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X-inactivation

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https://www.readbyqxmd.com/read/28027854/exome-sequencing-in-children-of-women-with-skewed-x-inactivation-identifies-atypical-cases-and-complex-phenotypes
#1
Elisa Giorgio, Alessandro Brussino, Elisa Biamino, Elga Fabia Belligni, Alessandro Bruselles, Andrea Ciolfi, Viviana Caputo, Simone Pizzi, Alessandro Calcia, Eleonora Di Gregorio, Simona Cavalieri, Cecilia Mancini, Elisa Pozzi, Marta Ferrero, Evelise Riberi, Iolanda Borelli, Antonio Amoroso, Giovanni Battista Ferrero, Marco Tartaglia, Alfredo Brusco
BACKGROUND: More than 100 X-linked intellectual disability (X-LID) genes have been identified to be involved in 10-15% of intellectual disability (ID). METHOD: To identify novel possible candidates, we selected 18 families with a male proband affected by isolated or syndromic ID. Pedigree and/or clinical presentation suggested an X-LID disorder. After exclusion of known genetic diseases, we identified seven cases whose mother showed a skewed X-inactivation (>80%) that underwent whole exome sequencing (WES, 50X average depth)...
December 19, 2016: European Journal of Paediatric Neurology: EJPN
https://www.readbyqxmd.com/read/27999427/cancer-genetics-x-inactivation-and-cancer-incidence
#2
Sarah Seton-Rogers
No abstract text is available yet for this article.
December 21, 2016: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/27995571/evaluating-the-feasibility-of-dna-methylation-analyses-using-long-term-archived-brain-formalin-fixed-paraffin-embedded-samples
#3
Stine T Bak, Nicklas H Staunstrup, Anna Starnawska, Tina F Daugaard, Jens R Nyengaard, Mette Nyegaard, Anders Børglum, Ole Mors, Karl-Anton Dorph-Petersen, Anders L Nielsen
We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques...
December 19, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27989770/human-naive-pluripotent-stem-cells-model-x-chromosome-dampening-and-x-inactivation
#4
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
#5
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/27929079/from-function-to-phenotype-impaired-dna-binding-and-clustering-correlates-with-clinical-severity-in-males-with-missense-mutations-in-mecp2
#6
Taimoor I Sheikh, Juan Ausió, Hannah Faghfoury, Josh Silver, Jane B Lane, James H Eubanks, Patrick MacLeod, Alan K Percy, John B Vincent
Mutations in the MECP2 gene cause Rett syndrome (RTT). MeCP2 binds to chromocentric DNA through its methyl CpG-binding domain (MBD) to regulate gene expression. In heterozygous females the variable phenotypic severity is modulated by non-random X-inactivation, thus making genotype-phenotype comparisons unreliable. However, genotype-phenotype correlations in males with hemizygousMECP2 mutations can provide more accurate insights in to the true biological effect of specific mutations. Here, we compared chromatin organization and binding dynamics for twelve MeCP2 missense mutations (including two novel and the five most common MBD missense RTT mutations) and identifiedacorrelation with phenotype in hemizygous males...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27880931/an-xist-related-small-rna-regulates-kras-g-quadruplex-formation-beyond-x-inactivation
#7
Yuli C Chang, Chien-Chih Chiu, Chung-Yee Yuo, Wen-Ling Chan, Ya-Sian Chang, Wen-Hsin Chang, Shou-Mei Wu, Han-Lin Chou, Ta-Chih Liu, Chi-Yu Lu, Wen-Kuang Yang, Jan-Gowth Chang
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex...
November 17, 2016: Oncotarget
https://www.readbyqxmd.com/read/27870409/cognitive-behavioral-and-neural-consequences-of-sex-chromosome-aneuploidy
#8
REVIEW
Frida Printzlau, Jeanne Wolstencroft, David H Skuse
The X chromosome has played a critical role in the development of sexually selected characteristics for over 300 million years, and during that time it has accumulated a disproportionate number of genes concerned with mental functions. There are relatively specific effects of X-linked genes on social cognition, language, emotional regulation, visuospatial, and numerical skills. Many human X-linked genes outside the X-Y pairing pseudoautosomal regions escape X-inactivation. Dosage differences in the expression of such genes (which constitute at least 15% of the total) are likely to play an important role in male-female neural differentiation, and in cognitive deficits and behavioral characteristics, particularly in the realm of social communication, that are associated with sex chromosome aneuploidies...
January 2, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27869828/tumor-suppressor-genes-that-escape-from-x-inactivation-contribute-to-cancer-sex-bias
#9
Andrew Dunford, David M Weinstock, Virginia Savova, Steven E Schumacher, John P Cleary, Akinori Yoda, Timothy J Sullivan, Julian M Hess, Alexander A Gimelbrant, Rameen Beroukhim, Michael S Lawrence, Gad Getz, Andrew A Lane
There is a striking and unexplained male predominance across many cancer types. A subset of X-chromosome genes can escape X-inactivation, which would protect females from complete functional loss by a single mutation. To identify putative 'escape from X-inactivation tumor-suppressor' (EXITS) genes, we examined somatic alterations from >4,100 cancers across 21 tumor types for sex bias. Six of 783 non-pseudoautosomal region (PAR) X-chromosome genes (ATRX, CNKSR2, DDX3X, KDM5C, KDM6A, and MAGEC3) harbored loss-of-function mutations more frequently in males (based on a false discovery rate < 0...
January 2017: Nature Genetics
https://www.readbyqxmd.com/read/27815372/female-mice-with-an-xy-sex-chromosome-complement-develop-severe-angiotensin-ii-induced-abdominal-aortic-aneurysms
#10
Yasir Alsiraj, Sean E Thatcher, Richard Charnigo, Chen Kuey, Eric Blalock, Alan Daugherty, Lisa A Cassis
BACKGROUND: -Abdominal aortic aneurysms (AAAs) are a deadly pathology with strong sexual dimorphism. Similar to humans, female mice exhibit far lower incidences of angiotensin II (AngII)-induced AAAs than males. In addition to sex hormones, the X and Y sex chromosomes, and their unique complements of genes, may contribute to sexually dimorphic AAA pathology. Here, we defined the effect of female (XX) versus male (XY) sex chromosome complement on AngII-induced AAA formation and rupture in phenotypically female mice...
November 4, 2016: Circulation
https://www.readbyqxmd.com/read/27739211/simpson-golabi-behmel-syndrome-in-a-female-a-case-report-and-an-unsolved-issue
#11
Alessandro Vaisfeld, Maria Grazia Pomponi, Roberta Pietrobono, Elisabetta Tabolacci, Giovanni Neri
Simpson-Golabi-Behmel syndrome is an X-linked recessive overgrowth condition caused by alterations in GPC3 gene, encoding for the cell surface receptor glypican 3, whose clinical manifestations in affected males are well known. Conversely, there is little information regarding affected females, with very few reported cases, and a clinical definition of this phenotype is still lacking. In the present report we describe an additional case, the first to receive a primary molecular diagnosis based on strong clinical suspicion...
January 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27622320/clonal-hematopoiesis-in-patients-with-dyskeratosis-congenita
#12
Nieves Perdigones, Juan C Perin, Irene Schiano, Peter Nicholas, Jaclyn A Biegel, Philip J Mason, Daria V Babushok, Monica Bessler
Dyskeratosis congenita (DC) is a rare inherited telomeropathy most frequently caused by mutations in a number of genes all thought to be involved in telomere maintenance. The main causes of mortality in DC are bone marrow failure as well as malignancies including leukemias and solid tumors. The clinical picture including the degree of bone marrow failure is highly variable and factors that contribute to this variability are poorly understood. Based on the recent finding of frequent clonal hematopoiesis in related bone marrow failure syndromes, we hypothesized that somatic mutations may also occur in DC and may contribute at least in part to the variability in blood production...
December 2016: American Journal of Hematology
https://www.readbyqxmd.com/read/27570172/investigation-of-chromosome-x-inactivation-and-clinical-phenotypes-in-female-carriers-of-dkc1-mutations
#13
Jialin Xu, Payal P Khincha, Neelam Giri, Blanche P Alter, Sharon A Savage, Judy M Y Wong
Dyskeratosis congenita (DC) is an inherited bone marrow failure and cancer susceptibility syndrome caused by germline mutations in telomere biology genes. Germline mutations in DKC1, which encodes the protein dyskerin, cause X-linked recessive DC. Because of skewed X-chromosome inactivation, female DKC1 mutation carriers do not typically develop clinical features of DC. This study evaluated female DKC1 mutation carriers with DC-associated phenotypes to elucidate the molecular features of their mutations, in comparison with unaffected carriers and mutation-negative female controls...
December 2016: American Journal of Hematology
https://www.readbyqxmd.com/read/27553879/effect-of-storage-time-on-gene-expression-data-acquired-from-unfrozen-archived-newborn-blood-spots
#14
Nhan T Ho, Julia V Busik, James H Resau, Nigel Paneth, Sok Kean Khoo
Unfrozen archived newborn blood spots (NBS) have been shown to retain sufficient messenger RNA (mRNA) for gene expression profiling. However, the effect of storage time at ambient temperature for NBS samples in relation to the quality of gene expression data is relatively unknown. Here, we evaluated mRNA expression from quantitative real-time PCR (qRT-PCR) and microarray data obtained from NBS samples stored at ambient temperature to determine the effect of storage time on the quality of gene expression. These data were generated in a previous case-control study examining NBS in 53 children with cerebral palsy (CP) and 53 matched controls...
November 2016: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/27550844/de-novo-and-inherited-mutations-in-the-x-linked-gene-clcn4-are-associated-with-syndromic-intellectual-disability-and-behavior-and-seizure-disorders-in-males-and-females
#15
E E Palmer, T Stuhlmann, S Weinert, E Haan, H Van Esch, M Holvoet, J Boyle, M Leffler, M Raynaud, C Moraine, H van Bokhoven, T Kleefstra, K Kahrizi, H Najmabadi, H-H Ropers, M R Delgado, D Sirsi, S Golla, A Sommer, M P Pietryga, W K Chung, J Wynn, L Rohena, E Bernardo, D Hamlin, B M Faux, D K Grange, L Manwaring, J Tolmie, S Joss, J M Cobben, F A M Duijkers, J M Goehringer, T D Challman, F Hennig, U Fischer, A Grimme, V Suckow, L Musante, J Nicholl, M Shaw, S P Lodh, Z Niu, J A Rosenfeld, P Stankiewicz, T J Jentsch, J Gecz, M Field, V M Kalscheuer
Variants in CLCN4, which encodes the chloride/hydrogen ion exchanger CIC-4 prominently expressed in brain, were recently described to cause X-linked intellectual disability and epilepsy. We present detailed phenotypic information on 52 individuals from 16 families with CLCN4-related disorder: 5 affected females and 2 affected males with a de novo variant in CLCN4 (6 individuals previously unreported) and 27 affected males, 3 affected females and 15 asymptomatic female carriers from 9 families with inherited CLCN4 variants (4 families previously unreported)...
August 23, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27528619/xist-and-tsix-transcription-dynamics-is-regulated-by-the-x-to-autosome-ratio-and-semistable-transcriptional-states
#16
Friedemann Loos, Cheryl Maduro, Agnese Loda, Johannes Lehmann, Gert-Jan Kremers, Derk Ten Berge, J Anton Grootegoed, Joost Gribnau
In female mammals, X chromosome inactivation (XCI) is a key process in the control of gene dosage compensation between X-linked genes and autosomes. Xist and Tsix, two overlapping antisense-transcribed noncoding genes, are central elements of the X inactivation center (Xic) regulating XCI. Xist upregulation results in the coating of the entire X chromosome by Xist RNA in cis, whereas Tsix transcription acts as a negative regulator of Xist Here, we generated Xist and Tsix reporter mouse embryonic stem (ES) cell lines to study the genetic and dynamic regulation of these genes upon differentiation...
November 1, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27501756/long-noncoding-rna-xist-acts-as-an-oncogene-in-non-small-cell-lung-cancer-by-epigenetically-repressing-klf2-expression
#17
Jing Fang, Cheng-Cao Sun, Cheng Gong
Recently, long noncoding RNAs (lncRNAs) have been identified as critical regulators in numerous types of cancers, including non-small cell lung cancer (NSCLC). X inactivate-specific transcript (XIST) has been found to be up-regulated and acts as an oncogene in gastric cancer and hepatocellular carcinoma, but little is known about its expression pattern, biological function and underlying mechanism in NSCLC. Here, we identified XIST as an oncogenic lncRNA by driving tumorigenesis in NSCLC. We found that XIST is over-expressed in NSCLC, and its increased level is associated with shorter survival and poorer prognosis...
September 16, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27498871/direct-transcriptional-consequences-of-somatic-mutation-in-breast-cancer
#18
Adam Shlien, Keiran Raine, Fabio Fuligni, Roland Arnold, Serena Nik-Zainal, Serge Dronov, Lira Mamanova, Andrej Rosic, Young Seok Ju, Susanna L Cooke, Manasa Ramakrishna, Elli Papaemmanuil, Helen R Davies, Patrick S Tarpey, Peter Van Loo, David C Wedge, David R Jones, Sancha Martin, John Marshall, Elizabeth Anderson, Claire Hardy, Violetta Barbashina, Samuel A J R Aparicio, Torill Sauer, Øystein Garred, Anne Vincent-Salomon, Odette Mariani, Sandrine Boyault, Aquila Fatima, Anita Langerød, Åke Borg, Gilles Thomas, Andrea L Richardson, Anne-Lise Børresen-Dale, Kornelia Polyak, Michael R Stratton, Peter J Campbell
Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells...
August 16, 2016: Cell Reports
https://www.readbyqxmd.com/read/27470653/clinical-and-molecular-characterization-of-a-boy-with-intellectual-disability-facial-dysmorphism-minor-digital-anomalies-and-a-complex-il1rapl1-intragenic-rearrangement
#19
Luigi Laino, Irene Bottillo, Caterina Piedimonte, Laura Bernardini, Barbara Torres, Barbara Grammatico, Simone Bargiacchi, Claudia Mulargia, Mauro Calvani, Francesco Cardona, Marco Castori, Paola Grammatico
X-linked intellectual disability accounts for 10-12% of cases of cognitive impairment in males. Mutations in IL1RAPL1 are an emerging form of apparently non-syndromic X-linked intellectual disability. We report a 8-year-old intellectually disabled boy with speech delay, and unusual facial and digital anomalies who showed a novel and complex IL1RAPL1 rearrangement. It was defined by two intragenic non-contiguous duplications inherited from the unaffected mother. Chromosome X inactivation study on the mother's blood leukocytes, urinary sediment and buccal swab did not show a significant skewed inactivation...
November 2016: European Journal of Paediatric Neurology: EJPN
https://www.readbyqxmd.com/read/27461945/long-non-coding-rna-xist-exerts-oncogenic-functions-in-human-nasopharyngeal-carcinoma-by-targeting-mir-34a-5p
#20
Peng Song, Lin-Feng Ye, Cen Zhang, Tao Peng, Xu-Hong Zhou
Long non-coding RNA (lncRNA) X inactivate-specific transcript (XIST) has been verified as an oncogenic gene in several human malignant tumors, and its dysregulation was closed associated with tumor initiation, development and progression. Nevertheless, whether the aberrant expression of XIST in human nasopharyngeal carcinoma (NPC) is corrected with malignancy, metastasis or prognosis has not been elaborated. Here, we discovered that XIST was up-regulated in NPC tissues and higher expression of XIST contributed to a markedly poorer survival time...
October 30, 2016: Gene
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