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X chromosome inactivation

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https://www.readbyqxmd.com/read/28533481/massively-parallel-sequencing-and-genome-wide-copy-number-analysis-revealed-a-clonal-relationship-in-benign-metastasizing-leiomyoma
#1
Ren-Chin Wu, An-Shine Chao, Li-Yu Lee, Gigin Lin, Shu-Jen Chen, Yen-Jung Lu, Huei-Jean Huang, Chi-Feng Yen, Chien Min Han, Yun-Shien Lee, Tzu-Hao Wang, Angel Chao
Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28528201/x-linked-carriers-of-chronic-granulomatous-disease-illness-lyonization-and-stability
#2
Beatriz E Marciano, Christa S Zerbe, E Liana Falcone, Li Ding, Suk See DeRavin, Janine Daub, Samantha Kreuzburg, Lynne Yockey, Sally Hunsberger, Ladan Foruraghi, Lisa A Barnhart, Kabir Matharu, Victoria Anderson, Dirk N Darnell, Cathleen Frein, Danielle L Fink, Karen P Lau, Debra A Long Priel, John I Gallin, Harry L Malech, Gulbu Uzel, Alexandra F Freeman, Douglas B Kuhns, Sergio D Rosenzweig, Steven M Holland
BACKGROUND: Chronic granulomatous disease (CGD) is characterized by recurrent life-threatening bacterial and fungal infections and aberrant inflammation. Mutations in CYBB cause X-linked CGD and account for 65%-70% of cases in western countries. OBJECTIVE: To understand the clinical manifestations associated with the X-linked CGD carrier state. METHODS: We undertook a comprehensive retrospective study of 162 affected females. We examined dihydrorhodamine oxidation (DHR) data for percent (%) X chromosome inactivation...
May 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28512193/dna-replication-timing-during-development-anticipates-transcriptional-programs-and-parallels-enhancer-activation
#3
Joseph C Siefert, Constantin Georgescu, Jonathan D Wren, Amnon Koren, Christopher L Sansam
In dividing cells, DNA replication occurs in a precise order, but many questions remain regarding the mechanisms of replication timing establishment and regulation. We now have generated genome-wide, high-resolution replication timing maps throughout zebrafish development. Unexpectedly, in the rapid cell cycles preceding the midblastula transition, a defined timing program was present that predicted the initial wave of zygotic transcription. Replication timing was thereafter progressively and continuously remodeled across the majority of the genome, and epigenetic changes involved in enhancer activation frequently paralleled developmental changes in replication timing...
May 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28502657/rpl10l-is-required-for-male-meiotic-division-by-compensating-for-rpl10-during-meiotic-sex-chromosome-inactivation-in-mice
#4
Long Jiang, Tao Li, Xingxia Zhang, Beibei Zhang, Changping Yu, Yang Li, Suixing Fan, Xiaohua Jiang, Teka Khan, Qiaomei Hao, Peng Xu, Daita Nadano, Mahmoud Huleihel, Eitan Lunenfeld, P Jeremy Wang, Yuanwei Zhang, Qinghua Shi
The mammalian sex chromosomes have undergone profound changes during their evolution from an ancestral pair of autosomes [1-4]. Specifically, the X chromosome has acquired a paradoxical sex-biased function by redistributing gene contents [5, 6] and has generated a disproportionately high number of retrogenes that are located on autosomes and exhibit male-biased expression patterns [6]. Several selection-based models have been proposed to explain this phenomenon, including a model of sexual antagonism driving X inactivation (SAXI) [6-8] and a compensatory mechanism based on meiotic sex chromosome inactivation (MSCI) [6, 8-11]...
May 22, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28491099/induction-of-pluripotent-stem-cells-from-a-manifesting-carrier-of-duchenne-muscular-dystrophy-and-characterization-of-their-x-inactivation-status
#5
Yuko Miyagoe-Suzuki, Takashi Nishiyama, Miho Nakamura, Asako Narita, Fusako Takemura, Satoru Masuda, Narihiro Minami, Kumiko Murayama, Hirofumi Komaki, Yu-Ichi Goto, Shin'ichi Takeda
Three to eight percent of female carriers of Duchenne muscular dystrophy (DMD) develop dystrophic symptoms ranging from mild muscle weakness to a rapidly progressive DMD-like muscular dystrophy due to skewed inactivation of X chromosomes during early development. Here, we generated human induced pluripotent stem cells (hiPSCs) from a manifesting female carrier using retroviral or Sendai viral (SeV) vectors and determined their X-inactivation status. Although manifesting carrier-derived iPS cells showed normal expression of human embryonic stem cell markers and formed well-differentiated teratomas in vivo, many hiPS clones showed bi-allelic expression of the androgen receptor (AR) gene and loss of X-inactivation-specific transcript and trimethyl-histone H3 (Lys27) signals on X chromosomes, suggesting that both X chromosomes of the hiPS cells are in an active state...
2017: Stem Cells International
https://www.readbyqxmd.com/read/28484201/epigenetic-analysis-of-bovine-parthenogenetic-embryonic-fibroblasts
#6
Masahiro Kaneda, Masashi Takahashi, Ken-Ichi Yamanaka, Koji Saito, Masanori Taniguchi, Satoshi Akagi, Shinya Watanabe, Takashi Nagai
Although more than 100 imprinted genes have already been identified in the mouse and human genomes, little is known about genomic imprinting in cattle. For a better understanding of these genes in cattle, parthenogenetically activated bovine blastocysts were transferred to recipient cows to obtain parthenotes, and fibroblasts derived from a Day 40 (Day 0 being the day of parthenogenetic activation) parthenogenetic embryo (BpEFs) were successfully obtained. Bovine embryonic fibroblasts (BEFs) were also isolated from a normal fertilized embryo obtained from an artificially inseminated cow...
May 6, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/28481423/the-pig-a-gene-mutation-assay-in-mice-and-human-cells-a-review
#7
Ann-Karin Olsen, Stephen D Dertinger, Christopher T Krüger, Dag M Eide, Christine Instanes, Gunnar Brunborg, Andrea Hartwig, Anne Graupner
This MiniReview describes the principle of mutation assays based on the endogenous Pig-a gene and summarizes results for two species of toxicological interest, mice and humans. The work summarized here largely avoids rat-based studies, as are summarized elsewhere. The Pig-a gene mutation assay has emerged as a valuable tool for quantifying in vivo and in vitro mutational events. The Pig-a locus is located at the X-chromosome, giving the advantage that one inactivated allele can give rise to a mutated phenotype, detectable by multi-colour flow cytometry...
May 8, 2017: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/28479596/the-x-chromosome-in-space
#8
REVIEW
Teddy Jégu, Eric Aeby, Jeannie T Lee
Extensive 3D folding is required to package a genome into the tiny nuclear space, and this packaging must be compatible with proper gene expression. Thus, in the well-hierarchized nucleus, chromosomes occupy discrete territories and adopt specific 3D organizational structures that facilitate interactions between regulatory elements for gene expression. The mammalian X chromosome exemplifies this structure-function relationship. Recent studies have shown that, upon X-chromosome inactivation, active and inactive X chromosomes localize to different subnuclear positions and adopt distinct chromosomal architectures that reflect their activity states...
June 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28468635/prc2-represses-transcribed-genes-on-the-imprinted-inactive-x-chromosome-in-mice
#9
Emily Maclary, Michael Hinten, Clair Harris, Shriya Sethuraman, Srimonta Gayen, Sundeep Kalantry
BACKGROUND: Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression broadly, it remains unclear why some but not other PRC2 target genes require PRC2 and H3K27me3 for silencing. RESULTS: Here we define the transcriptional and chromatin features that predict which PRC2 target genes require PRC2/H3K27me3 for silencing by interrogating imprinted mouse X-chromosome inactivation...
May 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28463240/incorrect-dosage-of-iqsec2-a-known-intellectual-disability-and-epilepsy-gene-disrupts-dendritic-spine-morphogenesis
#10
S J Hinze, M R Jackson, S Lie, L Jolly, M Field, S C Barry, R J Harvey, C Shoubridge
There is considerable genetic and phenotypic heterogeneity associated with intellectual disability (ID), specific learning disabilities, attention-deficit hyperactivity disorder, autism and epilepsy. The intelligence quotient (IQ) motif and SEC7 domain containing protein 2 gene (IQSEC2) is located on the X-chromosome and harbors mutations that contribute to non-syndromic ID with and without early-onset seizure phenotypes in both sexes. Although IQ and Sec7 domain mutations lead to partial loss of IQSEC2 enzymatic activity, the in vivo pathogenesis resulting from these mutations is not known...
May 2, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28456808/heterozygous-nonsense-mutation-in-the-androgen-receptor-gene-associated-with-partial-androgen-insensitivity-syndrome-in-an-individual-with-47-xxy-karyotype
#11
Rafael L Batista, Andresa S Rodrigues, Mirian Y Nishi, Alina C R Feitosa, Nathália L R A Gomes, José Antonia F Junior, Sorahia Domenice, Elaine M F Costa, Berenice B de Mendonça
There are only 2 patients with 47,XXY karyotype and androgen receptor (AR) gene mutation reported in the literature, and both are diagnosed as complete androgen insensitivity syndrome (CAIS). We report a 22-year-old female with 47,XXY karyotype and atypical external genitalia. Sequencing of AR revealed the heterozygous p.Asn849Lys*32 mutation, and extensive X chromosome microsatellite analysis showed homozygosity for Xp and heterozygosity for Xq, suggesting partial X maternal isodisomy. Partial androgen insensitivity syndrome (PAIS) developed in this case, probably because of the presence of the heterozygous AR mutation and random X- inactivation of the healthy allele...
April 29, 2017: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/28454580/association-of-skewed-x-chromosome-inactivation-with-fmr1-cgg-repeat-length-and-anti-mullerian-hormone-levels-a-cohort-study
#12
David H Barad, Sarah Darmon, Andrea Weghofer, Gary J Latham, Filipovic-Sadic, Qi Wang, Vitaly A Kushnir, David F Albertini, Norbert Gleicher
BACKGROUND: Premutation range CGGn repeats of the FMR1 gene denote risk toward primary ovarian insufficiency (POI), also called premature ovarian failure (POF). This prospective cohort study was undertaken to determine if X-chromosome inactivation skew (sXCI) is associated with variations in FMR1 CGG repeat length and, if so, is also associated with age adjusted antimüllerian hormone (AMH) levels as an indicator of functional ovarian reserve (FOR). METHODS: DNA samples of 58 women were analyzed for methylation status and confirmation of CGGn repeat length...
April 28, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/28446708/structural-and-functional-analysis-of-oceanobacillus-iheyensis-macrodomain-reveals-a-network-of-waters-involved-in-substrate-binding-and-catalysis
#13
Rubén Zapata-Pérez, Fernando Gil-Ortiz, Ana Belén Martínez-Moñino, Antonio Ginés García-Saura, Jordi Juanhuix, Álvaro Sánchez-Ferrer
Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28443134/characterization-of-x-chromosome-gene-expression-in-bovine-blastocysts-derived-by-in-vitro-fertilization-and-somatic-cell-nuclear-transfer
#14
Byungkuk Min, Jung Sun Park, Kyuheum Jeon, Yong-Kook Kang
To better understand X-chromosome reactivation (XCR) during early development, we analyzed transcriptomic data obtained from bovine male and female blastocysts derived by in-vitro fertilization (IVF) or somatic-cell nuclear transfer (SCNT). We found that X-linked genes were upregulated by almost two-fold in female compared with male IVF blastocysts. The upregulation of X-linked genes in female IVFs indicated a transcriptional dimorphism between the sexes, because the mean autosomal gene expression levels were relatively constant, regardless of sex...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28414775/xp11-22-deletions-encompassing-cenpvl1-cenpvl2-maged1-and-gspt2-as-a-cause-of-syndromic-x-linked-intellectual-disability
#15
Christina Grau, Molly Starkovich, Mahshid S Azamian, Fan Xia, Sau Wai Cheung, Patricia Evans, Alex Henderson, Seema R Lalani, Daryl A Scott
By searching a clinical database of over 60,000 individuals referred for array-based CNV analyses and online resources, we identified four males from three families with intellectual disability, developmental delay, hypotonia, joint hypermobility and relative macrocephaly who carried small, overlapping deletions of Xp11.22. The maximum region of overlap between their deletions spanned ~430 kb and included two pseudogenes, CENPVL1 and CENPVL2, whose functions are not known, and two protein coding genes-the G1 to S phase transition 2 gene (GSPT2) and the MAGE family member D1 gene (MAGED1)...
2017: PloS One
https://www.readbyqxmd.com/read/28408975/x-chromosome-inactivation-new-players-in-the-initiation-of-gene-silencing
#16
REVIEW
Ines Pinheiro, Edith Heard
X chromosome inactivation (XCI) is a dosage compensation process that was adopted by female mammals to balance gene dosage between XX females and XY males. XCI starts with the upregulation of the non-coding RNA Xist, after which most X-linked genes are silenced and acquire a repressive chromatin state. Even though the chromatin marks of the inactive X have been fairly well described, the mechanisms responsible for the initiation of XCI remain largely unknown. In this review, we discuss recent developments that revealed unexpected factors playing a role in XCI and that might be of crucial importance to understand the mechanisms responsible for the very first steps of this chromosome-wide gene-silencing event...
2017: F1000Research
https://www.readbyqxmd.com/read/28403217/embryonic-loss-of-human-females-with-partial-trisomy-19-identifies-region-critical-for-the-single-active-x
#17
Barbara R Migeon, Michael A Beer, Hans T Bjornsson
To compensate for the sex difference in the number of X chromosomes, human females, like human males have only one active X. The other X chromosomes in cells of both sexes are silenced in utero by XIST, the Inactive X Specific Transcript gene, that is present on all X chromosomes. To investigate the means by which the human active X is protected from silencing by XIST, we updated the search for a key dosage sensitive XIST repressor using new cytogenetic data with more precise resolution. Here, based on a previously unknown sex bias in copy number variations, we identify a unique region in our genome, and propose candidate genes that lie within, as they could inactivate XIST...
2017: PloS One
https://www.readbyqxmd.com/read/28401797/the-state-of-skewed-x-chromosome-inactivation-is-retained-in-the-induced-pluripotent-stem-cells-from-a-female-with-hemophilia-b
#18
Cuicui Lyu, Jun Shen, Jianping Zhang, Feng Xue, Xiaofan Liu, Wei Liu, Rongfeng Fu, Liyan Zhang, Huiyuan Li, Donglei Zhang, Xiaobing Zhang, Tao Cheng, Renchi Yang, Lei Zhang
Skewed X chromosome inactivation (XCI) is a rare reason for hemophilia B in females. It is indefinite whether X chromosome reactivation (XCR) would occur when cells of hemophilia B patients with skewed XCI were reprogrammed into induced pluripotent stem cells (iPSCs). In this study, we investigated a female hemophilia B patient with a known F9 gene mutation: c.676C>T, p.Arg226Trp . We demonstrated that skewed XCI was the pathogenesis of the patient, and we successfully generated numerous iPSC colonies of the patient from peripheral blood mononuclear cells (PBMNCs), which was the first time for generating hemophilia-specific iPSCs from PBMNCs...
March 22, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28391319/allele-specific-expression-analysis-does-not-support-sex-chromosome-inactivation-on-the-chicken-z-chromosome
#19
Qiong Wang, Judith E Mank, Junying Li, Ning Yang, Lujiang Qu
Heterogametic sex chromosomes have evolved many times independently, and in many cases, the loss of functional genes from the sex-limited Y or W chromosome leaves only one functional gene copy on the corresponding X or Z chromosome in the heterogametic sex. Because gene dose often correlates with gene expression level, this difference in gene dose between males and females for X- or Z-linked genes in some cases has selected for chromosome-wide transcriptional dosage compensation mechanisms to counteract any reduction in expression in the heterogametic sex...
March 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28387970/mutation-of-the-xist-gene-upregulates-expression-of-x-linked-genes-but-decreases-the-developmental-rates-of-cloned-male-porcine-embryos
#20
Yang Yang, Dan Wu, Dewu Liu, Junsong Shi, Rong Zhou, Xiaoyan He, Jianping Quan, Gengyuan Cai, Enqin Zheng, Zhenfang Wu, Zicong Li
XIST is an X-linked, non-coding gene responsible for the cis induction of X-chromosome inactivation (XCI). Knockout of the XIST allele on an active X chromosome abolishes erroneous XCI and enhances the in vivo development of cloned mouse embryos by more than 10-fold. This study aimed to investigate whether a similar manipulation would improve cloning efficiency in pigs. A male, porcine kidney cell line containing an EGFP insert in exon 1 of the XIST gene, resulting in a knockout allele (XIST-KO), was generated by homologous recombination using transcription activator-like effector nucleases (TALENs)...
April 7, 2017: Molecular Reproduction and Development
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