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Polymorphism chromatin

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https://www.readbyqxmd.com/read/29339533/learning-dependent-chromatin-remodeling-highlights-noncoding-regulatory-regions-linked-to-autism
#1
John N Koberstein, Shane G Poplawski, Mathieu E Wimmer, Giulia Porcari, Charlly Kao, Bruce Gomes, Davide Risso, Hakon Hakonarson, Nancy R Zhang, Robert T Schultz, Ted Abel, Lucia Peixoto
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder that is associated with genetic risk factors. Most human disease-associated single-nucleotide polymorphisms (SNPs) are not located in genes but rather are in regulatory regions that control gene expression. The function of regulatory regions is determined through epigenetic mechanisms. Parallels between the cellular basis of development and the formation of long-term memory have long been recognized, particularly the role of epigenetic mechanisms in both processes...
January 16, 2018: Science Signaling
https://www.readbyqxmd.com/read/29317594/polymorphism-in-tmem132d-regulates-expression-and-anxiety-related-behavior-through-binding-of-rna-polymerase-ii-complex
#2
Roshan R Naik, Sergey V Sotnikov, Rebekka P Diepold, Stella Iurato, Patrick O Markt, Andrea Bultmann, Nadine Brehm, Tobias Mattheus, Beat Lutz, Angelika Erhardt, Elisabeth B Binder, Ulrike Schmidt, Florian Holsboer, Rainer Landgraf, Ludwig Czibere
TMEM132D is a candidate gene, where risk genotypes have been associated with anxiety severity along with higher mRNA expression in the frontal cortex of panic disorder patients. Concurrently, in a high (HAB) and low (LAB) trait anxiety mouse model, Tmem132d was found to show increased expression in the anterior cingulate cortex (aCC) of HAB as compared to LAB mice. To understand the molecular underpinnings underlying the differential expression, we sequenced the gene and found two single-nucleotide polymorphisms (SNPs) in the promoter differing between both lines which could explain the observed mRNA expression profiles using gene reporter assays...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29301971/intracranial-aneurysm-associated-single-nucleotide-polymorphisms-alter-regulatory-dna-in-the-human-circle-of-willis
#3
Melanie D Laarman, Marit W Vermunt, Rachel Kleinloog, Jelkje J de Boer-Bergsma, Netherlands Brain Bank, Gabriël J E Rinkel, Menno P Creyghton, Michal Mokry, Jeroen Bakkers, Ynte M Ruigrok
BACKGROUND AND PURPOSE: Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in 6 genomic loci. To gain insight into the relevance of these IA-associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop. METHODS: We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in postmortem specimens of the human CoW...
January 4, 2018: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/29300379/the-role-of-smad3-in-the-genetic-predisposition-to-papillary-thyroid-carcinoma
#4
Yanqiang Wang, Huiling He, Sandya Liyanarachchi, Luke K Genutis, Wei Li, Lianbo Yu, John E Phay, Rulong Shen, Pamela Brock, Albert de la Chapelle
PurposeTo identify and characterize the functional variants, regulatory gene networks, and potential binding targets of SMAD3 in the 15q22 thyroid cancer risk locus.MethodsWe performed linkage disequilibrium (LD) and haplotype analyses to fine map the 15q22 locus. Luciferase reporter assays were applied to evaluate the regulatory effects of the candidate variants. Knockdown by small interfering RNA, microarray analysis, chromatin immunoprecipitation (ChIP) and quantitative real-time polymerase chain reaction assays were performed to reveal the regulatory gene network and identify its binding targets...
January 4, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29259117/effects-of-mutation-and-selection-on-plasticity-of-a-promoter-activity-in-saccharomyces-cerevisiae
#5
Fabien Duveau, David C Yuan, Brian P H Metzger, Andrea Hodgins-Davis, Patricia J Wittkopp
Phenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single-nucleotide mutations in the Saccharomyces cerevisiae TDH3 promoter (PTDH3 ) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild-type allele...
December 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29250096/methylation-sensitive-amplification-polymorphism-sequencing-msap-seq-a-method-for-high-throughput-analysis-of-differentially-methylated-ccgg-sites-in-plants-with-large-genomes
#6
Karolina Chwialkowska, Urszula Korotko, Joanna Kosinska, Iwona Szarejko, Miroslaw Kwasniewski
Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29239112/male-reproductive-tract-and-spermatozoa-ultrastructure-in-the-grasshopper-orphulella-punctata-de-geer-1773-insecta-orthoptera-caelifera
#7
Daniela Santos Martins Silva, Jamile Fernanda Silva Cossolin, Marcelo Ribeiro Pereira, José Lino-Neto, Carlos Frankl Sperber, José Eduardo Serrão
Identification Orphulellini grasshoppers (Acrididae: Gomphocerinae) species has been difficult due to high polymorphism rate. Orphulella Giglio-Tos, 1894 is a genus with widespread geographical distribution and poor descriptions. Orphulella punctata (De Geer, 1773) has an extensive record of occurrence and available information about the phallic complex, however, there is poor data describing other parts of the male reproductive tract. The objective of this study was characterizes the internal organs of the male reproductive system and spermatozoa of O...
December 14, 2017: Microscopy Research and Technique
https://www.readbyqxmd.com/read/29233832/exome-wide-association-study-identifies-four-novel-loci-for-systemic-lupus-erythematosus-in-han-chinese-population
#8
Leilei Wen, Caihong Zhu, Zhengwei Zhu, Chao Yang, Xiaodong Zheng, Lu Liu, Xianbo Zuo, Yujun Sheng, Huayang Tang, Bo Liang, Yi Zhou, Pan Li, Jun Zhu, Yantao Ding, Gang Chen, Jinping Gao, Lili Tang, Yuyan Cheng, Jingying Sun, Tamilselvi Elango, Anjana Kafle, Ruixing Yu, Ke Xue, Yaohua Zhang, Feng Li, Zhanguo Li, Jianping Guo, Xuan Zhang, Chen Zhou, Yuanjia Tang, Nan Shen, Meng Wang, Xueqing Yu, Shengxiu Liu, Xing Fan, Min Gao, Fengli Xiao, Peiguang Wang, Zaixing Wang, Anping Zhang, Fusheng Zhou, Liangdan Sun, Sen Yang, Jinhua Xu, Xianyong Yin, Yong Cui, Xuejun Zhang
OBJECTIVES: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of considerable genetic predisposition. Genome-wide association studies have identified tens of common variants for SLE. However, the majority of them reside in non-coding sequences. The contributions of coding variants have not yet been systematically evaluated. METHODS: We performed a large-scale exome-wide study in 5004 SLE cases and 8179 healthy controls in a Han Chinese population using a custom exome array, and then genotyped 32 variants with suggestive evidence in an independent cohort of 13 246 samples...
December 12, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29218911/convergent-downstream-candidate-mechanisms-of-independent-intergenic-polymorphisms-between-co-classified-diseases-implicate-epistasis-among-noncoding-elements
#9
Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo Pesce, Ian Foster, Haiquan Li, Yves A Lussier
Eighty percent of DNA outside protein coding regions was shown biochemically functional by the ENCODE project, enabling studies of their interactions. Studies have since explored how convergent downstream mechanisms arise from independent genetic risks of one complex disease. However, the cross-talk and epistasis between intergenic risks associated with distinct complex diseases have not been comprehensively characterized. Our recent integrative genomic analysis unveiled downstream biological effectors of disease-specific polymorphisms buried in intergenic regions, and we then validated their genetic synergy and antagonism in distinct GWAS...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29208650/transcriptional-profiling-of-saccharomyces-cerevisiae-reveals-the-impact-of-variation-of-a-single-transcription-factor-on-differential-gene-expression-in-4nqo-fermentable-and-non-fermentable-carbon-sources
#10
Xiaqing Rong-Mullins, Michael C Ayers, Mahmoud Summers, Jennifer E G Gallagher
Cellular metabolism can change the potency of a chemical's tumorigenicity. 4-nitroquinoline-1-oxide (4NQO) is a tumorigenic drug widely used on animal models for cancer research. Polymorphisms of the transcription factor, Yrr1, confer different levels of resistance to 4NQO in Saccharomyces cerevisiae To study how different Yrr1 alleles regulate gene expression leading to resistance, transcriptomes of three isogenic Scerevisiae strains carrying different Yrr1 alleles were profiled via RNA sequencing (RNA-Seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) in presence and absence of 4NQO...
December 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29183316/rna-sequencing-reveals-candidate-genes-and-polymorphisms-related-to-sperm-dna-integrity-in-testis-tissue-from-boars
#11
Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else-Berit Stenseth, Teklu Tewoldebrhan Zeremichael, Eli Grindflek
BACKGROUND: Sperm DNA is protected against fragmentation by a high degree of chromatin packaging. It has been demonstrated that proper chromatin packaging is important for boar fertility outcome. However, little is known about the molecular mechanisms underlying differences in sperm DNA fragmentation. Knowledge of sequence variation influencing this sperm parameter could be beneficial in selecting the best artificial insemination (AI) boars for commercial production. The aim of this study was to identify genes differentially expressed in testis tissue of Norwegian Landrace and Duroc boars, with high and low sperm DNA fragmentation index (DFI), using transcriptome sequencing...
November 28, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29168327/distinct-cerebellar-foliation-anomalies-in-a-chd7-haploinsufficient-mouse-model-of-charge-syndrome
#12
Danielle E Whittaker, Sahrunizam Kasah, Alex P A Donovan, Jacob Ellegood, Kimberley L H Riegman, Holger A Volk, Imelda McGonnell, Jason P Lerch, M Albert Basson
Mutations in the gene encoding the ATP dependent chromatin-remodeling factor, CHD7 are the major cause of CHARGE (Coloboma, Heart defects, Atresia of the choanae, Retarded growth and development, Genital-urinary anomalies, and Ear defects) syndrome. Neurodevelopmental defects and a range of neurological signs have been identified in individuals with CHARGE syndrome, including developmental delay, lack of coordination, intellectual disability, and autistic traits. We previously identified cerebellar vermis hypoplasia and abnormal cerebellar foliation in individuals with CHARGE syndrome...
November 23, 2017: American Journal of Medical Genetics. Part C, Seminars in Medical Genetics
https://www.readbyqxmd.com/read/29168119/clinical-and-biological-significance-of-a-%C3%A2-73a%C3%A2-%C3%A2-c-variation-in-the-cdh1-promoter-of-patients-with-sporadic-gastric-carcinoma
#13
Baozhen Zhang, Jing Zhou, Zhaojun Liu, Liankun Gu, Jiafu Ji, Woo Ho Kim, Dajun Deng
BACKGROUND: CDH1 germline mutations lead to hereditary diffuse gastric carcinomas. However, it is unclear whether genetic variations in the CDH1 promoter affect the progression of sporadic gastric carcinomas (SGCs). METHODS: SGC patients in two independent cohorts with follow-up data were enrolled. The CDH1 genotypes, including the - 73A > C polymorphism (rs28372783), were determined by PCR sequencing. The CDH1 promoter activity was determined using reporter assays...
November 22, 2017: Gastric Cancer
https://www.readbyqxmd.com/read/29162933/deep-characterization-of-a-common-d4z4-variant-identifies-biallelic-dux4-expression-as-a-modifier-for-disease-penetrance-in-fshd2
#14
Richard Jlf Lemmers, Patrick J van der Vliet, Judit Balog, Jelle J Goeman, Wibowo Arindrarto, Yvonne D Krom, Kirsten R Straasheijm, Rashmie D Debipersad, Gizem Özel, Janet Sowden, Lauren Snider, Karlien Mul, Sabrina Sacconi, Baziel van Engelen, Stephen J Tapscott, Rabi Tawil, Silvère M van der Maarel
Facioscapulohumeral muscular dystrophy is caused by incomplete repression of the transcription factor DUX4 in skeletal muscle as a consequence of D4Z4 macrosatellite repeat contraction in chromosome 4q35 (FSHD1) or variants in genes encoding D4Z4 chromatin repressors (FSHD2). A clinical hallmark of FSHD is variability in onset and progression suggesting the presence of disease modifiers. A well-known cis modifier is the polymorphic DUX4 polyadenylation signal (PAS) that defines FSHD permissive alleles: D4Z4 chromatin relaxation on non-permissive alleles which lack the DUX4-PAS cannot cause disease in the absence of stable DUX4 mRNA...
November 21, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29149895/novel-insights-into-chromosomal-conformations-in-cancer
#15
REVIEW
Ruobing Jia, Peiwei Chai, He Zhang, Xianqun Fan
Exploring gene function is critical for understanding the complexity of life. DNA sequences and the three-dimensional organization of chromatin (chromosomal interactions) are considered enigmatic factors underlying gene function, and interactions between two distant fragments can regulate transactivation activity via mediator proteins. Thus, a series of chromosome conformation capture techniques have been developed, including chromosome conformation capture (3C), circular chromosome conformation capture (4C), chromosome conformation capture carbon copy (5C), and high-resolution chromosome conformation capture (Hi-C)...
November 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29138238/a-resource-for-the-allele-specific-analysis-of-dna-methylation-at-multiple-genomically-imprinted-loci-in-mice
#16
Jadiel A Wasson, Onur Birol, David J Katz
Genomically imprinted loci are expressed mono-allelically dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent of origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele-specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult...
November 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29126153/an-empirical-bayes-test-for-allelic-imbalance-detection-in-chip-seq
#17
Qi Zhang, Sündüz Keles
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has enabled discovery of genomic regions enriched with biological signals such as transcription factor binding and histone modifications. Allelic-imbalance (ALI) detection is a complementary analysis of ChIP-seq data for associating biological signals with single nucleotide polymorphisms (SNPs). It has been successfully used in elucidating functional roles of non-coding SNPs. Commonly used statistical approaches for ALI detection are often based on binomial testing and mixture models, both of which rely on strong assumptions on the distribution of the unobserved allelic probability, and have significant practical shortcomings...
November 3, 2017: Biostatistics
https://www.readbyqxmd.com/read/29121402/incorporating-functional-genomic-information-to-enhance-polygenic-signal-and-identify-variants-involved-in-gene-by-environment-interaction-for-young-adult-alcohol-problems
#18
Jessica E Salvatore, Jeanne E Savage, Peter Barr, Aaron R Wolen, Fazil Aliev, Eero Vuoksimaa, Antti Latvala, Lea Pulkkinen, Richard J Rose, Jaakko Kaprio, Danielle M Dick
BACKGROUND: Characterizing aggregate genetic risk for alcohol misuse and identifying variants involved in gene-by-environment interaction (G×E) effects has so far been a major challenge. We hypothesized that functional genomic information could be used to enhance detection of polygenic signal underlying alcohol misuse, and to prioritize identification of single nucleotide polymorphisms (SNPs) most likely to exhibit G×E effects. METHODS: We examined these questions in the young adult FinnTwin12 sample (n=1170)...
November 9, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29098179/dna-topology-in-chromatin-is-defined-by-nucleosome-spacing
#19
Tatiana Nikitina, Davood Norouzi, Sergei A Grigoryev, Victor B Zhurkin
In eukaryotic nucleosomes, DNA makes ~1.7 superhelical turns around histone octamer. However, there is a long-standing discrepancy between the nucleosome core structure determined by x-ray crystallography and measurements of DNA topology in circular minichromosomes, indicating that there is only ~1.0 superhelical turn per nucleosome. Although several theoretical assumptions were put forward to explain this paradox by conformational variability of the nucleosome linker, none was tested experimentally. We analyzed topological properties of DNA in circular nucleosome arrays with precisely positioned nucleosomes...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29093029/chromatin-conformation-links-distal-target-genes-to-ckd-loci
#20
Maarten M Brandt, Claartje A Meddens, Laura Louzao-Martinez, Noortje A M van den Dungen, Nico R Lansu, Edward E S Nieuwenhuis, Dirk J Duncker, Marianne C Verhaar, Jaap A Joles, Michal Mokry, Caroline Cheng
Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes...
November 1, 2017: Journal of the American Society of Nephrology: JASN
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