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Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation

BACKGROUND: Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a...

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Autores principales: Buckberry, Sam, Bianco-Miotto, Tina, Bent, Stephen J., Clifton, Vicki, Shoubridge, Cheryl, Shankar, Kartik, Roberts, Claire T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209944/
https://www.ncbi.nlm.nih.gov/pubmed/28049421
http://dx.doi.org/10.1186/s12864-016-3384-9
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author Buckberry, Sam
Bianco-Miotto, Tina
Bent, Stephen J.
Clifton, Vicki
Shoubridge, Cheryl
Shankar, Kartik
Roberts, Claire T.
author_facet Buckberry, Sam
Bianco-Miotto, Tina
Bent, Stephen J.
Clifton, Vicki
Shoubridge, Cheryl
Shankar, Kartik
Roberts, Claire T.
author_sort Buckberry, Sam
collection PubMed
description BACKGROUND: Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS: In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation. We identified modules of co-expressed genes that are preserved across human gestation, and also identifed modules conserved in the mouse indicating conserved molecular networks involved in placental development and gene expression patterns more specific to late gestation. Analysis of co-expressed gene flanking sequences indicated that conserved co-expression modules in the placenta are regulated by a core set of transcription factors, including ZNF423 and EBF1. Additionally, we identified a gene co-expression module enriched for genes implicated in the pregnancy pathology preeclampsia. By using an independnet transcriptome dataset, we show that these co-expressed genes are differentially expressed in preeclampsia. CONCLUSIONS: This study represents a comprehensive characterisation of placental co-expression and provides insight into potential transcriptional regulators that govern conserved molecular programs fundamental to placental development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3384-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-52099442017-01-04 Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation Buckberry, Sam Bianco-Miotto, Tina Bent, Stephen J. Clifton, Vicki Shoubridge, Cheryl Shankar, Kartik Roberts, Claire T. BMC Genomics Research Article BACKGROUND: Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS: In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation. We identified modules of co-expressed genes that are preserved across human gestation, and also identifed modules conserved in the mouse indicating conserved molecular networks involved in placental development and gene expression patterns more specific to late gestation. Analysis of co-expressed gene flanking sequences indicated that conserved co-expression modules in the placenta are regulated by a core set of transcription factors, including ZNF423 and EBF1. Additionally, we identified a gene co-expression module enriched for genes implicated in the pregnancy pathology preeclampsia. By using an independnet transcriptome dataset, we show that these co-expressed genes are differentially expressed in preeclampsia. CONCLUSIONS: This study represents a comprehensive characterisation of placental co-expression and provides insight into potential transcriptional regulators that govern conserved molecular programs fundamental to placental development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3384-9) contains supplementary material, which is available to authorized users. BioMed Central 2017-01-03 /pmc/articles/PMC5209944/ /pubmed/28049421 http://dx.doi.org/10.1186/s12864-016-3384-9 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Buckberry, Sam
Bianco-Miotto, Tina
Bent, Stephen J.
Clifton, Vicki
Shoubridge, Cheryl
Shankar, Kartik
Roberts, Claire T.
Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
title Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
title_full Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
title_fullStr Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
title_full_unstemmed Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
title_short Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
title_sort placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209944/
https://www.ncbi.nlm.nih.gov/pubmed/28049421
http://dx.doi.org/10.1186/s12864-016-3384-9
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