Profiling the small non-coding RNA transcriptome of the human placenta

Abstract

Proper functioning of the human placenta is critical for maternal and fetal health. While microRNAs (miRNAs) are known to impact placental gene expression, the effects of other small non-coding RNAs (sncRNAs) on the placental transcriptome are not well-established, and are emerging topics in the study of environmental influence on fetal development and reproductive health. Here, we assembled a cohort of 30 placental chorionic villi samples of varying gestational ages (M ± SD = 23.7 ± 11.3 weeks) to delineate the human placental sncRNA transcriptome through small RNA sequence analysis. We observed expression of 1544 sncRNAs, which include 48 miRNAs previously unannotated in humans. Additionally, 18,003 miRNA variants (isomiRs) were identified from the 654 observed miRNA species. This characterization of the term and pre-term placental sncRNA transcriptomes provides data fundamental to future investigations of their regulatory functions in the human placenta, and the baseline expression pattern needed for identifying changes in response to environmental factors, or under disease conditions.

Small Non-Coding RNAs in the Human Placenta: Regulatory Roles and Clinical Utility

“…The role of sncRNAs has been extensively researched in various cancer subtypes, with several studies showing their expression levels to be altered in malignant tissue ( Ferreira and Esteller 2018 ). SncRNA transcriptome profiling of placentas ranging from early gestation to term revealed that microRNAs (miRNAs) were the most abundant sncRNA species, followed by Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), and finally transfer RNAs (tRNAs) ( Martinez et al, 2021a ). SncRNA species are potential disease biomarkers or clinically actionable targets—for example, miRNA hsa-miR-16 can directly downregulate the VEGF gene, which is vital in establishing and maintaining the placental vasculature, by binding specifically to its 3’ untranslated region (UTR) ( Zhu et al, 2016 ).…”

Visual Analytics for Robust Investigations of Placental Aquaporin Gene Expression in Response to Maternal SARS-CoV-2 Infection

“…Maternal viral infection, such as infection of the enveloped ribonucleic acid (RNA) single-stranded Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), during pregnancy is a risk factor for pregnancy complications, neonatal and fetal complications, and long-term health issues [4,5]. Placental gene expression profiling (placental transcriptomics) studies have revealed evidence of differential expression at different stages of a placenta's development, physiology, and pathology [6][7][8][9][10]. Typically, genes are categorized into gene families or gene groups based on a variety of characteristics, including shared protein sequences and function [11].…”