Transcriptome landscape of the human placenta
<p>Abstract</p> <p>Background</p> <p>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 patho...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/115 |
| _version_ | 1818963720143896576 |
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| author | Kim Jinsil Zhao Keyan Jiang Peng Lu Zhi-xiang Wang Jinkai Murray Jeffrey C Xing Yi |
| author_facet | Kim Jinsil Zhao Keyan Jiang Peng Lu Zhi-xiang Wang Jinkai Murray Jeffrey C Xing Yi |
| author_sort | Kim Jinsil |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>ESRP1 </it>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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-20T12:49:42Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T12:49:42Z |
| publishDate | 2012-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b2036fe76bc64d47aae06f0fec5f9ba92022-12-21T19:40:11ZengBMCBMC Genomics1471-21642012-03-0113111510.1186/1471-2164-13-115Transcriptome landscape of the human placentaKim JinsilZhao KeyanJiang PengLu Zhi-xiangWang JinkaiMurray Jeffrey CXing Yi<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>ESRP1 </it>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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/13/115PlacentaAmnionChorionDeciduaRNA-SeqTranscriptomeAlternative splicingFunctional interaction networkNovel transcriptional active region |
| spellingShingle | Kim Jinsil Zhao Keyan Jiang Peng Lu Zhi-xiang Wang Jinkai Murray Jeffrey C Xing Yi Transcriptome landscape of the human placenta BMC Genomics Placenta Amnion Chorion Decidua RNA-Seq Transcriptome Alternative splicing Functional interaction network Novel transcriptional active region |
| title | Transcriptome landscape of the human placenta |
| title_full | Transcriptome landscape of the human placenta |
| title_fullStr | Transcriptome landscape of the human placenta |
| title_full_unstemmed | Transcriptome landscape of the human placenta |
| title_short | Transcriptome landscape of the human placenta |
| title_sort | transcriptome landscape of the human placenta |
| topic | Placenta Amnion Chorion Decidua RNA-Seq Transcriptome Alternative splicing Functional interaction network Novel transcriptional active region |
| url | http://www.biomedcentral.com/1471-2164/13/115 |
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