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https://www.readbyqxmd.com/read/28438634/structural-insights-into-baf47-and-baf155-complex-formation
#1
Li Yan, Si Xie, Yongming Du, Chengmin Qian
Mammalian BAF complexes are a subfamily of SWI/SNF ATP-dependent chromatin remodelers that dynamically modulate chromatin structure to regulate fundamental cellular processes including gene transcription, cell cycle control and DNA damage response. So far many distinct BAF complexes have been identified with polymorphic assemblies of up to 15 subunits from 29 genes. The evolutionarily conserved BRG1/BRM, BAF47 and BAF155/BAF170 form a stable complex that carries out essential chromatin remodeling activity and therefore have been regarded as the core components of BAF complex...
April 21, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28427211/association-of-brm-promoter-polymorphisms-and-esophageal-adenocarcinoma-outcome
#2
Grzegorz J Korpanty, Lawson Eng, Xin Qiu, Olusola Olusesan Faluyi, Daniel J Renouf, Dangxiao Cheng, Devalben Patel, Zhuo Chen, Brandon C Tse, Jennifer J Knox, Lorin Dodbiba, Jennifer Teichman, Abul Kalam Azad, Rebecca Wong, Gail Darling, David Reisman, Sinead Cuffe, Geoffrey Liu, Wei Xu
PURPOSE: Brahma (BRM) is a critical catalytic subunit of the SWI/SNF chromatin remodeling complex; expression of BRM is commonly lost in various cancer types. BRM promoter polymorphisms (BRM-741; BRM-1321) are associated with loss of BRM expression, and with cancer risk/survival. We evaluated these two polymorphisms in the overall survival (OS) of esophageal adenocarcinoma (EAC) patients. RESULTS: Of 270 patients, 37% were stage IV. Minor allele frequencies were 47-49%; 15% were double-homozygotes...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416631/mutation-of-neuron-specific-chromatin-remodeling-subunit-baf53b-rescue-of-plasticity-and-memory-by-manipulating-actin-remodeling
#3
Annie Vogel Ciernia, Enikö A Kramár, Dina P Matheos, Robbert Havekes, Thekla J Hemstedt, Christophe N Magnan, Keith Sakata, Ashley Tran, Soraya Azzawi, Alberto Lopez, Richard Dang, Weisheng Wang, Brian Trieu, Joyce Tong, Ruth M Barrett, Rebecca J Post, Pierre Baldi, Ted Abel, Gary Lynch, Marcelo A Wood
Recent human exome-sequencing studies have implicated polymorphic Brg1-associated factor (BAF) complexes (mammalian SWI/SNF chromatin remodeling complexes) in several intellectual disabilities and cognitive disorders, including autism. However, it remains unclear how mutations in BAF complexes result in impaired cognitive function. Post-mitotic neurons express a neuron-specific assembly, nBAF, characterized by the neuron-specific subunit BAF53b. Subdomain 2 of BAF53b is essential for the differentiation of neuronal precursor cells into neurons...
May 2017: Learning & Memory
https://www.readbyqxmd.com/read/28361702/a-sequence-based-method-to-predict-the-impact-of-regulatory-variants-using-random-forest
#4
Qiao Liu, Mingxin Gan, Rui Jiang
BACKGROUND: Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their hosting regulatory elements, it remains a great challenge to characterize the risk of a genetic variant within the implicated genome sequence. Therefore, it is essential to develop an effective computational model that is not only capable of predicting the potential risk of a genetic variant but also valid in interpreting how the function of the genome is affected with the occurrence of the variant...
March 14, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28359301/bromodomain-protein-4-discriminates-tissue-specific-super-enhancers-containing-disease-specific-susceptibility-loci-in-prostate-and-breast-cancer
#5
Verena Zuber, Francesco Bettella, Aree Witoelar, Ole A Andreassen, Ian G Mills, Alfonso Urbanucci
BACKGROUND: Epigenetic information can be used to identify clinically relevant genomic variants single nucleotide polymorphisms (SNPs) of functional importance in cancer development. Super-enhancers are cell-specific DNA elements, acting to determine tissue or cell identity and driving tumor progression. Although previous approaches have been tried to explain risk associated with SNPs in regulatory DNA elements, so far epigenetic readers such as bromodomain containing protein 4 (BRD4) and super-enhancers have not been used to annotate SNPs...
March 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28358394/long-read-chia-pet-for-base-pair-resolution-mapping-of-haplotype-specific-chromatin-interactions
#6
Xingwang Li, Oscar Junhong Luo, Ping Wang, Meizhen Zheng, Danjuan Wang, Emaly Piecuch, Jacqueline Jufen Zhu, Simon Zhongyuan Tian, Zhonghui Tang, Guoliang Li, Yijun Ruan
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method for capturing genome-wide chromatin interactions. Unlike other 3C-based methods, it includes a chromatin immunoprecipitation (ChIP) step that enriches for interactions mediated by specific target proteins. This unique feature allows ChIA-PET to provide the functional specificity and higher resolution needed to detect chromatin interactions, which chromosome conformation capture (3C)/Hi-C approaches have not achieved. The original ChIA-PET protocol generates short paired-end tags (2 × 20 base pairs (bp)) to detect two genomic loci that are far apart on linear chromosomes but are in spatial proximity in the folded genome...
May 2017: Nature Protocols
https://www.readbyqxmd.com/read/28346410/quality-of-tcr-signaling-determined-by-differential-affinities-of-enhancers-for-the-composite-batf-irf4-transcription-factor-complex
#7
Arifumi Iwata, Vivek Durai, Roxane Tussiwand, Carlos G Briseño, Xiaodi Wu, Gary E Grajales-Reyes, Takeshi Egawa, Theresa L Murphy, Kenneth M Murphy
Variable strengths of signaling via the T cell antigen receptor (TCR) can produce divergent outcomes, but the mechanism of this remains obscure. The abundance of the transcription factor IRF4 increases with TCR signal strength, but how this would induce distinct types of responses is unclear. We compared the expression of genes in the TH2 subset of helper T cells to enhancer occupancy by the BATF-IRF4 transcription factor complex at varying strengths of TCR stimulation. Genes dependent on BATF-IRF4 clustered into groups with distinct TCR sensitivities...
May 2017: Nature Immunology
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#8
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28322451/genome-wide-association-studies-with-proteomics-data-reveal-genes-important-for-synthesis-transport-and-packaging-of-globulins-in-legume-seeds
#9
Christine Le Signor, Delphine Aimé, Amandine Bordat, Maya Belghazi, Valérie Labas, Jérôme Gouzy, Nevin D Young, Jean-Marie Prosperi, Olivier Leprince, Richard D Thompson, Julia Buitink, Judith Burstin, Karine Gallardo
Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop...
March 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28304185/modulation-of-transcription-factor-binding-and-epigenetic-regulation-of-the-mlh1-cpg-island-and-shore-by-polymorphism-rs1800734-in-colorectal-cancer
#10
Andrea J Savio, Bharati Bapat
The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG)...
March 17, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28302752/lower-circulating-folate-induced-by-a-fidgetin-intronic-variant-is-associated-with-reduced-congenital-heart-disease-susceptibility
#11
Dan Wang, Feng Wang, Kai-Hu Shi, Hui Tao, Yang Li, Rui Zhao, Han Lu, Wenyuan Duan, Bin Qiao, Shi-Min Zhao, Hongyan Wang, Jian-Yuan Zhao
Background -Folate deficiency is an independent risk factor for congenital heart disease (CHD); however, the maternal plasma folate level is paradoxically not a good diagnostic marker. Genome-wide surveys have identified variants of non-folate metabolic genes associated with the plasma folate level, suggesting that these genetic polymorphisms are potential risk factors for CHD. Methods -To examine the effects of folate concentration-related variations on CHD risk in the Han Chinese population, we performed three independent case-control studies including a total of 1,489 CHD patients and 1,745 controls...
March 16, 2017: Circulation
https://www.readbyqxmd.com/read/28302177/cepip-context-dependent-epigenomic-weighting-for-prioritization-of-regulatory-variants-and-disease-associated-genes
#12
Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S Liu, Junwen Wang
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential. We present cepip, a joint likelihood framework, for estimating a variant's regulatory probability in a context-dependent manner. Our method exhibits significant GWAS signal enrichment and is superior to existing cell type-specific methods...
March 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28287101/identification-of-common-non-coding-variants-at-1p22-that-are-functional-for-non-syndromic-orofacial-clefting
#13
Huan Liu, Elizabeth J Leslie, Jenna C Carlson, Terri H Beaty, Mary L Marazita, Andrew C Lidral, Robert A Cornell
Genome-wide association studies (GWAS) do not distinguish between single nucleotide polymorphisms (SNPs) that are causal and those that are merely in linkage-disequilibrium with causal mutations. Here we describe a versatile, functional pipeline and apply it to SNPs at 1p22, a locus identified in several GWAS for non-syndromic cleft lip with or without cleft palate (NS CL/P). First we amplified DNA elements containing the ten most-highly risk-associated SNPs and tested their enhancer activity in vitro, identifying three SNPs with allele-dependent effects on such activity...
March 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28280564/methylation-of-avpr1a-in-the-cortex-of-wild-prairie-voles-effects-of-cpg-position-and-polymorphism
#14
M Okhovat, S M Maguire, S M Phelps
DNA methylation can cause stable changes in neuronal gene expression, but we know little about its role in individual differences in the wild. In this study, we focus on the vasopressin 1a receptor (avpr1a), a gene extensively implicated in vertebrate social behaviour, and explore natural variation in DNA methylation, genetic polymorphism and neuronal gene expression among 30 wild prairie voles (Microtus ochrogaster). Examination of CpG density across 8 kb of the locus revealed two distinct CpG islands overlapping promoter and first exon, characterized by few CpG polymorphisms...
January 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28265118/risk-alleles-of-genes-with-monoallelic-expression-are-enriched-in-gain-of-function-variants-and-depleted-in-loss-of-function-variants-for-neurodevelopmental-disorders
#15
V Savova, S Vinogradova, D Pruss, A A Gimelbrant, L A Weiss
Over 3000 human genes can be expressed from a single allele in one cell, and from the other allele-or both-in neighboring cells. Little is known about the consequences of this epigenetic phenomenon, monoallelic expression (MAE). We hypothesized that MAE increases expression variability, with a potential impact on human disease. Here, we use a chromatin signature to infer MAE for genes in lymphoblastoid cell lines and human fetal brain tissue. We confirm that across clones MAE status correlates with expression level, and that in human tissue data sets, MAE genes show increased expression variability...
March 7, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28226269/the-causes-and-consequences-of-dna-methylome-variation-in-plants
#16
REVIEW
Danelle K Seymour, Claude Becker
Epigenetic variation - polymorphisms at the level of DNA methylation or histone modifications - modulates chromatin accessibility, which can perturb transcriptional activity and spur phenotypic variation. Determining the origin, frequency spectrum, and consequences of epigenetic variants is key to understanding the role of this variation in generating stable phenotypic variation in plants. Here we review recent literature on DNA methylation variation in both model and crop plant species with a focus on the link between genotype, epigenotype, and transcription...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28219892/an-infectious-disease-associated-il12b-polymorphism-regulates-il-12-23-p40-transcription-involving-poly-adp-ribose-polymerase-1
#17
Quanju Zhao, Qinglin Du, Fang Wei, Jianping Xie, Xiaojing Ma
IL-12 and IL-23 are important host defense factors produced by APCs against certain intracellular and extracellular pathogens. Their dysregulation has also been implicated in several autoimmune diseases. The nucleotide polymorphism in the promoter region of Il12b (rs41292470 consisting of the long or short allele) encoding the shared subunit of IL-12 and IL-23, p40, has been reported to associate with susceptibility to infectious diseases and autoimmune disorders. How these genetic variants impact Il12b expression at the molecular level was unclear...
April 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28211977/1q21-3-deletion-involving-gatad2b-an-emerging-recurrent-microdeletion-syndrome
#18
Thipwimol Tim-Aroon, Natini Jinawath, Weerin Thammachote, Praweena Sinpitak, Anchalee Limrungsikul, Chaiyos Khongkhatithum, Duangrurdee Wattanasirichaigoon
GATAD2B gene is involved in chromatin modification and transcription activity. Loss-of-function mutations of GATAD2B have recently been defined to cause a recognizable syndrome with intellectual disability (ID). Human TPM3 gene encoding thin filament protein is associated with myopathies. Both genes are located on chromosome 1q21.3. We herein report an infant with feeding difficulty, developmental delay, hypotonia, and dysmorphic features including small palpebral fissures, telecanthus, sparse hair and eyebrow, cup-shaped ears, and clinodactyly...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28205384/cribriform-adenocarcinoma-of-the-minor-salivary-gland-arising-in-the-tonsil-with-metastasis-to-a-cervical-lymph-node-a-case-report-with-description-of-fine-needle-aspiration-cytology
#19
Alexa Pagano, Katie Dennis
Cribriform adenocarcinoma of minor salivary gland (CAMSG) is a rare tumor of the head and neck. We report a case of a 70-year-old female who presented with a 4-5-month history of a left neck mass. CT scan of the neck showed a left neck mass just inferior to the angle of the mandible and left tonsillar prominence. Fine-needle aspiration (FNA) of the neck mass showed epithelial groups with focal cribriform architecture. The cells had round to oval nuclei and fine chromatin. The background contained scattered lymphocytes...
February 16, 2017: Diagnostic Cytopathology
https://www.readbyqxmd.com/read/28202009/development-of-intron-targeting-it-markers-specific-for-chromosome-arm-4vs-of-haynaldia-villosa-by-chromosome-sorting-and-next-generation-sequencing
#20
Haiyan Wang, Keli Dai, Jin Xiao, Chunxia Yuan, Renhui Zhao, Jaroslav Doležel, Yufeng Wu, Aizhong Cao, Peidu Chen, Shouzhong Zhang, Xiue Wang
BACKGROUND: Haynaldia villosa (L.) Schur (syn. Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance gene Wss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) of H. villosa. We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as to H...
February 15, 2017: BMC Genomics
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