Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus

JC virus (JCV), as an archetype, establishes a lifelong latent or persistent infection in many healthy individuals. In immunocompromised patients, prototype JCV with variable mutations in the non-coding control region (NCCR) causes progressive multifocal leukoencephalopathy (PML), a severe demyelina...

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Autores principales:	Kazuo Nakamichi, Toshio Shimokawa
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	database JC virus non-coding control region mutational pattern transcription factor binding sites statistical analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ea5c31566b2b4db4a36613136bea2a5f
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spelling	oai:doaj.org-article:ea5c31566b2b4db4a36613136bea2a5f2021-11-25T19:14:29ZDatabase and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus10.3390/v131123141999-4915https://doaj.org/article/ea5c31566b2b4db4a36613136bea2a5f2021-11-01T00:00:00Zhttps://www.mdpi.com/1999-4915/13/11/2314https://doaj.org/toc/1999-4915JC virus (JCV), as an archetype, establishes a lifelong latent or persistent infection in many healthy individuals. In immunocompromised patients, prototype JCV with variable mutations in the non-coding control region (NCCR) causes progressive multifocal leukoencephalopathy (PML), a severe demyelinating disease. This study was conducted to create a database of NCCR sequences annotated with transcription factor binding sites (TFBSs) and statistically analyze the mutational pattern of the JCV NCCR. JCV NCCRs were extracted from >1000 sequences registered in GenBank, and TFBSs within each NCCR were identified by computer simulation, followed by examination of their prevalence, multiplicity, and location by statistical analyses. In the NCCRs of the prototype JCV, the limited types of TFBSs, which are mainly present in regions D through F of archetype JCV, were significantly reduced. By contrast, modeling count data revealed that several TFBSs located in regions C and E tended to overlap in the prototype NCCRs. Based on data from the BioGPS database, genes encoding transcription factors that bind to these TFBSs were expressed not only in the brain but also in the peripheral sites. The database and NCCR patterns obtained in this study could be a suitable platform for analyzing JCV mutations and pathogenicity.Kazuo NakamichiToshio ShimokawaMDPI AGarticledatabaseJC virusnon-coding control regionmutational patterntranscription factor binding sitesstatistical analysisMicrobiologyQR1-502ENViruses, Vol 13, Iss 2314, p 2314 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	database JC virus non-coding control region mutational pattern transcription factor binding sites statistical analysis Microbiology QR1-502
spellingShingle	database JC virus non-coding control region mutational pattern transcription factor binding sites statistical analysis Microbiology QR1-502 Kazuo Nakamichi Toshio Shimokawa Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus
description	JC virus (JCV), as an archetype, establishes a lifelong latent or persistent infection in many healthy individuals. In immunocompromised patients, prototype JCV with variable mutations in the non-coding control region (NCCR) causes progressive multifocal leukoencephalopathy (PML), a severe demyelinating disease. This study was conducted to create a database of NCCR sequences annotated with transcription factor binding sites (TFBSs) and statistically analyze the mutational pattern of the JCV NCCR. JCV NCCRs were extracted from >1000 sequences registered in GenBank, and TFBSs within each NCCR were identified by computer simulation, followed by examination of their prevalence, multiplicity, and location by statistical analyses. In the NCCRs of the prototype JCV, the limited types of TFBSs, which are mainly present in regions D through F of archetype JCV, were significantly reduced. By contrast, modeling count data revealed that several TFBSs located in regions C and E tended to overlap in the prototype NCCRs. Based on data from the BioGPS database, genes encoding transcription factors that bind to these TFBSs were expressed not only in the brain but also in the peripheral sites. The database and NCCR patterns obtained in this study could be a suitable platform for analyzing JCV mutations and pathogenicity.
format	article
author	Kazuo Nakamichi Toshio Shimokawa
author_facet	Kazuo Nakamichi Toshio Shimokawa
author_sort	Kazuo Nakamichi
title	Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus
title_short	Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus
title_full	Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus
title_fullStr	Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus
title_full_unstemmed	Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus
title_sort	database and statistical analyses of transcription factor binding sites in the non-coding control region of jc virus
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/ea5c31566b2b4db4a36613136bea2a5f
work_keys_str_mv	AT kazuonakamichi databaseandstatisticalanalysesoftranscriptionfactorbindingsitesinthenoncodingcontrolregionofjcvirus AT toshioshimokawa databaseandstatisticalanalysesoftranscriptionfactorbindingsitesinthenoncodingcontrolregionofjcvirus
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Database and Statistical Analyses of Transcription Factor Binding Sites in the Non-Coding Control Region of JC Virus

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