Transcriptome landscape of the human placenta

BMC Genomics

Research Article

Jinsil Kim¹  Peng Jiang²  Zhi-xiang Lu²  Keyan Zhao²  Jinkai Wang²  Yi Xing³  Jeffrey C Murray⁴ 

[1] Department of Anatomy and Cell Biology, University of Iowa, 52242, Iowa City, IA, USA;Department of Internal Medicine, University of Iowa, 52242, Iowa City, IA, USA;Department of Internal Medicine, University of Iowa, 52242, Iowa City, IA, USA;Department of Biomedical Engineering, University of Iowa, 52242, Iowa City, IA, USA;Department of Biostatistics, University of Iowa, 52242, Iowa City, IA, USA;Department of Pediatrics, University of Iowa, 52242, Iowa City, IA, USA;Department of Biology, University of Iowa, 52242, Iowa City, IA, USA;Department of Epidemiology, University of Iowa, 52242, Iowa City, IA, USA;

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

DOI  :  10.1186/1471-2164-13-115

 received in 2011-12-02, accepted in 2012-03-27,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Kim et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.