Transcriptome profile of the human placenta

Abstract

The human placenta is a particular organ that inseparably binds the mother and the fetus. The proper development and survival of the conceptus relies on the essential interplay between maternal and fetal factors involved in cooperation within the placenta. In our study, high-throughput sequencing (RNA-seq) was applied to analyze the global transcriptome of the human placenta during uncomplicated pregnancies. The RNA-seq was utilized to identify the global pattern of the gene expression in placentas (N = 4) from women in single and twin pregnancies. During analyses, we obtained 228,044 transcripts. More than 91% of them were multi-exon, and among them 134 were potentially unknown protein coding genes. Expression levels (FPKM) were estimated for 38,948 transcriptional active regions, and more than 3000 of genes were expressed with FPKM >20 in each sample. Additionally, all unannotated transcripts with estimated FPKM values were localized on the human genome. Highly covered splice junctions unannotated in the human genome (6497) were identified, and among them 30 were novel. To gain a better understanding of the biological implications, the assembled transcripts were annotated with gene ontology (GO) terms. Single nucleotide variants were predicted for the transcripts assigned to each analyzed GO category. Our results may be useful for establishing a general pattern of the gene expression in the human placenta. Characterizing placental transcriptome, which is crucial for a pregnancy’s outcome, can serve as a basis for identifying the mechanisms underlying physiological pregnancy, as well as may be useful for an early detection of the genomic defects.Electronic supplementary materialThe online version of this article (doi:10.1007/s10142-017-0555-y) contains supplementary material, which is available to authorized users.

De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.)

“…The top represented GO terms within the biological process, molecular function and cellular component GO category were transcription, DNA-templated, binding function of ATP and integral component of membrane, respectively. In similar studies, concerning the general landscape of the human placental transcriptome (Majewska et al 2017 ), overrepresented GO terms are convergent with the annotations generated in our study. Some differences in gene number assigned to each GO category may indicate interspecies variability of placenta physiology at a molecular level.…”

“…Differences in placental physiology between eutherians may be an adaptation to diversified reproductive strategies (Knox and Baker 2008 ). Our data fit into trends concerning studies of tissue-specific expression (Bogacka et al 2017 ; Majewska et al 2017 ; Lipka et al 2017b ). The availability of RNA-Seq data from multiple studies in the SRA database create the possibility to compare results from different tissues, physiological conditions or various species (Hou et al 2012 ).…”

“…2 ), as well as splice variants identified in beaver placenta (Fig. 6 ), may contribute to embryo development and pregnancy maintenance, as was previously described for human placenta (Soleymanlou et al 2005 ; Majewska et al 2017 ).…”

“…Physiological development and proper function of the placenta are under influence of sophisticated pathways related with expression of substantial genes throughout pregnancy. Therefore, any alterations affecting gene expression or posttranslational modification may lead to disorders manifested in pregnancy disorders (Majewska et al 2017 ). Studies of the transcriptome provide knowledge concerning placental evolution and create the opportunity to define specific, common genes engaged in reproductive physiology in eutherians (Hou et al 2012 ; Carter 2018 ).…”

“…The placenta is a key component required for pregnancy maintenance. Characterizing genes crucial for placental development can serve as a basis for identifying mechanisms underlying effective reproduction (Majewska et al 2017 ). Detailing the beaver placental transcriptome may provide a valuable genetic resource required for founding stock selection.…”