High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci

Abstract Cellular responses to stimuli are rapid and continuous and yet the vast majority of investigations of transcriptional responses during developmental transitions typically use long interval time courses; limiting the available interpretive power. Moreover, such experiments typically focus on...

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Autores principales:	Brian S. Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b8a06b814e0248288830020045d527fd
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spelling	oai:doaj.org-article:b8a06b814e0248288830020045d527fd2021-12-02T15:05:18ZHigh resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci10.1038/s41598-017-06110-52045-2322https://doaj.org/article/b8a06b814e0248288830020045d527fd2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06110-5https://doaj.org/toc/2045-2322Abstract Cellular responses to stimuli are rapid and continuous and yet the vast majority of investigations of transcriptional responses during developmental transitions typically use long interval time courses; limiting the available interpretive power. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We therefore evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report new insight into molecular processes and genome organization. We present a highly resolved differentiation cascade that exhibits coding and noncoding transcriptional alterations, transcription factor network interactions and alternative splicing events, little of which can be resolved by long-interval developmental time-courses. We describe novel short lived and cycling patterns of gene expression and dissect temporally ordered gene expression changes in response to transcription factors. We elucidate patterns in gene co-expression across the genome, describe asynchronous transcription at bidirectional promoters and functionally annotate known and novel regulatory lncRNAs. These findings highlight the complex and dynamic molecular events underlying mammalian differentiation that can only be observed though a temporally resolved time course.Brian S. GlossBethany SignalSeth W. CheethamFranziska GruhlDominik C. KaczorowskiAndrew C. PerkinsMarcel E. DingerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Brian S. Gloss Bethany Signal Seth W. Cheetham Franziska Gruhl Dominik C. Kaczorowski Andrew C. Perkins Marcel E. Dinger High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
description	Abstract Cellular responses to stimuli are rapid and continuous and yet the vast majority of investigations of transcriptional responses during developmental transitions typically use long interval time courses; limiting the available interpretive power. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We therefore evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report new insight into molecular processes and genome organization. We present a highly resolved differentiation cascade that exhibits coding and noncoding transcriptional alterations, transcription factor network interactions and alternative splicing events, little of which can be resolved by long-interval developmental time-courses. We describe novel short lived and cycling patterns of gene expression and dissect temporally ordered gene expression changes in response to transcription factors. We elucidate patterns in gene co-expression across the genome, describe asynchronous transcription at bidirectional promoters and functionally annotate known and novel regulatory lncRNAs. These findings highlight the complex and dynamic molecular events underlying mammalian differentiation that can only be observed though a temporally resolved time course.
format	article
author	Brian S. Gloss Bethany Signal Seth W. Cheetham Franziska Gruhl Dominik C. Kaczorowski Andrew C. Perkins Marcel E. Dinger
author_facet	Brian S. Gloss Bethany Signal Seth W. Cheetham Franziska Gruhl Dominik C. Kaczorowski Andrew C. Perkins Marcel E. Dinger
author_sort	Brian S. Gloss
title	High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
title_short	High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
title_full	High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
title_fullStr	High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
title_full_unstemmed	High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
title_sort	high resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b8a06b814e0248288830020045d527fd
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High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci

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