[Show abstract][Hide abstract] ABSTRACT: To characterize the genetic variation of alternative splicing, we develop GLiMMPS, a
robust statistical method for detecting splicing quantitative trait loci (sQTLs) from
RNA-seq data. GLiMMPS takes into account the individual variation in sequencing
coverage and the noise prevalent in RNA-seq data. Analyses of simulated and real
RNA-seq datasets demonstrate that GLiMMPS outperforms competing statistical models.
Quantitative RT-PCR tests of 26 randomly selected GLiMMPS sQTLs yielded a validation
rate of 100%. As population-scale RNA-seq studies become increasingly affordable and
popular, GLiMMPS provides a useful tool for elucidating the genetic variation of
alternative splicing in humans and model organisms.
[Show abstract][Hide abstract] ABSTRACT: Tables S1 and S2 and Figures S1-3 Supplemental Table S1. Mapping statistics of RNA-Seq data from placenta and HBM2.0 tissues. Supplemental Table S2. Distribution of gene expression level (FPKM) of RNA-Seq data from placenta and HBM2.0 tissues. Figure S1. Distribution of gene expression values (FPKM) for all tissues examined in the study. Figure S2. qRT-PCR validation of placenta-enriched SFs ESRP1 and MBNL3. Figure S3. Functional interaction network analysis of genes with enriched expression (EE) and differential splicing (DS) that intersect all three placental tissues: module 2. Circular node: a query gene. Diamond-shaped node: a linker gene. Node color was determined based on whether the query gene shows EE (green), DS (pink), or both (red). The most significantly enriched pathways were highlighted in bigger node size: integrin signaling pathway and ECM-receptor interaction pathway.
[Show abstract][Hide abstract] ABSTRACT: 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.
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.
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.