18 results match your criteria multitissue transcriptomes

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, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs.

Front Genet 2021 15;12:628192. Epub 2021 Apr 15.

College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.

Tibetan pigs are native mammalian species on the Tibetan Plateau that have evolved distinct physiological traits that allow them to tolerate high-altitude hypoxic environments. However, the genetic mechanism underlying this adaptation remains elusive. Here, based on multitissue transcriptional data from high-altitude Tibetan pigs and low-altitude Rongchang pigs, we performed a weighted correlation network analysis (WGCNA) and identified key modules related to these tissues. Read More

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Chromosome level reference of Atlantic halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems.

Mol Ecol Resour 2021 Mar 2. Epub 2021 Mar 2.

Biology Department, Dalhousie University, Halifax, NS, Canada.

Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multitissue transcriptomes, and reduced representation population data for the Atlantic halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged (0.9-3. Read More

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Transcriptomic signatures across human tissues identify functional rare genetic variation.

Science 2020 09 10;369(6509). Epub 2020 Sep 10.

University of Mississippi Medical Center, Jackson, MS, USA.

Rare genetic variants are abundant across the human genome, and identifying their function and phenotypic impact is a major challenge. Measuring aberrant gene expression has aided in identifying functional, large-effect rare variants (RVs). Here, we expanded detection of genetically driven transcriptome abnormalities by analyzing gene expression, allele-specific expression, and alternative splicing from multitissue RNA-sequencing data, and demonstrate that each signal informs unique classes of RVs. Read More

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September 2020

Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments.

Sci Adv 2020 May 22;6(21):eaba3388. Epub 2020 May 22.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.

Phenotypic plasticity refers to environment-induced phenotypic changes without mutation and is present in all organisms. The role of phenotypic plasticity in organismal adaptations to novel environments has attracted much attention, but its role in readaptations to ancestral environments is understudied. To address this question, we use the reciprocal transplant approach to investigate the multitissue transcriptomes of chickens adapted to the Tibetan Plateau and adjacent lowland. Read More

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Understanding osteoarthritis pathogenesis: a multiomics system-based approach.

Curr Opin Rheumatol 2020 01;32(1):80-91

Arthritis Program.

Purpose Of Review: Osteoarthritis is a heterogeneous, multifactorial condition regulated by complex biological interactions at multiple levels. Comprehensive understanding of these regulatory interactions is required to develop feasible advances to improve patient outcomes. Improvements in technology have made extensive genomic, transcriptomic, epigenomic, proteomic, and metabolomic profiling possible. Read More

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January 2020

Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression.

J Allergy Clin Immunol 2020 04 9;145(4):1208-1218. Epub 2019 Nov 9.

Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.

Background: Fifteen percent of atopic dermatitis (AD) liability-scale heritability could be attributed to 31 susceptibility loci identified by using genome-wide association studies, with only 3 of them (IL13, IL-6 receptor [IL6R], and filaggrin [FLG]) resolved to protein-coding variants.

Objective: We examined whether a significant portion of unexplained AD heritability is further explained by low-frequency and rare variants in the gene-coding sequence.

Methods: We evaluated common, low-frequency, and rare protein-coding variants using exome chip and replication genotype data of 15,574 patients and 377,839 control subjects combined with whole-transcriptome data on lesional, nonlesional, and healthy skin samples of 27 patients and 38 control subjects. Read More

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Breakdown of multiple sclerosis genetics to identify an integrated disease network and potential variant mechanisms.

Physiol Genomics 2019 11 4;51(11):562-577. Epub 2019 Sep 4.

Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.

Genetics of multiple sclerosis (MS) are highly polygenic with few insights into mechanistic associations with pathology. In this study, we assessed MS genetics through linkage disequilibrium and missense variant interpretation to yield a MS gene network. This network of 96 genes was taken through pathway analysis, tissue expression profiles, single cell expression segregation, expression quantitative trait loci (eQTLs), genome annotations, transcription factor (TF) binding profiles, structural genome looping, and overlap with additional associated genetic traits. Read More

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November 2019

Transcriptional changes in the hypothalamus, pituitary, and mammary gland underlying decreased lactation performance in mice under heat stress.

FASEB J 2019 11 31;33(11):12588-12601. Epub 2019 Aug 31.

College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China; and.

Because of climate change, heat stress (HS) causes more and more impacts on dairy animals to decrease lactation performance. The neuroendocrine system is key in regulating systemic physiological processes and milk synthesis. However, the hypothalamic-pituitary axis response to HS is still unclear. Read More

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November 2019

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses.

Genome Res 2019 04 11;29(4):697-709. Epub 2019 Mar 11.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.

Aging is accompanied by the functional decline of tissues. However, a systematic study of epigenomic and transcriptomic changes across tissues during aging is missing. Here, we generated chromatin maps and transcriptomes from four tissues and one cell type from young, middle-aged, and old mice-yielding 143 high-quality data sets. Read More

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Prenatal Bisphenol A Exposure in Mice Induces Multitissue Multiomics Disruptions Linking to Cardiometabolic Disorders.

Endocrinology 2019 02;160(2):409-429

Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California.

The health impacts of endocrine-disrupting chemicals (EDCs) remain debated, and their tissue and molecular targets are poorly understood. In this study, we leveraged systems biology approaches to assess the target tissues, molecular pathways, and gene regulatory networks associated with prenatal exposure to the model EDC bisphenol A (BPA). Prenatal BPA exposure at 5 mg/kg/d, a dose below most reported no-observed-adverse-effect levels, led to tens to thousands of transcriptomic and methylomic alterations in the adipose, hypothalamus, and liver tissues in male offspring in mice, with cross-tissue perturbations in lipid metabolism as well as tissue-specific alterations in histone subunits, glucose metabolism, and extracellular matrix. Read More

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February 2019

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.

Gigascience 2018 01;7(1):1-7

Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia.

Background: Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Read More

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January 2018

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

Nat Genet 2017 Dec 30;49(12):1714-1721. Epub 2017 Oct 30.

McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. Read More

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December 2017

Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders.

Genome Biol Evol 2016 Jan 5;8(1):228-42. Epub 2016 Jan 5.

Department of Biological Sciences, University of Massachusetts, Lowell

Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. Read More

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January 2016

Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.


Science 2015 May 7;348(6235):648-60. Epub 2015 May 7.

Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. Read More

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Highly variable recombinational landscape modulates efficacy of natural selection in birds.

Genome Biol Evol 2014 Aug;6(8):2061-75

Department of Animal and Plant Sciences, University of Sheffield, United Kingdom

Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two passerine birds, great tit and zebra finch (Taeniopygia guttata), using the chicken genome (Gallus gallus) as an outgroup. We investigated whether a special feature of avian genomes, the highly variable recombinational landscape, modulates the efficacy of natural selection through the effects of Hill-Robertson interference, which predicts that selection should be more effective in removing deleterious mutations and incorporating beneficial mutations in high-recombination regions than in low-recombination regions. Read More

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Multitissue molecular, genomic, and developmental effects of the Deepwater Horizon oil spill on resident Gulf killifish (Fundulus grandis).

Environ Sci Technol 2013 May 9;47(10):5074-82. Epub 2013 May 9.

Louisiana State University, Department of Biological Sciences, 208 Life Sciences Building, Baton Rouge, Louisiana 70803, United States.

The Deepwater Horizon oil rig disaster resulted in crude oil contamination along the Gulf coast in sensitive estuaries. Toxicity from exposure to crude oil can affect populations of fish that live or breed in oiled habitats as seen following the Exxon Valdez oil spill. In an ongoing study of the effects of Deepwater Horizon crude oil on fish, Gulf killifish ( Fundulus grandis ) were collected from an oiled site (Grande Terre, LA) and two reference locations (coastal MS and AL) and monitored for measures of exposure to crude oil. Read More

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Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate.

Proc Natl Acad Sci U S A 2004 Nov 18;101(48):16970-5. Epub 2004 Nov 18.

School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L39 7ZB, United Kindgom.

How do organisms respond adaptively to environmental stress? Although some gene-specific responses have been explored, others remain to be identified, and there is a very poor understanding of the system-wide integration of response, particularly in complex, multitissue animals. Here, we adopt a transcript screening approach to explore the mechanisms underpinning a major, whole-body phenotypic transition in a vertebrate animal that naturally experiences extreme environmental stress. Carp were exposed to increasing levels of cold, and responses across seven tissues were assessed by using a microarray composed of 13,440 cDNA probes. Read More

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November 2004

Computational dissection of tissue contamination for identification of colon cancer-specific expression profiles.

FASEB J 2003 Mar;17(3):376-85

III. Medizinische Klinik und Poliklinik, Johannes Gutenberg Universität Mainz, D-55131 Mainz, Germany.

Microarray profiles of bulk tumor tissues reflect gene expression corresponding to malignant cells as well as to many different types of contaminating normal cells. In this report, we assess the feasibility of querying baseline multitissue transcriptome databases to dissect disease-specific genes. Using colon cancer as a model tumor, we show that the application of Boolean operators (AND, OR, BUTNOT) for database searches leads to genes with expression patterns of interest. Read More

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