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Open Access Highly Accessed Research article

Transcriptome landscape of the human placenta

Jinsil Kim1, Keyan Zhao2, Peng Jiang2, Zhi-xiang Lu2, Jinkai Wang2, Jeffrey C Murray345* and Yi Xing267*

Author Affiliations

1 Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA

2 Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA

3 Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA

4 Department of Biology, University of Iowa, Iowa City, IA 52242, USA

5 Department of Epidemiology, University of Iowa, Iowa City, IA 52242, USA

6 Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA

7 Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA

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BMC Genomics 2012, 13:115  doi:10.1186/1471-2164-13-115

Published: 27 March 2012

Abstract

Background

The placenta is a key component in understanding the physiological processes involved in pregnancy. Characterizing genes critical for placental function can serve as a basis for identifying mechanisms underlying both normal and pathologic pregnancies. Detailing the placental tissue transcriptome could provide a valuable resource for genomic studies related to placental disease.

Results

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.

Conclusions

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.

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