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Cis-regulation

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https://www.readbyqxmd.com/read/29331478/comprehensive-analysis-of-lncrnas-and-mrnas-with-associated-co-expression-and-cerna-networks-in-c2c12-myoblasts-and-myotubes
#1
Rui Chen, Ting Jiang, Yanling She, Sidong Xie, Shanyao Zhou, Cheng Li, Jun Ou, Yulin Liu
Long non-coding RNAs (lncRNAs) are emerging as important regulators in the modulation of muscle development and muscle-related diseases. To explore potential regulators of muscle differentiation, we determined the expression profiles of lncRNAs and mRNAs in C2C12 mouse myoblast cell line using microarray analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to explore their function. We also constructed co-expression, cis/trans-regulation, and competing endogenous RNA (ceRNA) networks with bioinformatics methods...
January 10, 2018: Gene
https://www.readbyqxmd.com/read/29331019/cis-regulator-runaway-and-divergence-in-asexuals
#2
Frédéric Fyon, Thomas Lenormand
With the advent of new sequencing technologies, the evolution of gene expression is becoming a subject of intensive genomic research, with sparking debates upon the role played by these kinds of changes in adaptive evolution and speciation. In this paper, we model expression evolution in species differing by their reproductive systems. We consider different rates of sexual versus asexual reproduction and the different type of parthenogenesis (apomixis and the various modes of automixis). We show that competition for expression leads to two selective processes on cis-regulatory regions that act independently to organism-level adaptation...
January 13, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29316023/sj%C3%A3-gren-s-syndrome-x-chromosome-dose-effect-an-epigenetic-perspective
#3
REVIEW
Jean-Luc C Mougeot, Braxton Noll, Farah K Bahrani Mougeot
Sjögren's syndrome (SS) is a chronic autoimmune disease affecting exocrine glands leading to mouth and eyes dryness. The extent to which epigenetic DNA methylation changes are responsible for an X-chromosome dose effect has yet to be determined. Our objectives were to (i) describe how epigenetic DNA methylation changes could explain an X-chromosome dose effect in SS for women with normal 46,XX genotype and (ii) determine the relevant relationships to this dose effect, between X-linked genes, genes controlling X-chromosome inactivation (XCI) and genes encoding associated transcription factors, all of which are differentially expressed and/or differentially methylated in the salivary glands of SS patients...
January 9, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29311643/lncrna-nef-antagonized-epithelial-to-mesenchymal-transition-and-cancer-metastasis-via-cis-regulating-foxa2-and-inactivating-wnt-%C3%AE-catenin-signaling
#4
Wei-Cheng Liang, Jia-Lin Ren, Cheuk-Wa Wong, Sun-On Chan, Mary Miu-Yee Waye, Wei-Ming Fu, Jin-Fang Zhang
Emerging evidence indicates that the long noncoding RNAs extensively participate in cancer progression. Nevertheless, the molecular pathogenesis of how these lncRNAs regulate tumorigenesis has not been fully elucidated especially in hepatocellular carcinoma (HCC). Here, we sought to define the role of a novel lncRNA named lncRNA-NEF in modulating epithelial to mesenchymal transition (EMT) in HCC. It was found that the lncRNA-NEF was transcriptionally activated by EMT suppressor FOXA2 and frequently downregulated in HCC cell lines as well as clinical specimens...
January 9, 2018: Oncogene
https://www.readbyqxmd.com/read/29242531/long-noncoding-rna-expression-profile-reveals-lncrnas-signature-associated-with-extracellular-matrix-degradation-in-kashin-beck-disease
#5
Cuiyan Wu, Huan Liu, Feng'e Zhang, Wanzhen Shao, Lei Yang, Yujie Ning, Sen Wang, Guanghui Zhao, Byeong Jae Lee, Mikko Lammi, Xiong Guo
Kashin-Beck disease (KBD) is a deformative, endemic osteochondropathy involving degeneration and necrosis of growth plates and articular cartilage. The pathogenesis of KBD is related to gene expression and regulation mechanisms, but long noncoding RNAs (lncRNAs) in KBD have not been investigated. In this study, we identified 316 up-regulated and 631 down-regulated lncRNAs (≥ 2-fold change) in KBD chondrocytes using microarray analysis, of which more than three-quarters were intergenic lncRNAs and antisense lncRNAs...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29237423/deciphering-the-genetic-regulation-of-peripheral-blood-transcriptome-in-pigs-through-expression-genome-wide-association-study-and-allele-specific-expression-analysis
#6
T Maroilley, G Lemonnier, J Lecardonnel, D Esquerré, Y Ramayo-Caldas, M J Mercat, C Rogel-Gaillard, J Estellé
BACKGROUND: Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity...
December 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29225039/a-massively-parallel-reporter-assay-of-3-utr-sequences-identifies-in%C3%A2-vivo-rules-for-mrna-degradation
#7
Michal Rabani, Lindsey Pieper, Guo-Liang Chew, Alexander F Schier
The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR-seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens of thousands of 3' UTR sequences during early zebrafish embryogenesis. UTR-seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation...
November 30, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29202958/transcriptome-wide-association-study-revealed-two-novel-genes-associated-with-nonobstructive-azoospermia-in-a-chinese-population
#8
Tingting Jiang, Yuzhuo Wang, Meng Zhu, Yifeng Wang, Mingtao Huang, Guangfu Jin, Xuejiang Guo, Jiahao Sha, Juncheng Dai, Zhibin Hu
OBJECTIVE: To investigate the associations between genetically cis-regulated gene expression levels and nonobstructive azoospermia (NOA) susceptibility. DESIGN: Transcriptome-wide association study (TWAS). SETTING: Medical university. INTERVENTIONS: None. MAIN OUTCOME MEASURE(S): The cis-hg2 values for each gene were estimated with GCTA software. The effect sizes of cis-single-nucleotide polymorphisms (SNPs) on gene expression were measured using GEMMA software...
December 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/29187214/synthetic-enhancer-design-by-in-silico-compensatory-evolution-reveals-flexibility-and-constraint-in-cis-regulation
#9
Kenneth A Barr, Carlos Martinez, Jennifer R Moran, Ah-Ram Kim, Alexandre F Ramos, John Reinitz
BACKGROUND: Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite this, the minimum set of mechanisms required to reconstruct an enhancer from its constituent parts is not known. Synthetic biology offers the potential to test the sufficiency of known mechanisms to describe the activity of enhancers, as well as to uncover constraints on the number, order, and spacing of motifs...
November 29, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29167272/direct-testing-for-allele-specific-expression-differences-between-conditions
#10
Luis Leon-Novelo, Alison R Gerken, Rita M Graze, Lauren M McIntyre, Fabio Marroni
Allelic imbalance (AI) indicates the presence of functional variation in cis regulatory regions. Detecting cis regulatory differences using AI is widespread, yet there is no formal statistical methodology that tests whether AI differs between conditions. Here we present a novel model and formally test differences in AI across conditions using Bayesian credible intervals. The approach tests AI by environment (GxE) interactions and can be used to test AI between environments, genotypes, sex, and any other condition...
November 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#11
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29116104/germline-copy-number-variations-are-associated-with-breast-cancer-risk-and-prognosis
#12
Mahalakshmi Kumaran, Carol E Cass, Kathryn Graham, John R Mackey, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Breast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29062693/computational-deciphering-of-biotic-stress-associated-genes-in-tomato-solanum-lycopersicum
#13
G Tandon, S Singh, S Kaur, Sarika, M A Iquebal, A Rai, D Kumar
Tomato (Solanum lycopersicum) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though > 1.5 M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14 M catalogued markers can be used to introgress specific desirable genes in varietal improvement program...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29029442/transcriptomic-profiling-of-long-non-coding-rnas-in-hepatitis-b-virus-related-hepatocellular-carcinoma
#14
Hongxia Fan, Qiaoge Zhang, Xiaopei Zhao, Ping Lv, Min Liu, Hua Tang
Long non-coding RNAs (lncRNAs) have been reported to be involved in the development and progression of hepatocellular carcinoma (HCC). However, few studies have focus on the dyregulation and the role of lncRNAs in HBV-related HCC. We performed a comprehensive analysis of lncRNAs expression profile in HBV-related HCC tissues samples using deep sequencing. We revealed that a total of 1242 lncRNA transcripts (983 up-regulated and 259 down-regulated) and 1841 mRNA transcripts were significantly differentially expressed in HBV-related HCC patients...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29021289/quantifying-the-regulatory-effect-size-of-cis-acting-genetic-variation-using-allelic-fold-change
#15
Pejman Mohammadi, Stephane E Castel, Andrew A Brown, Tuuli Lappalainen
Mapping cis-acting expression quantitative trait loci (cis-eQTL) has become a popular approach for characterizing proximal genetic regulatory variants. In this paper, we describe and characterize log allelic fold change (aFC), the magnitude of expression change associated with a given genetic variant, as a biologically interpretable unit for quantifying the effect size of cis-eQTLs and a mathematically convenient approach for systematic modeling of cis-regulation. This measure is mathematically independent from expression level and allele frequency, additive, applicable to multiallelic variants, and generalizable to multiple independent variants...
November 2017: Genome Research
https://www.readbyqxmd.com/read/28993676/properties-analysis-of-transcription-factor-gene-tasmyb36-from-trichoderma-asperellum-cbs433-97-and-its-heterogeneous-transfomation-to-improve-antifungal-ability-of-populus
#16
Shida Ji, Zhiying Wang, Jinjie Wang, Haijuan Fan, Yucheng Wang, Zhihua Liu
The transcription of TasMYB36 in the biocontrol species T. asperellum was upregulated in four different pathogenic fermentation broths, suggesting that TasMYB36 plays an important role in the response to biotic stresses. Seventy-nine MYB transcription factors that were homologous to TasMYB36 from six sequenced Trichoderma genomes were analyzed. They were distributed in fourteen clades in the phylogenetic tree. The 79 MYBs contained 113 DNA binding domains, and their amino acid sequences were conserved and were different to those in plants...
October 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28902707/impact-of-human-ca8-on-thermal-antinociception-in-relation-to-morphine-equivalence-in-mice
#17
Eugene S Fu, Diana M Erasso, Gerald Z Zhuang, Udita Upadhyay, Mehtap Ozdemir, Timothy Wiltshire, Konstantinos D Sarantopoulos, Shad B Smith, William Maixner, Eden R Martin, Roy C Levitt
Recently, we showed that murine dorsal root ganglion (DRG) Car8 expression is a cis-regulated eQTL that determines analgesic responses. In this report, we show that transduction through sciatic nerve injection of DRG with human wild-type carbonic anhydrase-8 using adeno-associated virus viral particles (AAV8-V5-CA8WT) produces analgesia in naive male C57BL/6J mice and antihyperalgesia after carrageenan treatment. A peak mean increase of about 4 s in thermal hindpaw withdrawal latency equaled increases in thermal withdrawal latency produced by 10 mg/kg intraperitoneal morphine in these mice...
December 13, 2017: Neuroreport
https://www.readbyqxmd.com/read/28860661/long-intergenic-non-coding-rna-galmd3-in-chicken-marek-s-disease
#18
Bo Han, Yanghua He, Li Zhang, Yi Ding, Ling Lian, Chunfang Zhao, Jiuzhou Song, Ning Yang
Long intergenic non-coding RNAs (lincRNAs) are transcribed from non-coding DNA sequences. Studies have revealed that aberrant expressions of lincRNAs are associated with various types of cancers and neurological disorders. Marek's disease (MD) is a highly contagious T-cell lymphoid neoplasia of chicken induced by Marek's disease virus (MDV). In this study, we first identified and validated linc-GALMD3 highly expressed in MDV-infected CD4+ T cells by RNA-Seq and qRT-PCR. By RNA-Seq analysis in MDCC-MSB1 cells after loss of function of linc-GALMD3 by shRNA, we found that linc-GALMD3 could positively cis-regulate its downstream gga-miR-223 gene expression...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28843809/cis-and-trans-acting-lncrnas-in-pluripotency-and-reprogramming
#19
REVIEW
Pixi Yan, Sai Luo, J Yuyang Lu, Xiaohua Shen
Pervasive transcription in mammalian genomes produces thousands of long noncoding RNA (lncRNA) transcripts. Although they have been implicated in diverse biological processes, the functional relevance of most lncRNAs remains unknown. Recent studies reveal the prevalence of lncRNA-mediated cis regulation on nearby transcription. In this review, we summarize cis- and trans-acting lncRNAs involved in stem cell pluripotency and reprogramming, highlighting the role of regulatory lncRNAs in providing an additional layer of complexity to the regulation of genes that govern cell fate during development...
August 19, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28836940/genome-wide-identification-of-novel-intergenic-enhancer-like-elements-implications-in-the-regulation-of-transcription-in-plasmodium-falciparum
#20
Suyog Ubhe, Mukul Rawat, Srikant Verma, Krishanpal Anamika, Krishanpal Karmodiya
BACKGROUND: The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of cis-regulatory elements are known to operate in transcriptional regulation. Here, we employed an epigenetic signature based approach to identify significance of previously uncharacterised intergenic regions enriched with histone modification marks leading to discovery of enhancer-like elements...
August 23, 2017: BMC Genomics
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