1. LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
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Louise Harewood, Duncan T. Odom, Paul Flicek, Aisling M. Redmond, Diego Villar, Maša Roller, Raghavendra Ramachanderan, Osagie G. Izuogu, Ericca Stamper, Fergal J. Martin, Flicek, Paul [0000-0002-3897-7955], and Apollo - University of Cambridge Repository
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Transposable element ,LINE L1 ,LINE L2 ,lcsh:QH426-470 ,Retroelements ,Retrotransposon ,Regulome ,Biology ,Regulatory Sequences, Nucleic Acid ,Computer Science::Digital Libraries ,Mathematics::Numerical Analysis ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Enhancers ,Animals ,Humans ,Enhancer ,Promoter Regions, Genetic ,Gene ,lcsh:QH301-705.5 ,Conserved Sequence ,030304 developmental biology ,Regulation of gene expression ,Mammals ,0303 health sciences ,Research ,Chromosome Mapping ,Promoter ,Computer Science::Computers and Society ,Gene regulation ,lcsh:Genetics ,Regulatory evolution ,Enhancer Elements, Genetic ,Long Interspersed Nucleotide Elements ,lcsh:Biology (General) ,Gene Expression Regulation ,Evolutionary biology ,Regulatory sequence ,Organ Specificity ,Promoters ,Transposable elements ,030217 neurology & neurosurgery ,Long Interspersed Nuclear Elements (LINEs) - Abstract
Funder: Helmholtz Society, Funder: European Molecular Biology Laboratory; doi: http://dx.doi.org/10.13039/100013060, BACKGROUND: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. RESULTS: The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species. CONCLUSIONS: Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.
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