FUNCTIONAL MAPPING OF NON-CODING RNA-MEDIATED GENE REGULATION IN DEVELOPMENT

Abstract

A new class of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have become essential regulators of gene expression in developmental processes. They tune transcriptional and post-transcriptional pathways of action using various cis- and trans-acting pathways, cellular differentiation, tissue specifications, and organogenesis. Although a lot of progress has been made, the overall functional mapping of ncRNA-mediated regulatory networks in development has not been done. This paper will set out to systematize the regulatory functions of ncRNAs by combining multi-omics data and computational strategies. The data of high-throughput RNA sequencing (RNA-seq) were processed to determine differentially expressed ncRNAs in various development stages. This was followed by the use of interaction prediction models and network-based predictions to create ncRNA-mRNA regulatory networks, differentiating between local (cis) and distal (trans) regulatory interactions. Functional enrichment studies were done to explain the biological pathways related to important ncRNAs. The findings show a multifaceted and dynamic landscape of ncRNAmediated regulation, with multiple hub lncRNAs and miRNAs, which have critical roles in developmental signaling cascades, including cell differentiation, proliferation, and morphogenesis. Network analysis also shows that ncRNAs are important modulators in gene regulatory pathways, and that they put forward the coordination of various gene expression layers. Conclusively, ncRNAs play a role in developmental gene regulation in multifaceted and hierarchical ways. The integrative model developed in this paper offers important insights on the ncRNA role, and forms the basis of future studies in developmental biology, disease modeling, and precision
medicine.