Limits...
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.

Show MeSH

Related in: MedlinePlus

Validation of differentially spliced exons between placental and other tissues.(a) Correlation of exon inclusion level differences between placental and HBM2.0 tissues estimated by RNA-Seq (x-axis) and by RT-PCR (y-axis). The dots are color-coded based on the placental compartment to which the values for other tissues were compared. The grey line indicates y = x. Two dashed lines indicate the 0.1 inclusion level difference, which was used to select target exons for validation. (b) Significant enrichment of ESRP1 targets among exons that are differentially spliced between amnion and other tissues. The darker and lighter shades indicate the proportions of exons with and without splicing differences (according to RNA-Seq) between amnion and other tissues, respectively. P-value was determined by Fisher's exact test. (c) An example of ESRP1 target exons differentially spliced in amnion. Shown are a wiggle plot of RNA-Seq read coverage for MINK1 (top) and a gel image of RTPCR products (bottom). Exon inclusion level for each tissue is shown on the top of the gel picture. Star mark in gel picture (c) denotes PCR products of unexpected sizes possibly resulting from the usage of cryptic splice sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3368734&req=5

Figure 6: Validation of differentially spliced exons between placental and other tissues.(a) Correlation of exon inclusion level differences between placental and HBM2.0 tissues estimated by RNA-Seq (x-axis) and by RT-PCR (y-axis). The dots are color-coded based on the placental compartment to which the values for other tissues were compared. The grey line indicates y = x. Two dashed lines indicate the 0.1 inclusion level difference, which was used to select target exons for validation. (b) Significant enrichment of ESRP1 targets among exons that are differentially spliced between amnion and other tissues. The darker and lighter shades indicate the proportions of exons with and without splicing differences (according to RNA-Seq) between amnion and other tissues, respectively. P-value was determined by Fisher's exact test. (c) An example of ESRP1 target exons differentially spliced in amnion. Shown are a wiggle plot of RNA-Seq read coverage for MINK1 (top) and a gel image of RTPCR products (bottom). Exon inclusion level for each tissue is shown on the top of the gel picture. Star mark in gel picture (c) denotes PCR products of unexpected sizes possibly resulting from the usage of cryptic splice sites.

Mentions: To further confirm the RNA-Seq results of exon splicing, we randomly selected 34 exons in total (including the 3 aformentioned exons) for fluorescently labeled RT-PCR. Using an independent set of term placental samples (N = 4) that were not used in the RNA-Seq experiments, we validated the predicted differential splicing events of 27 exons, yielding a validation rate of 79%. The RNA-Seq difference in exon inclusion levels between the placental tissues and the pooled non-placental tissues strongly matched the RT-PCR results (Pearson's correlation coefficient = 0.78) (Figure 6a).


Transcriptome landscape of the human placenta.

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

Validation of differentially spliced exons between placental and other tissues.(a) Correlation of exon inclusion level differences between placental and HBM2.0 tissues estimated by RNA-Seq (x-axis) and by RT-PCR (y-axis). The dots are color-coded based on the placental compartment to which the values for other tissues were compared. The grey line indicates y = x. Two dashed lines indicate the 0.1 inclusion level difference, which was used to select target exons for validation. (b) Significant enrichment of ESRP1 targets among exons that are differentially spliced between amnion and other tissues. The darker and lighter shades indicate the proportions of exons with and without splicing differences (according to RNA-Seq) between amnion and other tissues, respectively. P-value was determined by Fisher's exact test. (c) An example of ESRP1 target exons differentially spliced in amnion. Shown are a wiggle plot of RNA-Seq read coverage for MINK1 (top) and a gel image of RTPCR products (bottom). Exon inclusion level for each tissue is shown on the top of the gel picture. Star mark in gel picture (c) denotes PCR products of unexpected sizes possibly resulting from the usage of cryptic splice sites.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368734&req=5

Figure 6: Validation of differentially spliced exons between placental and other tissues.(a) Correlation of exon inclusion level differences between placental and HBM2.0 tissues estimated by RNA-Seq (x-axis) and by RT-PCR (y-axis). The dots are color-coded based on the placental compartment to which the values for other tissues were compared. The grey line indicates y = x. Two dashed lines indicate the 0.1 inclusion level difference, which was used to select target exons for validation. (b) Significant enrichment of ESRP1 targets among exons that are differentially spliced between amnion and other tissues. The darker and lighter shades indicate the proportions of exons with and without splicing differences (according to RNA-Seq) between amnion and other tissues, respectively. P-value was determined by Fisher's exact test. (c) An example of ESRP1 target exons differentially spliced in amnion. Shown are a wiggle plot of RNA-Seq read coverage for MINK1 (top) and a gel image of RTPCR products (bottom). Exon inclusion level for each tissue is shown on the top of the gel picture. Star mark in gel picture (c) denotes PCR products of unexpected sizes possibly resulting from the usage of cryptic splice sites.
Mentions: To further confirm the RNA-Seq results of exon splicing, we randomly selected 34 exons in total (including the 3 aformentioned exons) for fluorescently labeled RT-PCR. Using an independent set of term placental samples (N = 4) that were not used in the RNA-Seq experiments, we validated the predicted differential splicing events of 27 exons, yielding a validation rate of 79%. The RNA-Seq difference in exon inclusion levels between the placental tissues and the pooled non-placental tissues strongly matched the RT-PCR results (Pearson's correlation coefficient = 0.78) (Figure 6a).

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