title: Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.|University of Western Australia, Harry Perkins Institute of Medical Research, Perth, 6009, Australia.|University of Western Australia, Australian Research Council Centre of Excellence in Plant Energy Biology, Perth, 6009, Australia.
authors.forename: Sam
authors.initials: S
authors.lastname: Buckberry
authors.affiliation: The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.|The University of Adelaide, School of agriculture, food and wine, Adelaide, 5005, Australia.
authors.forename: Tina
authors.initials: T
authors.lastname: Bianco-Miotto
authors.affiliation: The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Bent
authors.affiliation: The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
authors.forename: Vicki
authors.initials: V
authors.lastname: Clifton
authors.affiliation: The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Shoubridge
authors.affiliation: University of Arkansas for Medical Sciences, The Department of Pediatrics, Little Rock, 72202, USA.
authors.forename: Kartik
authors.initials: K
authors.lastname: Shankar
authors.affiliation: The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia. claire.roberts@adelaide.edu.au.
authors.forename: Claire T
authors.initials: CT
authors.lastname: Roberts
mesh_terms: D000818:Animals; D001665:Binding Sites; D016000:Cluster Analysis; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005865:Gestational Age; D006801:Humans; D051379:Mice; D010920:Placenta / Q000378:metabolism*; D011247:Pregnancy; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014157:Transcription Factors
keywords: Co-expression; Gene expression; Microarray; Placenta; Preeclampsia; RNA-seq