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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Autor*in:	Tomoyuki Yamanaka [verfasserIn] Haruko Miyazaki [verfasserIn] Asako Tosaki [verfasserIn] Sankar N. Maity [verfasserIn] Tomomi Shimogori [verfasserIn] Nobutaka Hattori [verfasserIn] Nobuyuki Nukina [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2020

Übergeordnetes Werk:	In: Scientific Reports - Nature Portfolio, 2011, 10(2020), 1, Seite 14
Übergeordnetes Werk:	volume:10 ; year:2020 ; number:1 ; pages:14

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1038/s41598-020-78682-8

Katalog-ID:	DOAJ067806562

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allfields	10.1038/s41598-020-78682-8 doi (DE-627)DOAJ067806562 (DE-599)DOAJccbc7ee531b049c7937f687cdc397d5f DE-627 ger DE-627 rakwb eng Tomoyuki Yamanaka verfasserin aut Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Medicine R Science Q Haruko Miyazaki verfasserin aut Asako Tosaki verfasserin aut Sankar N. Maity verfasserin aut Tomomi Shimogori verfasserin aut Nobutaka Hattori verfasserin aut Nobuyuki Nukina verfasserin aut In Scientific Reports Nature Portfolio, 2011 10(2020), 1, Seite 14 (DE-627)663366712 (DE-600)2615211-3 20452322 nnns volume:10 year:2020 number:1 pages:14 https://doi.org/10.1038/s41598-020-78682-8 kostenfrei https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f kostenfrei https://doi.org/10.1038/s41598-020-78682-8 kostenfrei https://doaj.org/toc/2045-2322 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_381 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 1 14
spelling	10.1038/s41598-020-78682-8 doi (DE-627)DOAJ067806562 (DE-599)DOAJccbc7ee531b049c7937f687cdc397d5f DE-627 ger DE-627 rakwb eng Tomoyuki Yamanaka verfasserin aut Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Medicine R Science Q Haruko Miyazaki verfasserin aut Asako Tosaki verfasserin aut Sankar N. Maity verfasserin aut Tomomi Shimogori verfasserin aut Nobutaka Hattori verfasserin aut Nobuyuki Nukina verfasserin aut In Scientific Reports Nature Portfolio, 2011 10(2020), 1, Seite 14 (DE-627)663366712 (DE-600)2615211-3 20452322 nnns volume:10 year:2020 number:1 pages:14 https://doi.org/10.1038/s41598-020-78682-8 kostenfrei https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f kostenfrei https://doi.org/10.1038/s41598-020-78682-8 kostenfrei https://doaj.org/toc/2045-2322 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_381 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 1 14
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allfieldsSound	10.1038/s41598-020-78682-8 doi (DE-627)DOAJ067806562 (DE-599)DOAJccbc7ee531b049c7937f687cdc397d5f DE-627 ger DE-627 rakwb eng Tomoyuki Yamanaka verfasserin aut Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Medicine R Science Q Haruko Miyazaki verfasserin aut Asako Tosaki verfasserin aut Sankar N. Maity verfasserin aut Tomomi Shimogori verfasserin aut Nobutaka Hattori verfasserin aut Nobuyuki Nukina verfasserin aut In Scientific Reports Nature Portfolio, 2011 10(2020), 1, Seite 14 (DE-627)663366712 (DE-600)2615211-3 20452322 nnns volume:10 year:2020 number:1 pages:14 https://doi.org/10.1038/s41598-020-78682-8 kostenfrei https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f kostenfrei https://doi.org/10.1038/s41598-020-78682-8 kostenfrei https://doaj.org/toc/2045-2322 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_381 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2020 1 14
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authorswithroles_txt_mv	Tomoyuki Yamanaka @@aut@@ Haruko Miyazaki @@aut@@ Asako Tosaki @@aut@@ Sankar N. Maity @@aut@@ Tomomi Shimogori @@aut@@ Nobutaka Hattori @@aut@@ Nobuyuki Nukina @@aut@@
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author	Tomoyuki Yamanaka
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topic_title	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
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title	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
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title_full	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
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title_sort	gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by nf-y
title_auth	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
url	https://doi.org/10.1038/s41598-020-78682-8 https://doaj.org/article/ccbc7ee531b049c7937f687cdc397d5f https://doaj.org/toc/2045-2322
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Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y

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