Preliminary RNA-Seq Analysis of Long Non-Coding RNAs Expressed in Human Term Placenta

Abstract

Development of particular structures and proper functioning of the placenta are under the influence of sophisticated pathways, controlled by the expression of substantial genes that are additionally regulated by long non-coding RNAs (lncRNAs). To date, the expression profile of lncRNA in human term placenta has not been fully established. This study was conducted to characterize the lncRNA expression profile in human term placenta and to verify whether there are differences in the transcriptomic profile between the sex of the fetus and pregnancy multiplicity. RNA-Seq data were used to profile, quantify, and classify lncRNAs in human term placenta. The applied methodology enabled detection of the expression of 4463 isoforms from 2899 annotated lncRNA loci, plus 990 putative lncRNA transcripts from 607 intergenic regions. Those placentally expressed lncRNAs displayed features such as shorter transcript length, longer exon length, fewer exons, and lower expression levels compared to messenger RNAs (mRNAs). Among all placental transcripts, 175,268 were classified as mRNAs and 15,819 as lncRNAs, and 56,727 variants were discovered within unannotated regions. Five differentially expressed lncRNAs (HAND2-AS1, XIST, RP1-97J1.2, AC010084.1, TTTY15) were identified by a sex-bias comparison. Splicing events were detected within 37 genes and 4 lncRNA loci. Functional analysis of cis-related potential targets for lncRNAs identified 2021 enriched genes. It is presumed that the obtained data will expand the current knowledge of lncRNAs in placenta and human non-coding catalogs, making them more contemporary and specific.

Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

“…These lncRNAs were characterized by shorter transcript length, longer exons, lower estimated number of exons and lower expression levels. These properties were also observed in other reported lncRNAs within the genome [20,[35][36][37].…”

LncRNA de novo discovery reveals noncoding RNAs as major molecular mechanism associating coronary artery disease GWAS variants with causal genes to confer disease risk

“…In addition, they are usually smaller than mRNAs, for example, one study showed that lncRNA exhibit an average length of 1900 nt and that more than 30% of lncRNAs are in the range of 500-1000 nt. (Majewska et al 2018). Similarly, this study shows that lncRNA contain lower number of exons, as 38% of lncRNAs possess only 2 exons, while only 0.31% of lncRNAs had over 10 exons (Majewska et al 2018).…”

“…(Majewska et al 2018). Similarly, this study shows that lncRNA contain lower number of exons, as 38% of lncRNAs possess only 2 exons, while only 0.31% of lncRNAs had over 10 exons (Majewska et al 2018). In GENCODE v7 database, 42% of lncRNAs have two exons compared with 6% of protein-coding genes, while the median length equals 592 bp compared with 2453bp for protein-coding transcript (Derrien et al 2012).…”

Preeclampsia-Associated lncRNA INHBA-AS1 Regulates the Proliferation, Invasion, and Migration of Placental Trophoblast Cells

“…One of the major functions of lncRNAs is to recruit/inhibit transcription factors (TFs) to the promoter of their targeting genes. 40 , 41 Although the transcriptome sequencing has revealed a large number of lncRNAs in normal human placenta, 42 we do not know to what extent the lncRNAs might be involved in PE. In order to search for lncRNAs involved in PE, our group has recently carried out a transcriptome sequencing on placentae from patients with early-onset severe PE (EOSPE) and normal controls and identified 383 lncRNAs differentially expressed.…”