Associating transcription factors and conserved RNA structures with gene regulation in the human brain

Abstract Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcripti...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Nikolai Hecker, Stefan E. Seemann, Asli Silahtaroglu, Walter L. Ruzzo, Jan Gorodkin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/83d500d9e1854594a7000a1f6d217009
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:83d500d9e1854594a7000a1f6d217009
record_format	dspace
spelling	oai:doaj.org-article:83d500d9e1854594a7000a1f6d2170092021-12-02T15:05:01ZAssociating transcription factors and conserved RNA structures with gene regulation in the human brain10.1038/s41598-017-06200-42045-2322https://doaj.org/article/83d500d9e1854594a7000a1f6d2170092017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06200-4https://doaj.org/toc/2045-2322Abstract Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription factors (TF) and RNA secondary structures on the regulation of gene expression in the human brain. First, we modeled the expression of a gene as a linear combination of the expression of TFs. We devised an approach to select robust TF-gene interactions and to determine localized contributions to gene expression of TFs. Among the TFs with the most localized contributions, we identified EZH2 in the cerebellum, NR3C1 in the cerebral cortex and SRF in the basal forebrain. Our results suggest that EZH2 is involved in regulating ZIC2 and SHANK1 which have been linked to neurological diseases such as autism spectrum disorder. Second, we associated enriched regulatory elements inside differentially expressed mRNAs with RNA secondary structure motifs. We found a group of purine-uracil repeat RNA secondary structure motifs plus other motifs in neuron related genes such as ACSL4 and ERLIN2.Nikolai HeckerStefan E. SeemannAsli SilahtarogluWalter L. RuzzoJan GorodkinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-16 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nikolai Hecker Stefan E. Seemann Asli Silahtaroglu Walter L. Ruzzo Jan Gorodkin Associating transcription factors and conserved RNA structures with gene regulation in the human brain
description	Abstract Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription factors (TF) and RNA secondary structures on the regulation of gene expression in the human brain. First, we modeled the expression of a gene as a linear combination of the expression of TFs. We devised an approach to select robust TF-gene interactions and to determine localized contributions to gene expression of TFs. Among the TFs with the most localized contributions, we identified EZH2 in the cerebellum, NR3C1 in the cerebral cortex and SRF in the basal forebrain. Our results suggest that EZH2 is involved in regulating ZIC2 and SHANK1 which have been linked to neurological diseases such as autism spectrum disorder. Second, we associated enriched regulatory elements inside differentially expressed mRNAs with RNA secondary structure motifs. We found a group of purine-uracil repeat RNA secondary structure motifs plus other motifs in neuron related genes such as ACSL4 and ERLIN2.
format	article
author	Nikolai Hecker Stefan E. Seemann Asli Silahtaroglu Walter L. Ruzzo Jan Gorodkin
author_facet	Nikolai Hecker Stefan E. Seemann Asli Silahtaroglu Walter L. Ruzzo Jan Gorodkin
author_sort	Nikolai Hecker
title	Associating transcription factors and conserved RNA structures with gene regulation in the human brain
title_short	Associating transcription factors and conserved RNA structures with gene regulation in the human brain
title_full	Associating transcription factors and conserved RNA structures with gene regulation in the human brain
title_fullStr	Associating transcription factors and conserved RNA structures with gene regulation in the human brain
title_full_unstemmed	Associating transcription factors and conserved RNA structures with gene regulation in the human brain
title_sort	associating transcription factors and conserved rna structures with gene regulation in the human brain
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/83d500d9e1854594a7000a1f6d217009
work_keys_str_mv	AT nikolaihecker associatingtranscriptionfactorsandconservedrnastructureswithgeneregulationinthehumanbrain AT stefaneseemann associatingtranscriptionfactorsandconservedrnastructureswithgeneregulationinthehumanbrain AT aslisilahtaroglu associatingtranscriptionfactorsandconservedrnastructureswithgeneregulationinthehumanbrain AT walterlruzzo associatingtranscriptionfactorsandconservedrnastructureswithgeneregulationinthehumanbrain AT jangorodkin associatingtranscriptionfactorsandconservedrnastructureswithgeneregulationinthehumanbrain
_version_	1718388966434013184

Associating transcription factors and conserved RNA structures with gene regulation in the human brain

Ejemplares similares