LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

Genome Biology

Louise Harewood¹  Duncan T. Odom¹  Diego Villar¹  Aisling M. Redmond¹  Osagie Izuogu²  Paul Flicek²  Raghavendra Ramachanderan²  Maša Roller²  Ericca Stamper²  Fergal Martin² 

[1] Cancer Research UK Cambridge Institute, University of Cambridge;European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus;

关键词: Regulatory evolution;    Gene regulation;    Promoters;    Enhancers;    Transposable elements;    Long Interspersed Nuclear Elements (LINEs);   

DOI  :  10.1186/s13059-021-02260-y

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown