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https://www.readbyqxmd.com/read/29787736/g-quadruplexes-in-the-bap1-promoter-positively-regulate-its-expression
#1
Yingzhou Li, Xiao Zhang, Yang Gao, Jinming Shi, Liping Tang, Guangchao Sui
Accumulating evidence suggests a key role of BAP1 in oncogenesis, but mechanisms regulating BAP1 gene expression remain unexplored. In this report, we revealed that the BAP1 promoter contains multiple G-tracts in its negative strand with high potential of forming G-quadruplex (G4) structures. In circular dichroism studies, synthesized oligonucleotides within these G-rich regions upstream the BAP1 transcription start site showed molar ellipticity at specific wavelengths characteristic of G4 structures. Analyses of these oligonucleotides by native polyacrylamide gel electrophoresis revealed formation of multiple types of G4 structures...
May 19, 2018: Experimental Cell Research
https://www.readbyqxmd.com/read/29660852/etiology-and-functional-validation-of-gastrointestinal-motility-dysfunction-in-a-zebrafish-model-of-charge-syndrome
#2
Kellie Cloney, Shelby L Steele, Matthew R Stoyek, Roger P Croll, Frank M Smith, Sergey V Prykhozhij, Mary M Brown, Craig Midgen, Kim Blake, Jason N Berman
CHARGE syndrome is linked to autosomal dominant mutations in the CHD7 gene and results in a number of physiological and structural abnormalities, including heart defects, hearing and vision loss and gastrointestinal (GI) problems. Of these challenges, GI problems have a profound impact throughout an individual's life, resulting in increased morbidity and mortality. A homologue of CHD7 has been identified in the zebrafish, the loss of which recapitulates many of the features of the human disease. Using a morpholino chd7 knockdown model complemented by a chd7 null mutant zebrafish line, we examined GI structure, innervation, and motility in larval zebrafish...
April 16, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29653002/-genetic-analysis-of-two-children-patients-affected-with-charge-syndrome
#3
Guoqiang Li, Niu Li, Yufei Xu, Juan Li, Yu Ding, Yiping Shen, Xiumin Wang, Jian Wang
OBJECTIVE: To analyze two Chinese pediatric patients with multiple malformations and growth and development delay. METHODS: Both patients were subjected to targeted gene sequencing, and the results were analyzed with Ingenuity Variant Analysis software. Suspected pathogenic variations were verified by Sanger sequencing. RESULTS: High-throughput sequencing showed that both patients have carried heterozygous variants of the CHD7 gene. Patient 1 carried a nonsense mutation in exon 36 (c...
April 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29615807/an-intronic-mutation-in-chd7-creates-a-cryptic-splice-site-causing-aberrant-splicing-in-a-mouse-model-of-charge-syndrome
#4
Jacqueline M Ogier, Benedicta D Arhatari, Marina R Carpinelli, Bradley K McColl, Michael A Wilson, Rachel A Burt
Alternate splicing is a critical regulator of gene expression in eukaryotes, however genetic mutations can cause erroneous splicing and disease. Most recorded splicing disorders are caused by mutations of splice donor/acceptor sites, however intronic mutations can affect splicing. Clinical exome analyses largely ignore intronic sequence, limiting the detection of mutations to within coding regions. We describe 'Trooper', a novel mouse model of CHARGE syndrome harbouring a pathogenic point mutation in Chd7. The mutation is 18 nucleotides upstream of exon 10 and creates a cryptic acceptor site, causing exon skipping and partial intron retention...
April 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29536580/clinical-application-of-targeted-next-generation-sequencing-on-fetuses-with-congenital-heart-defects
#5
Ping Hu, Fengchang Qiao, Yan Wang, Lulu Meng, Xiuqing Ji, Chunyu Luo, Tianhui Xu, Ran Zhou, Jingjing Zhang, Bin Yu, Leilei Wang, Ting Wang, Qiong Pan, Dingyuan Ma, Dong Liang, Zhengfeng Xu
OBJECTIVES: This study aimed to determine the diagnostic yield of targeted next-generation sequencing (NGS) in prenatal diagnosis of congenital heart defects (CHDs) and for investigating the possible genetic etiology of prenatal CHD cases. METHODS: Forty-four fetuses with CHDs and normal molecular karyotypes underwent targeted NGS in this study. Fetal genomic DNA was directly extracted from amniotic fluid cells in each prenatal case. A customized targeted NGS panel containing 77 CHD-associated genes was designed to detect variants in the coding regions and the splicing sites of these genes...
March 13, 2018: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/29533783/sense-antisense-lncrna-pair-encoded-by-locus-6p22-3-determines-neuroblastoma-susceptibility-via-the-usp36-chd7-sox9-regulatory-axis
#6
Tanmoy Mondal, Prasanna Kumar Juvvuna, Agnete Kirkeby, Sanhita Mitra, Subazini Thankaswamy Kosalai, Larissa Traxler, Falk Hertwig, Sara Wernig-Zorc, Caroline Miranda, Lily Deland, Ruth Volland, Christoph Bartenhagen, Deniz Bartsch, Sashidhar Bandaru, Anne Engesser, Santhilal Subhash, Tommy Martinsson, Helena Carén, Levent M Akyürek, Leo Kurian, Meena Kanduri, Maite Huarte, Per Kogner, Matthias Fischer, Chandrasekhar Kanduri
Trait-associated loci often map to genomic regions encoding long noncoding RNAs (lncRNAs), but the role of these lncRNAs in disease etiology is largely unexplored. We show that a pair of sense/antisense lncRNA (6p22lncRNAs) encoded by CASC15 and NBAT1 located at the neuroblastoma (NB) risk-associated 6p22.3 locus are tumor suppressors and show reduced expression in high-risk NBs. Loss of functional synergy between 6p22lncRNAs results in an undifferentiated state that is maintained by a gene-regulatory network, including SOX9 located on 17q, a region frequently gained in NB...
March 12, 2018: Cancer Cell
https://www.readbyqxmd.com/read/29531775/an-unclassified-variant-of-chd7-activates-a-cryptic-splice-site-in-a-patient-with-charge-syndrome
#7
Yuko Katoh-Fukui, Shuichi Yatsuga, Hirohito Shima, Atsushi Hattori, Akie Nakamura, Kohji Okamura, Kumiko Yanagi, Manami Iso, Tadashi Kaname, Yoichi Matsubara, Maki Fukami
CHARGE syndrome is a rare autosomal dominant disease that is typically caused by heterozygous CHD7 mutations. A de novo variant in a CHD7 splicing acceptor site (NM_017780.3:c.7165-4A>G) was identified in a Japanese boy with CHARGE syndrome. This variant has been considered to be an "unclassified variant" due to its position outside the consensus splicing sites. In this study, abnormal splicing derived from this known variant was confirmed by cDNA sequencing.
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29467333/chd7-represses-the-retinoic-acid-synthesis-enzyme-aldh1a3-during-inner-ear-development
#8
Hui Yao, Sophie F Hill, Jennifer M Skidmore, Ethan D Sperry, Donald L Swiderski, Gilson J Sanchez, Cynthia F Bartels, Yehoash Raphael, Peter C Scacheri, Shigeki Iwase, Donna M Martin
CHD7, an ATP-dependent chromatin remodeler, is disrupted in CHARGE syndrome, an autosomal dominant disorder characterized by variably penetrant abnormalities in craniofacial, cardiac, and nervous system tissues. The inner ear is uniquely sensitive to CHD7 levels and is the most commonly affected organ in individuals with CHARGE. Interestingly, upregulation or downregulation of retinoic acid (RA) signaling during embryogenesis also leads to developmental defects similar to those in CHARGE syndrome, suggesting that CHD7 and RA may have common target genes or signaling pathways...
February 22, 2018: JCI Insight
https://www.readbyqxmd.com/read/29440260/chromatin-remodeler-chd7-regulates-the-stem-cell-identity-of-human-neural-progenitors
#9
MuhChyi Chai, Tsukasa Sanosaka, Hironobu Okuno, Zhi Zhou, Ikuko Koya, Satoe Banno, Tomoko Andoh-Noda, Yoshikuni Tabata, Rieko Shimamura, Tetsutaro Hayashi, Masashi Ebisawa, Yohei Sasagawa, Itoshi Nikaido, Hideyuki Okano, Jun Kohyama
Multiple congenital disorders often present complex phenotypes, but how the mutation of individual genetic factors can lead to multiple defects remains poorly understood. In the present study, we used human neuroepithelial (NE) cells and CHARGE patient-derived cells as an in vitro model system to identify the function of chromodomain helicase DNA-binding 7 (CHD7) in NE-neural crest bifurcation, thus revealing an etiological link between the central nervous system (CNS) and craniofacial anomalies observed in CHARGE syndrome...
January 15, 2018: Genes & Development
https://www.readbyqxmd.com/read/29434620/functional-analyses-of-a-novel-splice-variant-in-the-chd7-gene-found-by-next-generation-sequencing-confirm-its-pathogenicity-in-a-spanish-patient-and-diagnose-him-with-charge-syndrome
#10
Olatz Villate, Nekane Ibarluzea, Eugenia Fraile-Bethencourt, Alberto Valenzuela, Eladio A Velasco, Detelina Grozeva, F L Raymond, María P Botella, María-Isabel Tejada
Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosis. A splice donor variant in CHD7 (c.5665 + 1G > T) was identified. To study its potential pathogenicity, exons and flanking intronic sequences were amplified from patient DNA and cloned into the pSAD® splicing vector...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29432577/sema3a-plays-a-role-in-the-pathogenesis-of-charge-syndrome
#11
Roser Ufartes, Janina Schwenty-Lara, Luisa Freese, Christiane Neuhofer, Janika Möller, Peter Wehner, Conny M A van Ravenswaaij-Arts, Monica T Y Wong, Ina Schanze, Andreas Tzschach, Oliver Bartsch, Annette Borchers, Silke Pauli
CHARGE syndrome is an autosomal dominant malformation disorder caused by heterozygous loss of function mutations in the chromatin remodeler CHD7. Chd7 regulates the expression of Sema3a, which also contributes to the pathogenesis of Kallmann syndrome, a heterogeneous condition with the typical features hypogonadotropic hypogonadism and an impaired sense of smell. Both features are common in CHARGE syndrome suggesting that SEMA3A may provide a genetic link between these syndromes. Indeed, we find evidence that SEMA3A plays a role in the pathogenesis of CHARGE syndrome...
April 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29355723/a-case-of-charge-syndrome-associated-with-hyperinsulinemic-hypoglycemia-in-infancy
#12
Kazuhito Sekiguchi, Tomoyo Itonaga, Tomoki Maeda, Maki Fukami, Tohru Yorifuji, Kenji Ihara
CHARGE syndrome is a rare autosomal dominant disorder involving multiple organs. Chromodomain helicase DNA binding protein-7 (CHD7) is a major causative gene of CHARGE syndrome. We herein report a male infant born at full term with asphyxia who was diagnosed with CHARGE syndrome based on the typical anomalies. He showed a poor sucking ability and suffered from continuous hypoglycemia in early infancy, ultimately requiring tube feeding. While in a hypoglycemic status, inappropriate high insulin and low growth hormone levels were noticed...
January 20, 2018: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29353058/chd7-is-critical-for-early-t-cell-development-and-thymus-organogenesis-in-zebrafish
#13
Zhi-Zhi Liu, Zi-Long Wang, Tae-Ik Choi, Wen-Ting Huang, Han-Tsing Wang, Ying-Ying Han, Lou-Yin Zhu, Hyun-Taek Kim, Jung-Hwa Choi, Jin-Soo Lee, Hyung-Goo Kim, Jian Zhao, Yue Chen, Zhuo Lu, Xiao-Li Tian, Bing-Xing Pan, Bao-Ming Li, Cheol-Hee Kim, Hong A Xu
Coloboma, heart defect, atresia choanae, retarded growth and development, genital hypoplasia, ear anomalies/deafness (CHARGE) syndrome is a congenital disorder affecting multiple organs and mainly caused by mutations in CHD7, a gene encoding a chromatin-remodeling protein. Immunodeficiency and reduced T cells have been noted in CHARGE syndrome. However, the mechanisms underlying T lymphopenia are largely unexplored. Herein, we observed dramatic decrease of T cells in both chd7knockdown and knockout zebrafish embryos...
April 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29330883/genotype-phenotype-correlations-in-individuals-with-pathogenic-rere-variants
#14
Valerie K Jordan, Brieana Fregeau, Xiaoyan Ge, Jessica Giordano, Ronald J Wapner, Tugce B Balci, Melissa T Carter, John A Bernat, Amanda N Moccia, Anshika Srivastava, Donna M Martin, Stephanie L Bielas, John Pappas, Melissa D Svoboda, Marlène Rio, Nathalie Boddaert, Vincent Cantagrel, Andrea M Lewis, Fernando Scaglia, Jennefer N Kohler, Jonathan A Bernstein, Annika M Dries, Jill A Rosenfeld, Colette DeFilippo, Willa Thorson, Yaping Yang, Elliott H Sherr, Weimin Bi, Daryl A Scott
Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency...
January 13, 2018: Human Mutation
https://www.readbyqxmd.com/read/29321579/differentiation-potential-of-pluripotent-stem-cells-correlates-to-the-level-of-chd7
#15
Takako Yamamoto, Chiemi Takenaka, Yusuke Yoda, Yasuhiro Oshima, Kenichi Kagawa, Hiroshi Miyajima, Tetsuji Sasaki, Shin Kawamata
Embryonic Stem Cells (ESC) possesses two distinct features; self-renewal and the potential to differentiate. Here we show the differentiation potential and growth rate of ESC correlates positively with the expression level of the gene encoding chromodomain helicase DNA binding protein 7 (CHD7). When ESCs are maintained in feeder-free conditions and single cell seeding, ESC KhES-1 having 4520 copies or more of CHD7 in 5 ng total RNA show differentiation potential, but this is lost when the CHD7 copy number is reduced in KhES-1 to less than 696 by alternative culture conditions...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29311329/dysregulation-of-cotranscriptional-alternative-splicing-underlies-charge-syndrome
#16
Catherine Bélanger, Félix-Antoine Bérubé-Simard, Elizabeth Leduc, Guillaume Bernas, Philippe M Campeau, Seema R Lalani, Donna M Martin, Stephanie Bielas, Amanda Moccia, Anshika Srivastava, David W Silversides, Nicolas Pilon
CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in CHD7 (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for CHD7 mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined...
January 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29302581/novel-genetic-associations-between-lung-cancer-and-indoor-radon-exposure
#17
Jung Ran Choi, Sang-Baek Koh, Seong Yong Park, Hye Run Kim, Hyojin Lee, Dae Ryong Kang
Background: Lung cancer is the leading cause of cancer-related death worldwide, for which smoking is considered as the primary risk factor. The present study was conducted to determine whether genetic alterations induced by radon exposure are associated with the susceptible risk of lung cancer in never smokers. Methods: To accurately identify mutations within individual tumors, next generation sequencing was conduct for 19 pairs of lung cancer tissue. The associations of germline and somatic variations with radon exposure were visualized using OncoPrint and heatmap graphs...
December 2017: Journal of Cancer Prevention
https://www.readbyqxmd.com/read/29300383/genetic-analysis-of-charge-syndrome-identifies-overlapping-molecular-biology
#18
Amanda Moccia, Anshika Srivastava, Jennifer M Skidmore, John A Bernat, Marsha Wheeler, Jessica X Chong, Deborah Nickerson, Michael Bamshad, Margaret A Hefner, Donna M Martin, Stephanie L Bielas
PurposeCHARGE syndrome is an autosomal-dominant, multiple congenital anomaly condition characterized by vision and hearing loss, congenital heart disease, and malformations of craniofacial and other structures. Pathogenic variants in CHD7, encoding adenosine triphosphate-dependent chromodomain helicase DNA binding protein 7, are present in the majority of affected individuals. However, no causal variant can be found in 5-30% (depending on the cohort) of individuals with a clinical diagnosis of CHARGE syndrome...
January 4, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29280744/update-on-the-genetics-of-idiopathic-hypogonadotropic-hypogonadism
#19
A Kemal Topaloğlu
Traditionally, idiopathic hypogonadotropic hypogonadism (IHH) is divided into two major categories: Kallmann syndrome (KS) and normosmic IHH (nIHH). To date, inactivating variants in more than 50 genes have been reported to cause IHH. These mutations are estimated to account for up to 50% of all apparently hereditary cases. Identification of further causative gene mutations is expected to be more feasible with the increasing use of whole exome/genome sequencing. Presence of more than one IHH-associated mutant gene in a given patient/pedigree (oligogenic inheritance) is seen in 10-20% of all IHH cases...
December 30, 2017: Journal of Clinical Research in Pediatric Endocrinology
https://www.readbyqxmd.com/read/29277338/hypothalamic-abnormalities-growth-failure-due-to-defects-of-the-ghrh-receptor
#20
Manuel H Aguiar-Oliveira, Caridad Davalos, Viviane C Campos, Luiz A Oliveira Neto, Cindi G Marinho, Carla R P Oliveira
Several acquired or congenital hypothalamic abnormalities may cause growth failure (GF). We described two of these congenital abnormalities. First, a case of CHARGE syndrome, an epigenetic disorder mostly caused by heterozygous mutations in the gene encoding CHD7, a chromatin remodeling protein, causing several malformations, some life-threatening, with additional secondary hypothalamus-hypophyseal dysfunction, including GF. Second, a cohort of individuals with genetic isolated severe GH deficiency (IGHD), due to a homozygous mutation in the GH-releasing hormone (GHRH) receptor gene described in Itabaianinha County, in northeast Brazil...
February 2018: Growth Hormone & IGF Research
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