golzio, Cristina Gontan, Vera M Kalscheuer
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations...
May 4, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29727695/clonality-analysis-of-multifocal-ipsilateral-breast-carcinomas-using-x-chromosome-inactivation-patterns
#20
Hayeon Kim, Chung-Yeul Kim, Kyong Hwa Park, Aeree Kim
The definition of multifocal breast cancer is ambiguous, and its incidence varies depending on the definition and detection methods. Multifocal breast cancers either have the same clonal origin or arise from completely distinct progenitor cells. The current American Joint Committee on Cancer Staging system and College of American Pathologists breast tumor guidelines state that only the largest tumor needs to be staged and studied immunohistochemically, on the assumption that they are of the same origin. However, some multifocal tumors have been proven to have arisen from different clones...
May 1, 2018: Human Pathology
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