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X chromosome inactivation

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https://www.readbyqxmd.com/read/29623395/variable-x-chromosome-inactivation-and-enlargement-of-pericentral-glutamine-synthetase-zones-in-the-liver-of-heterozygous-females-with-otc-deficiency
#1
Dita Musalkova, Eva Sticova, Martin Reboun, Jitka Sokolova, Jakub Krijt, Jitka Honzikova, Jiri Gurka, Magdalena Neroldova, Tomas Honzik, Jiri Zeman, Milan Jirsa, Lenka Dvorakova, Martin Hrebicek
Ornithine transcarbamylase (OTC) deficiency is an X-linked disorder that causes recurrent and life-threatening episodes of hyperammonemia. The clinical picture in heterozygous females is highly diverse and derives from the genotype and the degree of inactivation of the mutated X chromosome in hepatocytes. Here, we describe molecular genetic, biochemical, and histopathological findings in the livers explanted from two female patients with late-onset OTC deficiency. Analysis of X-inactivation ratios by DNA methylation-based assays showed remarkable intra-organ variation ranging from 46:54 to 82:18 (average 70:30, n = 37), in favor of the active X chromosome carrying the mutation c...
April 6, 2018: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29620233/a-frameshift-mutation-in-the-chm-gene-causes-choroideremia-with-acute-angle%C3%A2-closure-glaucoma
#2
Pingbo Ouyang, Yun Li, Feng Zhang, Chengzhang Zhu, Beiji Zou, Jianlan Le, Lusi Zhang
Choroideremia is an X‑linked recessive chorioretinal degenerative disease that is characterized by progressive centripetal loss of the photoreceptor, retinal pigment epithelium (RPE), and choriocapillaris layers. The CHM gene [choroideremia (Rab escort protein 1)] has been identified as the pathogenic gene in choroideremia. The aim of the present study was to describe the clinical and genetic characteristics of a family with choroideremia family. In the present study, a family with choroideremia presenting with serious chorioretinal atrophy and pigment proliferation, shallow anterior chambers, angle closure and high intraocular pressure (IOP) were recruited...
April 5, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29615635/characterization-of-sex-based-dna-methylation-signatures-in-the-airways-during-early-life
#3
Cesar L Nino, Geovanny F Perez, Natalia Isaza, Maria J Gutierrez, Jose L Gomez, Gustavo Nino
Human respiratory conditions are largely influenced by the individual's sex resulting in overall higher risk for males. Sex-based respiratory differences are present at birth suggesting a strong genetic component. Our objective was to characterize early life sex-based genomic signatures determined by variable X-chromosome methylation in the airways. We compared male versus female genome-wide DNA methylation in nasal airway samples from newborns and infants aged 1-6 months (N = 12). We analyzed methylation signals across CpG sites mapped to each X-linked gene using an unsupervised classifier (principal components) followed by an internal evaluation and an exhaustive cross-validation...
April 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29606911/a-girl-with-10-mb-distal-xp-deletion-arising-from-maternal-pericentric-inversion-clinical-data-and-molecular-characterization
#4
Ioannis Papoulidis, Annalisa Vetro, Vassilis Paspaliaris, Monika Ziegler, Katharina Kreskowski, George Daskalakis, Vasilios Papadopoulos, Themistoklis Dagklis, Thomas Liehr, Loretta Thomaidis, Emmanouil Manolakos
Background: Short arm deletions of the X-chromosome are challenging issues for genetic counseling due to their low penetrance in population. Female carriers of these deletions have milder phenotype than male ones, considering the intellectual ability and social skills, probably because of the X-chromosome inactivation phenomenon. Case report: A female patient with a 10Mb distal Xp deletion and an Xq duplication, showing mild intellectual disability, is described in this report...
April 2018: Current Genomics
https://www.readbyqxmd.com/read/29605847/cpg-islands-in-cancer-heads-tails-and-sides
#5
Humberto J Ferreira, Manel Esteller
DNA methylation is a dynamic epigenetic mark that characterizes different cellular developmental stages, including tissue-specific profiles. This CpG dinucleotide modification cooperates in the regulation of the output of the cellular genetic content, in both healthy and pathological conditions. According to endogenous and exogenous stimuli, DNA methylation is involved in gene transcription, alternative splicing, imprinting, X-chromosome inactivation, and control of transposable elements. When these dinucleotides are organized in dense regions are called CpG islands (CGIs), being commonly known as transcriptional regulatory regions frequently associated with the promoter region of several genes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29568981/three-dimensional-organization-and-dynamics-of-the-genome
#6
REVIEW
Przemyslaw Szalaj, Dariusz Plewczynski
Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand...
March 22, 2018: Cell Biology and Toxicology
https://www.readbyqxmd.com/read/29553562/pooled-shrna-screen-for-reactivation-of-mecp2-on-the-inactive-x-chromosome
#7
Vid Leko, Smitha Sripathy, Robin L Adrianse, Taylor Loe, Angela Park, Uyen Lao, Eric J Foss, Marisa S Bartolomei, Antonio Bedalov
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi)...
March 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29546464/chromosome-wide-gene-dosage-rebalance-may-benefit-tumor-progression
#8
Honglei Zhang, Xing Yang, Xu Feng, Haibo Xu, Qin Yang, Li Zou, Mei Yan, Dequan Liu, Xiaosan Su, Baowei Jiao
The high-risk of tumor initiation in patients with Turner syndrome (TS) characterized by X chromosome monosomy in women has been well established and aneuploidy, defined as an abnormal number of chromosomes, is a common feature in human cancer. However, the underlying mechanisms of X chromosome aneuploidy promoting tumorigenesis remain obscure. We propose that chromosome-wide gene dosage imbalance (CDI) may serve as an important mechanism. Here, we assess the relative expression ratios of X chromosome and autosomes (expression ratios of X:AA) between tumor samples and adjacent normal samples across 16 tumor types using expression datasets from The Cancer Genome Atlas (TCGA) project...
March 15, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29530533/fabry-disease-revisited-management-and-treatment-recommendations-for-adult-patients
#9
REVIEW
Alberto Ortiz, Dominique P Germain, Robert J Desnick, Juan Politei, Michael Mauer, Alessandro Burlina, Christine Eng, Robert J Hopkin, Dawn Laney, Aleš Linhart, Stephen Waldek, Eric Wallace, Frank Weidemann, William R Wilcox
Fabry disease is an X-linked lysosomal storage disorder caused by mutations in the GLA gene leading to deficient α-galactosidase A activity, glycosphingolipid accumulation, and life-threatening complications. Phenotypes vary from the "classic" phenotype, with pediatric onset and multi-organ involvement, to later-onset, a predominantly cardiac phenotype. Manifestations are diverse in female patients in part due to variations in residual enzyme activity and X chromosome inactivation patterns. Enzyme replacement therapy (ERT) and adjunctive treatments can provide significant clinical benefit...
February 28, 2018: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29520293/analysis-of-parent-of-origin-effects-on-the-x-chromosome-in-asian-and-european-orofacial-cleft-triads-identifies-associations-with-dmd-fgf13-egfl6-and-additional-loci-at-xp22-2
#10
Øivind Skare, Rolv T Lie, Øystein A Haaland, Miriam Gjerdevik, Julia Romanowska, Håkon K Gjessing, Astanand Jugessur
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29519750/de-novo-hdac8-mutation-causes-rett-related-disorder-with-distinctive-facial-features-and-multiple-congenital-anomalies
#11
Tomoko Saikusa, Munetsugu Hara, Kazuhiro Iwama, Kotaro Yuge, Chihiro Ohba, Jun-Ichiro Okada, Tadashi Hisano, Yushiro Yamashita, Nobuhiko Okamoto, Hirotomo Saitsu, Naomichi Matsumoto, Toyojiro Matsuishi
We present a unique 11-year-old girl showing clinical features of Rett-related disorder with distinctive facial features and multiple congenital anomalies including ocular hypertelorism, arched eyebrows, a broad nose, dental anomalies, congenital heart disease, truncal obesity, and epilepsy. A novel de novo mutation in histone deacetylase 8 (HDAC8) (c.652G > T, p.Gly218Cys) was confirmed by whole exome sequencing and Sanger sequencing. X-chromosome inactivation analysis on DNA isolated from peripheral blood lymphocytes revealed a completely skewed pattern associated with an inactive maternal allele...
March 5, 2018: Brain & Development
https://www.readbyqxmd.com/read/29517003/corrigendum-landscape-of-x-chromosome-inactivation-across-human-tissues
#12
Taru Tukiainen, Alexandra-Chloé Villani, Angela Yen, Manuel A Rivas, Jamie L Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, Beryl B Cummings, Stephane E Castel, Konrad J Karczewski, François Aguet, Andrea Byrnes, GTEx Consortium, Tuuli Lappalainen, Aviv Regev, Kristin G Ardlie, Nir Hacohen, Daniel G MacArthur
This corrects the article DOI: 10.1038/nature24265.
March 7, 2018: Nature
https://www.readbyqxmd.com/read/29513658/brdt-is-an-essential-epigenetic-regulator-for-proper-chromatin-organization-silencing-of-sex-chromosomes-and-crossover-formation-in-male-meiosis
#13
Marcia Manterola, Taylor M Brown, Min Young Oh, Corey Garyn, Bryan J Gonzalez, Debra J Wolgemuth
The double bromodomain and extra-terminal domain (BET) proteins are critical epigenetic readers that bind to acetylated histones in chromatin and regulate transcriptional activity and modulate changes in chromatin structure and organization. The testis-specific BET member, BRDT, is essential for the normal progression of spermatogenesis as mutations in the Brdt gene result in complete male sterility. Although BRDT is expressed in both spermatocytes and spermatids, loss of the first bromodomain of BRDT leads to severe defects in spermiogenesis without overtly compromising meiosis...
March 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29499223/cd40lg-duplication-associated-autoimmune-disease-is-silenced-by-non-random-x-chromosome-inactivation
#14
Carole Le Coz, Melissa Trofa, Camille M Syrett, Anna Martin, Harumi Jyonouchi, Soma Jyonouchi, Montserrat C Anguera, Neil Romberg
An inherited syndrome of autoimmunity associated with CD40LG duplication is silenced by non-random X-chromosome inactivation and is treatable with CD40L directed therapy.
February 27, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29490426/demonstration-of-a-novel-xp22-2-microdeletion-as-the-cause-of-familial-extreme-skewing-of-x-inactivation-utilizing-case-parent-trio-snp-microarray-analysis
#15
Jane A Mason, Hnin T Aung, Adayapalam Nandini, Rickie G Woods, David J Fairbairn, John A Rowell, David Young, Rachel D Susman, Simon A Brown, Valentine J Hyland, Jeremy D Robertson
BACKGROUND: We report a kindred referred for molecular investigation of severe hemophilia A in a young female in which extremely skewed X-inactivation was observed in both the proband and her clinically normal mother. METHODS: Bidirectional Sanger sequencing of all F8 gene coding regions and exon/intron boundaries was undertaken. Methylation-sensitive restriction enzymes were utilized to investigate skewed X-inactivation using both a classical human androgen receptor (HUMARA) assay, and a novel method targeting differential methylation patterns in multiple informative X-chromosome SNPs...
February 28, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29472317/dynamic-control-of-chromosome-topology-and-gene-expression-by-a-chromatin-modification
#16
Qian Bian, Erika C Anderson, Katjuša Brejc, Barbara J Meyer
The function of chromatin modification in establishing higher-order chromosome structure during gene regulation has been elusive. We dissected the machinery and mechanism underlying the enrichment of histone modification H4K20me1 on hermaphrodite X chromosomes during Caenorhabditis elegans dosage compensation and discovered a key role for H4K20me1 in regulating X-chromosome topology and chromosome-wide gene expression. Structural and functional analysis of the dosage compensation complex (DCC) subunit DPY-21 revealed a novel Jumonji C demethylase subfamily that converts H4K20me2 to H4K20me1 in worms and mammals...
February 22, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29459630/development-of-ultra-deep-targeted-rna-sequencing-for-analyzing-x-chromosome-inactivation-in-female-dent-disease
#17
Shogo Minamikawa, Kandai Nozu, Yoshimi Nozu, Tomohiko Yamamura, Mariko Taniguchi-Ikeda, Keita Nakanishi, Junya Fujimura, Tomoko Horinouchi, Yuko Shima, Koichi Nakanishi, Masuji Hattori, Kyoko Kanda, Ryojiro Tanaka, Naoya Morisada, China Nagano, Nana Sakakibara, Hiroaki Nagase, Ichiro Morioka, Hiroshi Kaito, Kazumoto Iijima
The pattern of X-chromosome inactivation (XCI) can affect the clinical severity of X-linked disorders in females. XCI pattern analysis has been conducted mainly by HUMARA assay, a polymerase chain reaction-based assay using a methylation-sensitive restriction enzyme. However, this assay examines the XCI ratio of the androgen receptor gene at the genomic DNA level and does not reflect the ratio of either targeted gene directly or at the mRNA level. Here, we report four females with Dent disease, and we clarified the correlation between XCI and female cases of Dent disease using not only HUMARA assay but also a novel analytical method by RNA sequencing...
February 19, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29449410/conserved-microrna-targeting-reveals-preexisting-gene-dosage-sensitivities-that-shaped-amniote-sex-chromosome-evolution
#18
Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29401310/human-cis-acting-elements-regulating-escape-from-x-chromosome-inactivation-function-in-mouse
#19
Samantha B Peeters, Andrea J Korecki, Elizabeth M Simpson, Carolyn J Brown
A long-standing question concerning X-chromosome inactivation (XCI) has been how some genes avoid the otherwise stable chromosome-wide heterochromatinization of the inactive X chromosome. As 20% or more of human X-linked genes escape from inactivation, such genes are an important contributor to sex differences in gene expression. Although both human and mouse have genes that escape from XCI, more genes escape in humans than mice, with human escape genes often clustering in larger domains than the single escape genes of mouse...
February 1, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29386003/whole-exome-sequencing-of-benign-pulmonary-metastasizing-leiomyoma-reveals-mutation-in-the-bmp8b-gene
#20
Deniss Sõritsa, Hindrek Teder, Retlav Roosipuu, Hannes Tamm, Triin Laisk-Podar, Pille Soplepmann, Alan Altraja, Andres Salumets, Maire Peters
BACKGROUND: Benign metastasizing leiomyoma (BML) is an orphan neoplasm commonly characterized by pulmonary metastases consisting of smooth muscle cells. Patients with BML have usually a current or previous uterine leiomyoma, which is therefore suggested to be the most probable source of this tumour. The purpose of this case report was to determine the possible genetic grounds for pulmonary BML. CASE PRESENTATION: We present a case report in an asymptomatic 44-year-old female patient, who has developed uterine leiomyoma with subsequent pulmonary BML...
January 31, 2018: BMC Medical Genetics
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