Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes

Abstract Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (N...

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Autores principales:	Feinan Wu, Jie Yao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/07081384352f4780a38f186139293459
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spelling	oai:doaj.org-article:07081384352f4780a38f1861392934592021-12-02T12:32:52ZIdentifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes10.1038/s41598-017-00176-x2045-2322https://doaj.org/article/07081384352f4780a38f1861392934592017-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00176-xhttps://doaj.org/toc/2045-2322Abstract Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes. At the genome-wide scale, NL-association and H3K27me3 distinguishes two large gene classes with low transcriptional activities. Notably, NL-association is anti-correlated with both transcription and active histone mark levels among genes not significantly enriched with H3K9me3 or H3K27me3, suggesting that NL-association may represent a novel gene repression pathway. Interestingly, an NL gene subgroup is not significantly enriched with H3K9me3 or H3K27me3 and is transcribed at higher levels than the rest of NL genes. Furthermore, we identified distal enhancers associated with active NL genes and reported their epigenetic features.Feinan WuJie YaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Feinan Wu Jie Yao Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
description	Abstract Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes. At the genome-wide scale, NL-association and H3K27me3 distinguishes two large gene classes with low transcriptional activities. Notably, NL-association is anti-correlated with both transcription and active histone mark levels among genes not significantly enriched with H3K9me3 or H3K27me3, suggesting that NL-association may represent a novel gene repression pathway. Interestingly, an NL gene subgroup is not significantly enriched with H3K9me3 or H3K27me3 and is transcribed at higher levels than the rest of NL genes. Furthermore, we identified distal enhancers associated with active NL genes and reported their epigenetic features.
format	article
author	Feinan Wu Jie Yao
author_facet	Feinan Wu Jie Yao
author_sort	Feinan Wu
title	Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
title_short	Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
title_full	Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
title_fullStr	Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
title_full_unstemmed	Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes
title_sort	identifying novel transcriptional and epigenetic features of nuclear lamina-associated genes
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/07081384352f4780a38f186139293459
work_keys_str_mv	AT feinanwu identifyingnoveltranscriptionalandepigeneticfeaturesofnuclearlaminaassociatedgenes AT jieyao identifyingnoveltranscriptionalandepigeneticfeaturesofnuclearlaminaassociatedgenes
_version_	1718393899027791872

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes

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