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Transcriptome landscape of the human placenta.

Kim J, Zhao K, Jiang P, Lu ZX, Wang J, Murray JC, Xing Y - BMC Genomics (2012)

Bottom Line: 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.Importantly, genes with differential expression or splicing in the placenta are significantly enriched for genes implicated in placental abnormalities and preterm birth.These data are publicly available providing the community with a rich resource for placental physiology and disease-related studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA52242, USA.

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.

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Examples of exons with splicing differences between placental and HBM2.0 tissues. (a) Exon ENSE00000882762 in ITGA6. (b) Exon ENSE00001385284 in ITGB4. (c) Exon ENSE00000736978 in TCIRG1. Shown on the left-hand side are wiggle plots of RNA-Seq read coverage and RT-PCR gel images for validation of differential splicing events generated for placental and HBM2.0 tissues. UJC, DJC, and SJC indicate upstream, downstream, and skipping junction counts, respectively. Star mark in (c) indicates an additional alternatively spliced product detected by using the given primer pairs. Represented on the right-hand side are histograms showing exon inclusion levels obtained from RNA-Seq (blue bar) and RT-PCR (red bar) experiments. The values represented by red bars correspond to the numbers shown on the top of the gel pictures.
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Figure 5: Examples of exons with splicing differences between placental and HBM2.0 tissues. (a) Exon ENSE00000882762 in ITGA6. (b) Exon ENSE00001385284 in ITGB4. (c) Exon ENSE00000736978 in TCIRG1. Shown on the left-hand side are wiggle plots of RNA-Seq read coverage and RT-PCR gel images for validation of differential splicing events generated for placental and HBM2.0 tissues. UJC, DJC, and SJC indicate upstream, downstream, and skipping junction counts, respectively. Star mark in (c) indicates an additional alternatively spliced product detected by using the given primer pairs. Represented on the right-hand side are histograms showing exon inclusion levels obtained from RNA-Seq (blue bar) and RT-PCR (red bar) experiments. The values represented by red bars correspond to the numbers shown on the top of the gel pictures.

Mentions: In order to boost the power of RNA-Seq splicing analysis and obtain a robust set of splicing differences between the placental and non-placental tissues, we pooled the RNA-Seq data of all HBM2.0 tissues. We then compared the pooled data to that of each placental tissue. We identified 393, 637, and 402 differentially spliced exons (in 275, 464, and 289 genes) when comparing the pooled non-placental tissues to amnion, chorion, and decidua, respectively (Figure 4b). 129 exons (in 76 genes) were shared among the three placental tissues. On the other hand, the majority (74%) of differentially spliced exons identified were restricted to only one of the three placental tissues as compared to the non-placental tissues (Figure 4b). Importantly, among the 744 genes containing differentially spliced exons between placental and non-placental tissues, we observed a significant enrichment for genes in the MGI list (2.8% over 1.4% for the genome background, p = 0.001 based on Fisher's exact test), indicating the importance of tissue-specific AS in placental function and development. For example, one of these exons (ENSE00000882762) was in integrin, alpha 6 (ITGA6), which forms heterodimers with other integrin components and plays a crucial role in cell adhesion and migration [49,50]. We observed a high inclusion level of this exon in amnion and chorion compared to most of the other tissues, with close to 100% exon inclusion in amnion as validated by fluorescently labeled RT-PCR (Figure 5a). Exon (ENSE00001385284) in another integrin gene ITGB4 was frequently skipped in the placental tissues (Figure 5b). TCIRG1 (T-cell, immune regulator 1, ATPase, H + transporting, lysosomal V0 subunit A3) is another differentially spliced gene with multiple known isoforms produced by AS [51,52]. As shown in Figure 5c, the inclusion level of one of its exons (ENSE00000736978) was significantly lower in amnion.


Transcriptome landscape of the human placenta.

Kim J, Zhao K, Jiang P, Lu ZX, Wang J, Murray JC, Xing Y - BMC Genomics (2012)

Examples of exons with splicing differences between placental and HBM2.0 tissues. (a) Exon ENSE00000882762 in ITGA6. (b) Exon ENSE00001385284 in ITGB4. (c) Exon ENSE00000736978 in TCIRG1. Shown on the left-hand side are wiggle plots of RNA-Seq read coverage and RT-PCR gel images for validation of differential splicing events generated for placental and HBM2.0 tissues. UJC, DJC, and SJC indicate upstream, downstream, and skipping junction counts, respectively. Star mark in (c) indicates an additional alternatively spliced product detected by using the given primer pairs. Represented on the right-hand side are histograms showing exon inclusion levels obtained from RNA-Seq (blue bar) and RT-PCR (red bar) experiments. The values represented by red bars correspond to the numbers shown on the top of the gel pictures.
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Related In: Results  -  Collection

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Figure 5: Examples of exons with splicing differences between placental and HBM2.0 tissues. (a) Exon ENSE00000882762 in ITGA6. (b) Exon ENSE00001385284 in ITGB4. (c) Exon ENSE00000736978 in TCIRG1. Shown on the left-hand side are wiggle plots of RNA-Seq read coverage and RT-PCR gel images for validation of differential splicing events generated for placental and HBM2.0 tissues. UJC, DJC, and SJC indicate upstream, downstream, and skipping junction counts, respectively. Star mark in (c) indicates an additional alternatively spliced product detected by using the given primer pairs. Represented on the right-hand side are histograms showing exon inclusion levels obtained from RNA-Seq (blue bar) and RT-PCR (red bar) experiments. The values represented by red bars correspond to the numbers shown on the top of the gel pictures.
Mentions: In order to boost the power of RNA-Seq splicing analysis and obtain a robust set of splicing differences between the placental and non-placental tissues, we pooled the RNA-Seq data of all HBM2.0 tissues. We then compared the pooled data to that of each placental tissue. We identified 393, 637, and 402 differentially spliced exons (in 275, 464, and 289 genes) when comparing the pooled non-placental tissues to amnion, chorion, and decidua, respectively (Figure 4b). 129 exons (in 76 genes) were shared among the three placental tissues. On the other hand, the majority (74%) of differentially spliced exons identified were restricted to only one of the three placental tissues as compared to the non-placental tissues (Figure 4b). Importantly, among the 744 genes containing differentially spliced exons between placental and non-placental tissues, we observed a significant enrichment for genes in the MGI list (2.8% over 1.4% for the genome background, p = 0.001 based on Fisher's exact test), indicating the importance of tissue-specific AS in placental function and development. For example, one of these exons (ENSE00000882762) was in integrin, alpha 6 (ITGA6), which forms heterodimers with other integrin components and plays a crucial role in cell adhesion and migration [49,50]. We observed a high inclusion level of this exon in amnion and chorion compared to most of the other tissues, with close to 100% exon inclusion in amnion as validated by fluorescently labeled RT-PCR (Figure 5a). Exon (ENSE00001385284) in another integrin gene ITGB4 was frequently skipped in the placental tissues (Figure 5b). TCIRG1 (T-cell, immune regulator 1, ATPase, H + transporting, lysosomal V0 subunit A3) is another differentially spliced gene with multiple known isoforms produced by AS [51,52]. As shown in Figure 5c, the inclusion level of one of its exons (ENSE00000736978) was significantly lower in amnion.

Bottom Line: 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.Importantly, genes with differential expression or splicing in the placenta are significantly enriched for genes implicated in placental abnormalities and preterm birth.These data are publicly available providing the community with a rich resource for placental physiology and disease-related studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA52242, USA.

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.

Show MeSH
Related in: MedlinePlus