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

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Standard

Associating transcription factors and conserved RNA structures with gene regulation in the human brain. / Hecker, Nikolai; Seemann, Stefan E.; Silahtaroglu, Asli; Ruzzo, Walter L.; Gorodkin, Jan.

I: Scientific Reports, Bind 7, Nr. 1, 5776, 2017.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Hecker, N, Seemann, SE, Silahtaroglu, A, Ruzzo, WL & Gorodkin, J 2017, 'Associating transcription factors and conserved RNA structures with gene regulation in the human brain', Scientific Reports, bind 7, nr. 1, 5776. https://doi.org/10.1038/s41598-017-06200-4

APA

Hecker, N., Seemann, S. E., Silahtaroglu, A., Ruzzo, W. L., & Gorodkin, J. (2017). Associating transcription factors and conserved RNA structures with gene regulation in the human brain. Scientific Reports, 7(1), [5776]. https://doi.org/10.1038/s41598-017-06200-4

Vancouver

Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J. Associating transcription factors and conserved RNA structures with gene regulation in the human brain. Scientific Reports. 2017;7(1). 5776. https://doi.org/10.1038/s41598-017-06200-4

Author

Hecker, Nikolai ; Seemann, Stefan E. ; Silahtaroglu, Asli ; Ruzzo, Walter L. ; Gorodkin, Jan. / Associating transcription factors and conserved RNA structures with gene regulation in the human brain. I: Scientific Reports. 2017 ; Bind 7, Nr. 1.

Bibtex

@article{5aa4d2e266534bfea70f5f2aff7ea3df,
title = "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 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.",
author = "Nikolai Hecker and Seemann, {Stefan E.} and Asli Silahtaroglu and Ruzzo, {Walter L.} and Jan Gorodkin",
year = "2017",
doi = "10.1038/s41598-017-06200-4",
language = "English",
volume = "7",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "nature publishing group",
number = "1",

}

RIS

TY - JOUR

T1 - Associating transcription factors and conserved RNA structures with gene regulation in the human brain

AU - Hecker, Nikolai

AU - Seemann, Stefan E.

AU - Silahtaroglu, Asli

AU - Ruzzo, Walter L.

AU - Gorodkin, Jan

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

U2 - 10.1038/s41598-017-06200-4

DO - 10.1038/s41598-017-06200-4

M3 - Journal article

C2 - 28720872

AN - SCOPUS:85024881072

VL - 7

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 5776

ER -

ID: 183504492