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BMC Genomics  2012 

Transcriptome landscape of the human placenta

DOI: 10.1186/1471-2164-13-115

Keywords: Placenta, Amnion, Chorion, Decidua, RNA-Seq, Transcriptome, Alternative splicing, Functional interaction network, Novel transcriptional active region

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Abstract:

We have conducted a deep RNA sequencing (RNA-Seq) study on three tissue components (amnion, chorion, and decidua) of 5 human placentas from normal term pregnancies. We compared the placental RNA-Seq data to that of 16 other human tissues and observed a wide spectrum of transcriptome differences both between placenta and other human tissues and between distinct compartments of the placenta. Exon-level analysis of the RNA-Seq data revealed a large number of exons with differential splicing activities between placenta and other tissues, and 79% (27 out of 34) of the events selected for RT-PCR test were validated. The master splicing regulator ESRP1 is expressed at a proportionately higher level in amnion compared to all other analyzed human tissues, and there is a significant enrichment of ESRP1-regulated exons with tissue-specific splicing activities in amnion. This suggests an important role of alternative splicing in regulating gene function and activity in specific placental compartments. Importantly, genes with differential expression or splicing in the placenta are significantly enriched for genes implicated in placental abnormalities and preterm birth. In addition, we identified 604-1007 novel transcripts and 494-585 novel exons expressed in each of the three placental compartments.Our data demonstrate unique aspects of gene expression and splicing in placental tissues that provide a basis for disease investigation related to disruption of these mechanisms. These data are publicly available providing the community with a rich resource for placental physiology and disease-related studies.Pregnancy and parturition require an intricate interplay between maternal and fetal factors, orchestrated by the placenta, which lies at the interface between mother and fetus. The placenta performs multiple functions critical for fetal survival, growth, and development, including transport of gases, nutrients, and waste products, hormone production, protection of the fetus from

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