Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon–Intron Split Analysis (EISA)

Abstract

Epithelial–mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate ‘indirect’ miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon–Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.

Post-transcriptional Gene Regulation by MicroRNA-194 Promotes Neuroendocrine Transdifferentiation in Prostate Cancer

“…Exon Intron Split analysis (EISA) was performed as described previously (Pillman et al, 2019). To refine the miR-194 targetome, only post-transcriptionally downregulated genes (i.e., genes with log2FC(dExon-dIntron) < 0) and a FDR cutoff of 0.05) were considered as targets.…”

MicroRNA-194 promotes lineage plasticity in advanced prostate cancer

“…Exon Intron Split analysis (EISA) was performed as described previously (24). To refine the miR-194 targetome, only post-transcriptionally downregulated genes (i.e.…”

Modeling microRNA-driven post-transcriptional regulation by using exon-intron split analysis (EISA) in pigs

“…Several studies have addressed the effects of transcriptionally and post-transcriptionally perturbed genes in expression datasets [8][9][10] or how transcriptional dynamics can reflect the cellular transition between homeostasis and stress-induced responses or differentiation stages [11][12][13][14]. In an attempt to capture both regulatory components based on expression data, Gaidatzis et al [8] described the use of intronic mapping sequences as direct indicators of primary mRNA oscillations related to transcriptional activation.…”

“…Besides, the posttranscriptional effect was defined as a function of the expressed exonic and intronic fraction for each gene. Modelling the exonic and intronic contribution to gene expression changes between conditions, these and other authors could discern transcriptional and post-transcriptional responses within co-expressed mRNAs and their corresponding putative regulators [8][9][10]18]. Nevertheless, despite these promising results, the use of such methodologies to identify relevant regulatory effects in high throughput experiments is still limited.…”

“…We applied EISA analyses differentiate gene expression regulation based on transcriptional and post-transcriptional effects [8][9][10]. To this end, the exonic/intronic abundance of each annotated mRNA gene was estimated by separately assigning mapping reads from RNA-Seq data sets using Sscrofa11.1 v103 exon/intron custom annotation ranges previously generated.…”