干旱区生态环境知识资源中心(Arid): Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers

Arid

DOI	10.1073/pnas.1912008117
	Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers
	Ye, Mengliang 1; Goudot, Christel 1; Hoyler, Thomas 1; Lemoine, Benjamin 2; Amigorena, Sebastian 1; Zueva, Elina 1
通讯作者	Amigorena, Sebastian ; Zueva, Elina
来源期刊	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN	0027-8424
出版年	2020
卷号	117 期号:14 页码:7905-7916
英文摘要	Transposable elements (TEs) compose nearly half of mammalian genomes and provide building blocks for cis-regulatory elements. Using high-throughput sequencing, we show that 84 TE subfamilies are overrepresented, and distributed in a lineage-specific fashion in core and boundary domains of CD8(+) T cell enhancers. Endogenous retroviruses are most significantly enriched in core domains with accessible chromatin, and bear recognition motifs for immune-related transcription factors. In contrast, short interspersed elements (SINEs) are preferentially overrepresented in nucleosome-containing boundaries. A substantial proportion of these SINEs harbor a high density of the enhancer-specific histone mark H3K4me1 and carry sequences that match enhancer boundary nucleotide composition. Motifs with regulatory features are better preserved within enhancer-enriched TE copies compared to their subfamily equivalents located in gene deserts. TE-rich and TE-poor enhancers associate with both shared and unique gene groups and are enriched in overlapping functions related to lymphocyte and leukocyte biology. The majority of T cell enhancers are shared with other immune lineages and are accessible in common hematopoietic progenitors. A higher proportion of immune tissue-specific enhancers are TE-rich compared to enhancers specific to other tissues, correlating with higher TE occurrence in immune gene-associated genomic regions. Our results suggest that during evolution, TEs abundant in these regions and carrying motifs potentially beneficial for enhancer architecture and immune functions were particularly frequently incorporated by evolving enhancers. Their putative selection and regulatory cooption may have accelerated the evolution of immune regulatory networks.
英文关键词	transposable element enhancer T lymphocyte immune tissue
类型	Article
语种	英语
国家	France ; USA
开放获取类型	hybrid, Green Published
收录类别	SCI-E
WOS记录号	WOS:000524486300053
WOS关键词	TRANSCRIPTION FACTOR-BINDING ; IL-7 RECEPTOR EXPRESSION ; PHENOTYPIC ROBUSTNESS ; HISTONE MODIFICATIONS ; CHROMATIN ; EVOLUTION ; CELLS ; SIGNATURES ; PROTEINS ; DATABASE
WOS类目	Multidisciplinary Sciences
WOS研究方向	Science & Technology - Other Topics
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/315369
作者单位	1.Paris Sci & Lettres Res Univ, Inst Curie, INSERM, U932, F-75005 Paris, France; 2.Baylor Scott & White Res Inst, Genom Core, Dallas, TX 75204 USA
推荐引用方式 GB/T 7714	Ye, Mengliang,Goudot, Christel,Hoyler, Thomas,et al. Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers[J],2020,117(14):7905-7916.
APA	Ye, Mengliang,Goudot, Christel,Hoyler, Thomas,Lemoine, Benjamin,Amigorena, Sebastian,&Zueva, Elina.(2020).Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,117(14),7905-7916.
MLA	Ye, Mengliang,et al."Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 117.14(2020):7905-7916.