Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y

Abstract A heterotrimeric transcription factor NF-Y is crucial for cell-cycle progression in various types of cells. In contrast, studies using NF-YA knockout mice have unveiled its essential role in endoplasmic reticulum (ER) homeostasis in neuronal cells. However, whether NF-Y modulates a differen...

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Autores principales:	Tomoyuki Yamanaka, Haruko Miyazaki, Asako Tosaki, Sankar N. Maity, Tomomi Shimogori, Nobutaka Hattori, Nobuyuki Nukina
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f
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spelling	oai:doaj.org-article:ccbc7ee531b049c7937f687cdc397d5f2021-12-02T16:18:02ZGene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y10.1038/s41598-020-78682-82045-2322https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f2020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78682-8https://doaj.org/toc/2045-2322Abstract A heterotrimeric transcription factor NF-Y is crucial for cell-cycle progression in various types of cells. In contrast, studies using NF-YA knockout mice have unveiled its essential role in endoplasmic reticulum (ER) homeostasis in neuronal cells. However, whether NF-Y modulates a different transcriptome to mediate distinct cellular functions remains obscure. Here, we knocked down NF-Y in two types of neuronal cells, neuro2a neuroblastoma cells and mouse brain striatal cells, and performed gene expression profiling. We found that down-regulated genes preferentially contained NF-Y-binding motifs in their proximal promoters, and notably enriched genes related to ER functions rather than those for cell cycle. This contrasts with the profiling data of HeLa and embryonic stem cells in which distinct down-regulation of cell cycle-related genes was observed. Clustering analysis further identified several functional clusters where populations of the down-regulated genes were highly distinct. Further analyses using chromatin immunoprecipitation and RNA-seq data revealed that the transcriptomic difference was not correlated with DNA binding of NF-Y but with splicing of NF-YA. These data suggest that neuronal cells have a different type of transcriptome in which ER-related genes are dominantly modulated by NF-Y, and imply that NF-YA splicing alteration could be involved in this cell type-specific gene modulation.Tomoyuki YamanakaHaruko MiyazakiAsako TosakiSankar N. MaityTomomi ShimogoriNobutaka HattoriNobuyuki NukinaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-14 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tomoyuki Yamanaka Haruko Miyazaki Asako Tosaki Sankar N. Maity Tomomi Shimogori Nobutaka Hattori Nobuyuki Nukina Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
description	Abstract A heterotrimeric transcription factor NF-Y is crucial for cell-cycle progression in various types of cells. In contrast, studies using NF-YA knockout mice have unveiled its essential role in endoplasmic reticulum (ER) homeostasis in neuronal cells. However, whether NF-Y modulates a different transcriptome to mediate distinct cellular functions remains obscure. Here, we knocked down NF-Y in two types of neuronal cells, neuro2a neuroblastoma cells and mouse brain striatal cells, and performed gene expression profiling. We found that down-regulated genes preferentially contained NF-Y-binding motifs in their proximal promoters, and notably enriched genes related to ER functions rather than those for cell cycle. This contrasts with the profiling data of HeLa and embryonic stem cells in which distinct down-regulation of cell cycle-related genes was observed. Clustering analysis further identified several functional clusters where populations of the down-regulated genes were highly distinct. Further analyses using chromatin immunoprecipitation and RNA-seq data revealed that the transcriptomic difference was not correlated with DNA binding of NF-Y but with splicing of NF-YA. These data suggest that neuronal cells have a different type of transcriptome in which ER-related genes are dominantly modulated by NF-Y, and imply that NF-YA splicing alteration could be involved in this cell type-specific gene modulation.
format	article
author	Tomoyuki Yamanaka Haruko Miyazaki Asako Tosaki Sankar N. Maity Tomomi Shimogori Nobutaka Hattori Nobuyuki Nukina
author_facet	Tomoyuki Yamanaka Haruko Miyazaki Asako Tosaki Sankar N. Maity Tomomi Shimogori Nobutaka Hattori Nobuyuki Nukina
author_sort	Tomoyuki Yamanaka
title	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
title_short	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
title_full	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
title_fullStr	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
title_full_unstemmed	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
title_sort	gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by nf-y
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f
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Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y

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