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

Sam Buckberry, Tina Bianco-Miotto, Stephen J. Bent, Vicki Clifton, Cheryl Shoubridge, Kartik Shankar, Claire T. Roberts

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number10
JournalBMC Genomics
Volume18
Issue number1
DOIs
Publication statusPublished - 3 Jan 2017

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Transcriptome
Placentation
Pregnancy
Pre-Eclampsia
Genes
Genome
RNA Sequence Analysis
Gene Expression
Conserved Sequence
Gene Regulatory Networks
Placenta
Transcription Factors
Pathology
Datasets

Cite this

Buckberry, S., Bianco-Miotto, T., Bent, S. J., Clifton, V., Shoubridge, C., Shankar, K., & Roberts, C. T. (2017). Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics, 18(1), [10]. https://doi.org/10.1186/s12864-016-3384-9
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. In: BMC Genomics. 2017 ; Vol. 18, No. 1.
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Buckberry, S, Bianco-Miotto, T, Bent, SJ, Clifton, V, Shoubridge, C, Shankar, K & Roberts, CT 2017, 'Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation' BMC Genomics, vol. 18, no. 1, 10. https://doi.org/10.1186/s12864-016-3384-9

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.

In: BMC Genomics, Vol. 18, No. 1, 10, 03.01.2017.

Research output: Contribution to journalArticle

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AU - Bianco-Miotto, Tina

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AU - Shankar, Kartik

AU - Roberts, Claire T.

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