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Cis-regulation

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https://www.readbyqxmd.com/read/29116104/germline-copy-number-variations-are-associated-with-breast-cancer-risk-and-prognosis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
https://www.readbyqxmd.com/read/28793263/the-conserved-sonic-hedgehog-limb-enhancer-consists-of-discrete-functional-elements-that-regulate-precise-spatial-expression
#10
Laura A Lettice, Paul Devenney, Carlo De Angelis, Robert E Hill
Expression of sonic hedgehog (Shh) in the limb bud is regulated by an enhancer called the zone of polarizing activity regulatory sequence (ZRS), which, in evolution, belongs to an ancient group of highly conserved cis regulators found in all classes of vertebrates. Here, we examined the endogenous ZRS in mice, using genome editing to establish the relationship between enhancer composition and embryonic phenotype. We show that enhancer activity is a consolidation of distinct activity domains. Spatial restriction of Shh expression is mediated by a discrete repressor module, whereas levels of gene expression are controlled by large overlapping domains containing varying numbers of HOXD binding sites...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28756947/two-element-transcriptional-regulation-in-the-canonical-wnt-pathway
#11
Kibeom Kim, Jaehyoung Cho, Thomas S Hilzinger, Harry Nunns, Andrew Liu, Bryan E Ryba, Lea Goentoro
The canonical Wnt pathway regulates numerous fundamental processes throughout development and adult physiology and is often disrupted in diseases [1-4]. Signal in the pathway is transduced by β-catenin, which in complex with Tcf/Lef regulates transcription. Despite the many processes that the Wnt pathway governs, β-catenin acts primarily on a single cis element in the DNA, the Wnt-responsive element (WRE), at times potentiated by a nearby Helper site. In this study, working with Xenopus, mouse, and human systems, we identified a cis element, distinct from WRE, upon which β-catenin and Tcf act...
August 7, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28699901/transcriptomic-profiling-of-long-non-coding-rnas-in-hepatitis-b-virus-related-hepatocellular-carcinoma
#12
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...
June 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28698598/classification-and-function-of-small-open-reading-frames
#13
Juan-Pablo Couso, Pedro Patraquim
Small open reading frames (smORFs) of 100 codons or fewer are usually - if arbitrarily - excluded from proteome annotations. Despite this, the genomes of many metazoans, including humans, contain millions of smORFs, some of which fulfil key physiological functions. Recently, the transcriptome of Drosophila melanogaster was shown to contain thousands of smORFs of different classes that actively undergo translation, which produces peptides of mostly unknown function. Here, we present a comprehensive analysis of smORFs in flies, mice and humans...
September 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28638059/cis-regulatory-evolution-in-prokaryotes-revealed-by-interspecific-archaeal-hybrids
#14
Carlo G Artieri, Adit Naor, Israela Turgeman-Grott, Yiqi Zhou, Ryan York, Uri Gophna, Hunter B Fraser
The study of allele-specific expression (ASE) in interspecific hybrids has played a central role in our understanding of a wide range of phenomena, including genomic imprinting, X-chromosome inactivation, and cis-regulatory evolution. However across the hundreds of studies of hybrid ASE, all have been restricted to sexually reproducing eukaryotes, leaving a major gap in our understanding of the genomic patterns of cis-regulatory evolution in prokaryotes. Here we introduce a method to generate stable hybrids between two species of halophilic archaea, and measure genome-wide ASE in these hybrids with RNA-seq...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28581502/genome-wide-characterization-of-mammalian-promoters-with-distal-enhancer-functions
#15
COMPARATIVE STUDY
Lan T M Dao, Ariel O Galindo-Albarrán, Jaime A Castro-Mondragon, Charlotte Andrieu-Soler, Alejandra Medina-Rivera, Charbel Souaid, Guillaume Charbonnier, Aurélien Griffon, Laurent Vanhille, Tharshana Stephen, Jaafar Alomairi, David Martin, Magali Torres, Nicolas Fernandez, Eric Soler, Jacques van Helden, Denis Puthier, Salvatore Spicuglia
Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene promoters...
July 2017: Nature Genetics
https://www.readbyqxmd.com/read/28575045/the-effect-of-alcohol-on-the-differential-expression-of-cluster-of-differentiation-14-gene-associated-pathways-and-genetic-network
#16
COMPARATIVE STUDY
Diana X Zhou, Yinghong Zhao, Jessica A Baker, Qingqing Gu, Kristin M Hamre, Junming Yue, Byron C Jones, Melloni N Cook, Lu Lu
Alcohol consumption affects human health in part by compromising the immune system. In this study, we examined the expression of the Cd14 (cluster of differentiation 14) gene, which is involved in the immune system through a proinflammatory cascade. Expression was evaluated in BXD mice treated with saline or acute 1.8 g/kg i.p. ethanol (12.5% v/v). Hippocampal gene expression data were generated to examine differential expression and to perform systems genetics analyses. The Cd14 gene expression showed significant changes among the BXD strains after ethanol treatment, and eQTL mapping revealed that Cd14 is a cis-regulated gene...
2017: PloS One
https://www.readbyqxmd.com/read/28547032/car8-dorsal-root-ganglion-expression-and-genetic-regulation-of-analgesic-responses-are-associated-with-a-cis-eqtl-in-mice
#17
Roy C Levitt, Gerald Y Zhuang, Yuan Kang, Diana M Erasso, Udita Upadhyay, Mehtap Ozdemir, Eugene S Fu, Konstantinos D Sarantopoulos, Shad B Smith, William Maixner, Luda Diatchenko, Eden R Martin, Tim Wiltshire
Carbonic anhydrase-8 (Car8 mouse gene symbol) is devoid of enzymatic activity, but instead functions as an allosteric inhibitor of inositol trisphosphate receptor-1 (ITPR1) to regulate this intracellular calcium release channel important in synaptic functions and neuronal excitability. Causative mutations in ITPR1 and carbonic anhydrase-8 in mice and humans are associated with certain subtypes of spinal cerebellar ataxia (SCA). SCA mice are genetically deficient in dorsal root ganglia (DRG) Car8 expression and display mechanical and thermal hypersensitivity and susceptibility to subacute and chronic inflammatory pain behaviors...
October 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28499866/identification-and-characterization-of-novel-lncrnas-in-arabidopsis-thaliana
#18
Zhaogeng Lu, Xiao Xia, Bei Jiang, Kaibiao Ma, Likui Zhu, Li Wang, Biao Jin
Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified lncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (ssRNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel lncRNAs that we classified according to their localization. These novel identified lncRNAs showed low expression levels and sequence conservation...
June 24, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28475862/high-resolution-genetic-maps-identify-multiple-type-2-diabetes-loci-at-regulatory-hotspots-in-african-americans-and-europeans
#19
Winston Lau, Toby Andrew, Nikolas Maniatis
Interpretation of results from genome-wide association studies for T2D is challenging. Only very few loci have been replicated in African ancestry populations and the identification of the implicated functional genes remain largely undefined. We used genetic maps that capture detailed linkage disequilibrium information in European and African Americans and applied these to large T2D case-control samples in order to estimate locations for putative functional variants in both populations. Replicated T2D locations were tested for evidence of being regulatory hotspots using adipose expression...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28453813/identification-and-allelic-dissection-uncover-roles-of-lncrnas-in-secondary-growth-of-populus-tomentosa
#20
Daling Zhou, Qingzhang Du, Jinhui Chen, Qingshi Wang, Deqiang Zhang
Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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