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

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2021-02-18 DOI:10.1186/s13059-021-02260-y
Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T Odom, Paul Flicek
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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.

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LINE 反转座子是哺乳动物组织特异性和进化动态调控区域的特征。
背景:为了研究跨组织调控进化的驱动机制,我们通过实验绘制了十种不同哺乳动物肝脏、大脑、肌肉和睾丸中的启动子、增强子和基因表达图谱:基因周围的调控格局包括组织共享调控区和组织特异性调控区,其中组织特异性启动子和增强子的进化最为迅速。在启动子和增强子之间切换的基因组区域在不同物种之间更为常见,而在同一物种的不同组织之间则不太常见。长互套核元素(LINEs)在进化过程中反复发挥作用:LINE L1与组织特异性调控区相关,而更古老的LINE L2则与组织共享调控区以及在启动子和增强子之间跨物种切换的调控区相关:我们对启动子和增强子的组织特异性和进化稳定性的分析揭示了特定的LINE家族是如何帮助形成动态的哺乳动物调控组的。
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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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