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Polymorphism chromatin

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https://www.readbyqxmd.com/read/29138238/a-resource-for-the-allele-specific-analysis-of-dna-methylation-at-multiple-genomically-imprinted-loci-in-mice
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/29081688/noncoding-variants-functional-prioritization-methods-based-on-predicted-regulatory-factor-binding-sites
#6
REVIEW
Haoyue Fu, Xiangde Zhang
BACKGROUNDS: With the advent of the post genomic era, the research for the genetic mechanism of the diseases has found to be increasingly depended on the studies of the genes, the gene-networks and gene-protein interaction networks. To explore gene expression and regulation, the researchers have carried out many studies on transcription factors and their binding sites (TFBSs). Based on the large amount of transcription factor binding sites predicting values in the deep learning models, further computation and analysis have been done to reveal the relationship between the gene mutation and the occurrence of the disease...
August 2017: Current Genomics
https://www.readbyqxmd.com/read/29079706/genome-wide-association-study-identified-copy-number-variants-associated-with-sporadic-colorectal-cancer-risk
#7
Lai Fun Thean, Yee Syuen Low, Michelle Lo, Yik-Ying Teo, Woon-Puay Koh, Jian-Min Yuan, Min Hoe Chew, Choong Leong Tang, Peh Yean Cheah
BACKGROUND: Multiple single nucleotide polymorphisms (SNPs) have been associated with colorectal cancer (CRC) risk. The role of structural or copy number variants (CNV) in CRC, however, remained unclear. We investigated the role of CNVs in patients with sporadic CRC. METHODS: A genome-wide association study (GWAS) was performed on 1000 Singapore Chinese patients aged 50 years or more with no family history of CRC and 1000 ethnicity-matched, age-matched and gender-matched healthy controls using the Affymetrix SNP 6 platform...
October 27, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29036458/metabolic-syndrome-induces-over-expression-of-the-human-at1r-a-haplotype-dependent-effect-with-implications-on-cardio-renal-function
#8
Sudhir Jain, Nitin Puri, Anita Rana, Natalie Sirianni, Brahmaraju Mopidevi, Ashok Kumar
Background: The transcriptional regulation of the human AT1R gene in pathophysiologies, like the metabolic syndrome, is poorly understood. The human AT1R gene has polymorphisms in its promoter that can be arranged in two haplotypes. Variants -810T, -713T, -214A, and -153A always occur together (Hap-I) and variants -810A, -713G, -214C, and -153G form Hap-II. We have hypothesized that high fat diet will alter cellular transcriptional milieu and increase hAT1R gene expression in a haplotype-dependent manner...
October 5, 2017: American Journal of Hypertension
https://www.readbyqxmd.com/read/29025761/genome-wide-association-study-to-find-modifiers-for-tetralogy-of-fallot-in-the-22q11-2-deletion-syndrome-identifies-variants-in-the-gpr98-locus-on-5q14-3
#9
Tingwei Guo, Gabriela M Repetto, Donna M McDonald McGinn, Jonathan H Chung, Hiroko Nomaru, Christopher L Campbell, Anna Blonska, Anne S Bassett, Eva W C Chow, Elisabeth E Mlynarski, Ann Swillen, Joris Vermeesch, Koen Devriendt, Doron Gothelf, Miri Carmel, Elena Michaelovsky, Maude Schneider, Stephan Eliez, Stylianos E Antonarakis, Karlene Coleman, Aoy Tomita-Mitchell, Michael E Mitchell, M Cristina Digilio, Bruno Dallapiccola, Bruno Marino, Nicole Philip, Tiffany Busa, Leila Kushan-Wells, Carrie E Bearden, Małgorzata Piotrowicz, Wanda Hawuła, Amy E Roberts, Flora Tassone, Tony J Simon, Esther D A van Duin, Thérèse A van Amelsvoort, Wendy R Kates, Elaine Zackai, H Richard Johnston, David J Cutler, A J Agopian, Elizabeth Goldmuntz, Laura E Mitchell, Tao Wang, Beverly S Emanuel, Bernice E Morrow
BACKGROUND: The 22q11.2 deletion syndrome (22q11.2DS; DiGeorge syndrome/velocardiofacial syndrome) occurs in 1 of 4000 live births, and 60% to 70% of affected individuals have congenital heart disease, ranging from mild to severe. In our cohort of 1472 subjects with 22q11.2DS, a total of 62% (n=906) have congenital heart disease and 36% (n=326) of these have tetralogy of Fallot (TOF), comprising the largest subset of severe congenital heart disease in the cohort. METHODS AND RESULTS: To identify common genetic variants associated with TOF in individuals with 22q11...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29020618/hotspots-of-de-novo-point-mutations-in-induced-pluripotent-stem-cells
#10
Masahito Yoshihara, Ryoko Araki, Yasuji Kasama, Misato Sunayama, Masumi Abe, Kohji Nishida, Hideya Kawaji, Yoshihide Hayashizaki, Yasuhiro Murakawa
Induced pluripotent stem cells (iPSCs) are generated by direct reprogramming of somatic cells and hold great promise for novel therapies. However, several studies have reported genetic variations in iPSC genomes. Here, we investigated point mutations identified by whole-genome sequencing in mouse and human iPSCs in the context of epigenetic status. In contrast to disease-causing single-nucleotide polymorphisms, de novo point mutations introduced during reprogramming were underrepresented in protein-coding genes and in open chromatin regions, including transcription factor binding sites...
October 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28978027/functional-dissection-of-breast-cancer-risk-associated-tert-promoter-variants
#11
Sonja Helbig, Leesa Wockner, Annick Bouendeu, Ursula Hille-Betz, Karen McCue, Juliet D French, Stacey L Edwards, Hilda A Pickett, Roger R Reddel, Georgia Chenevix-Trench, Thilo Dörk, Jonathan Beesley
The multi-cancer susceptibility locus at 5p15.33 includes TERT, encoding the telomerase catalytic subunit. Genome-wide association studies (GWAS) have identified six single nucleotide polymorphisms (SNPs) in the TERT promoter associated with decreased breast cancer risk, although the precise causal variants and their mechanisms of action have remained elusive. Luciferase reporter assays indicated that the protective haplotype reduced TERT promoter activity in human mammary epithelial and cancer cells in an estrogen-independent manner...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28973384/characterization-of-breakpoint-regions-of-large-structural-autosomal-mosaic-events
#12
Mitchell J Machiela, Lea Jessop, Weiyin Zhou, Meredith Yeager, Stephen J Chanock
Recent studies have reported a higher than anticipated frequency of large clonal autosomal mosaic events >2 Mb in size in the aging population. Mosaic events are detected from analyses of intensity parameters of linear stretches with deviations in heterozygous probes of single nucleotide polymorphism microarrays. The non-random distribution of detected mosaic events throughout the genome suggests common mechanisms could influence the formation of mosaic events. Here we use publicly available data tracks from the University of California Santa Cruz Genome Browser to investigate the genomic characteristics of the regions at the terminal ends of two frequent types of large structural mosaic events: telomeric neutral events and interstitial losses...
November 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28973302/pseudoexfoliation-and-alzheimer-s-associated-clu-risk-variant-rs2279590-lies-within-an-enhancer-element-and-regulates-clu-ephx2-and-ptk2b-gene-expression
#13
Biswajit Padhy, Bushra Hayat, Gargi Gouranga Nanda, Pranjya Paramita Mohanty, Debasmita Pankaj Alone
Genetic variants at PTK2B-CLU locus pose as high-risk factors for many age-related disorders. However, the role of these variants in disease progression is less characterized. In this study, we aimed to investigate the functional significance of a clusterin intronic SNP, rs2279590, that has been associated with pseudoexfoliation, Alzheimer's disease (AD) and diabetes. We have previously shown that the alleles at rs2279590 differentially regulate clusterin (CLU) gene expression in lens capsule tissues. This polymorphism resides in an active regulatory region marked by H3K27Ac and DNase I hypersensitive site and is an eQTL for CLU expression...
November 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28957459/functional-mechanisms-of-microsatellite-dna-in-eukaryotic-genomes
#14
Andrew T M Bagshaw
Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28957321/identification-of-breast-cancer-associated-variants-that-modulate-transcription-factor-binding
#15
Yunxian Liu, Ninad M Walavalkar, Mikhail G Dozmorov, Stephen S Rich, Mete Civelek, Michael J Guertin
Genome-wide association studies (GWAS) have discovered thousands loci associated with disease risk and quantitative traits, yet most of the variants responsible for risk remain uncharacterized. The majority of GWAS-identified loci are enriched for non-coding single-nucleotide polymorphisms (SNPs) and defining the molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter transcription factor (TF) binding sites as the mechanism by which they affect organismal phenotypes...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28931929/a-resource-of-large-scale-molecular-markers-for-monitoring-agropyron-cristatum-chromatin-introgression-in-wheat-background-based-on-transcriptome-sequences
#16
Jinpeng Zhang, Weihua Liu, Yuqing Lu, Qunxing Liu, Xinming Yang, Xiuquan Li, Lihui Li
Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28910411/molecular-population-genetics-of-the-polycomb-genes-in-drosophila-subobscura
#17
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. Herein, we have studied the nucleotide polymorphism of PcG genes in a natural population of D...
2017: PloS One
https://www.readbyqxmd.com/read/28892201/two-brm-promoter-polymorphisms-predict-poor-survival-in-patients-with-hepatocellular-carcinoma
#18
Ivan Pasic, Kit Man Wong, Jonghun John Lee, Osvaldo Espin-Garcia, Yonathan Brhane, Dangxiao Cheng, Zhuo Chen, Devalben Patel, Catherine Brown, Roxana Bucur, David Reisman, Jennifer J Knox, Wei Xu, Rayjean J Hung, Geoffrey Guo, Sean P Cleary
BACKGROUND: Polymorphisms in the promoter of the BRM gene, a critical subunit of the chromatin remodeling SWI/SNF complex, have previously been implicated in risk and prognosis in Caucasian-predominant lung, head and neck, esophageal, and pancreatic cancers, and in hepatocellular cancers in Asians. We investigated the role of these polymorphisms in hepatocellular carcinoma (HCC) risk and prognosis. METHODS: HCC cases were recruited in a comprehensive cancer centre while the matched controls were recruited from family practice units from the same catchment area...
September 11, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28879201/wnt-%C3%AE-catenin-pathway-and-epigenetic-mechanisms-regulate-the-pitt-hopkins-syndrome-and-schizophrenia-risk-gene-tcf4
#19
Krista M Hennig, Daniel M Fass, Wen-Ning Zhao, Steven D Sheridan, Ting Fu, Serkan Erdin, Alexei Stortchevoi, Diane Lucente, Jannine D Cody, David Sweetser, James F Gusella, Michael E Talkowski, Stephen J Haggarty
Genetic variation within the transcription factor TCF4 locus can cause the intellectual disability and developmental disorder Pitt-Hopkins syndrome (PTHS), whereas single-nucleotide polymorphisms within noncoding regions are associated with schizophrenia. These genetic findings position TCF4 as a link between transcription and cognition; however, the neurobiology of TCF4 remains poorly understood. Here, we quantitated multiple distinct TCF4 transcript levels in human induced pluripotent stem cell-derived neural progenitors and differentiated neurons, and PTHS patient fibroblasts...
July 2017: Molecular Neuropsychiatry
https://www.readbyqxmd.com/read/28877499/h4-tails-potentially-produce-the-diversity-in-the-orientation-of-two-nucleosomes
#20
Hisashi Ishida, Hidetoshi Kono
Histone tails play an important role in internucleosomal interaction and chromatin compaction. To understand how the H4 tails are involved in the internucleosomal interaction, an adaptively biased molecular dynamics simulation of 63 models of two stacked nucleosomes, each with the H4 tails in different locations, was carried out. This simulation generated a variety of orientations of the separated nucleosomes depending on the formation of the H4 tail bridge between the H4 tails and the DNA of the neighboring nucleosomes...
September 5, 2017: Biophysical Journal
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