Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribut...
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Autor*in:	Yuzhuo Li [verfasserIn] Hairui Fan [verfasserIn] Weiyun Qin [verfasserIn] Yejun Wang [verfasserIn] Shuai Chen [verfasserIn] Wenbin Bao [verfasserIn] Ming-an Sun [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Transposable element Endogenous retrovirus Pig spleen 3D chromatin organization CTCF Hi-C

Übergeordnetes Werk:	In: Computational and Structural Biotechnology Journal - Elsevier, 2013, 21(2023), Seite 4580-4588
Übergeordnetes Werk:	volume:21 ; year:2023 ; pages:4580-4588

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1016/j.csbj.2023.09.029

Katalog-ID:	DOAJ096685972

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520			\|a Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribution of TEs for the 3D chromatin organization in three pig tissues, focusing on spleen which is crucial for both adaptive and innate immunity. We identified dozens of TE families overrepresented with CTCF binding sites, including LTR22_SS, LTR15_SS and LTR16_SSc which are pig-specific families of endogenous retroviruses (ERVs). Interestingly, LTR22_SS elements harbor a CTCF motif and create hundreds of CTCF binding sites that are associated with adaptive immunity. We further applied Hi-C to profile the 3D chromatin structure in spleen and found that TE-derived CTCF binding sites correlate with chromatin insulation and frequently overlap TAD borders and loop anchors. Notably, one LTR22_SS-derived CTCF binding site demarcate a TAD boundary upstream of XCL1, which is a spleen-enriched chemokine gene important for lymphocyte trafficking and inflammation. Overall, this study represents a first step toward understanding the function of TEs on 3D chromatin organization regulation in pigs and expands our understanding about the functional importance of TEs in mammals.
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language	English
source	In Computational and Structural Biotechnology Journal 21(2023), Seite 4580-4588 volume:21 year:2023 pages:4580-4588
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topic_facet	Transposable element Endogenous retrovirus Pig spleen 3D chromatin organization CTCF Hi-C Biotechnology
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authorswithroles_txt_mv	Yuzhuo Li @@aut@@ Hairui Fan @@aut@@ Weiyun Qin @@aut@@ Yejun Wang @@aut@@ Shuai Chen @@aut@@ Wenbin Bao @@aut@@ Ming-an Sun @@aut@@
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callnumber-first	T - Technology
author	Yuzhuo Li
spellingShingle	Yuzhuo Li misc TP248.13-248.65 misc Transposable element misc Endogenous retrovirus misc Pig spleen misc 3D chromatin organization misc CTCF misc Hi-C misc Biotechnology Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
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topic_title	TP248.13-248.65 Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen Transposable element Endogenous retrovirus Pig spleen 3D chromatin organization CTCF Hi-C
topic	misc TP248.13-248.65 misc Transposable element misc Endogenous retrovirus misc Pig spleen misc 3D chromatin organization misc CTCF misc Hi-C misc Biotechnology
topic_unstemmed	misc TP248.13-248.65 misc Transposable element misc Endogenous retrovirus misc Pig spleen misc 3D chromatin organization misc CTCF misc Hi-C misc Biotechnology
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title	Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
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title_full	Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
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title_sort	regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
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title_auth	Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
abstract	Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribution of TEs for the 3D chromatin organization in three pig tissues, focusing on spleen which is crucial for both adaptive and innate immunity. We identified dozens of TE families overrepresented with CTCF binding sites, including LTR22_SS, LTR15_SS and LTR16_SSc which are pig-specific families of endogenous retroviruses (ERVs). Interestingly, LTR22_SS elements harbor a CTCF motif and create hundreds of CTCF binding sites that are associated with adaptive immunity. We further applied Hi-C to profile the 3D chromatin structure in spleen and found that TE-derived CTCF binding sites correlate with chromatin insulation and frequently overlap TAD borders and loop anchors. Notably, one LTR22_SS-derived CTCF binding site demarcate a TAD boundary upstream of XCL1, which is a spleen-enriched chemokine gene important for lymphocyte trafficking and inflammation. Overall, this study represents a first step toward understanding the function of TEs on 3D chromatin organization regulation in pigs and expands our understanding about the functional importance of TEs in mammals.
abstractGer	Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribution of TEs for the 3D chromatin organization in three pig tissues, focusing on spleen which is crucial for both adaptive and innate immunity. We identified dozens of TE families overrepresented with CTCF binding sites, including LTR22_SS, LTR15_SS and LTR16_SSc which are pig-specific families of endogenous retroviruses (ERVs). Interestingly, LTR22_SS elements harbor a CTCF motif and create hundreds of CTCF binding sites that are associated with adaptive immunity. We further applied Hi-C to profile the 3D chromatin structure in spleen and found that TE-derived CTCF binding sites correlate with chromatin insulation and frequently overlap TAD borders and loop anchors. Notably, one LTR22_SS-derived CTCF binding site demarcate a TAD boundary upstream of XCL1, which is a spleen-enriched chemokine gene important for lymphocyte trafficking and inflammation. Overall, this study represents a first step toward understanding the function of TEs on 3D chromatin organization regulation in pigs and expands our understanding about the functional importance of TEs in mammals.
abstract_unstemmed	Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribution of TEs for the 3D chromatin organization in three pig tissues, focusing on spleen which is crucial for both adaptive and innate immunity. We identified dozens of TE families overrepresented with CTCF binding sites, including LTR22_SS, LTR15_SS and LTR16_SSc which are pig-specific families of endogenous retroviruses (ERVs). Interestingly, LTR22_SS elements harbor a CTCF motif and create hundreds of CTCF binding sites that are associated with adaptive immunity. We further applied Hi-C to profile the 3D chromatin structure in spleen and found that TE-derived CTCF binding sites correlate with chromatin insulation and frequently overlap TAD borders and loop anchors. Notably, one LTR22_SS-derived CTCF binding site demarcate a TAD boundary upstream of XCL1, which is a spleen-enriched chemokine gene important for lymphocyte trafficking and inflammation. Overall, this study represents a first step toward understanding the function of TEs on 3D chromatin organization regulation in pigs and expands our understanding about the functional importance of TEs in mammals.
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title_short	Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
url	https://doi.org/10.1016/j.csbj.2023.09.029 https://doaj.org/article/c91e15f2946e4c48be1ec2850dfafa23 http://www.sciencedirect.com/science/article/pii/S2001037023003410 https://doaj.org/toc/2001-0370
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Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

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