Multiple Alu exonization in 3’UTR of a primate specific isoform of CYP20A1 creates a potential miRNA sponge

Abstract

Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Our study highlights how exonized Alus could nucleate large-scale mRNA-miRNA interactions. Using a functional genomics approach, we characterize a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) that has exonization of 23 Alus in its 3’UTR. CYP20A1_Alu-LT, confirmed by 3’RACE, is an outlier in length (9 kb 3’UTR) and widely expressed. Using publically available datasets, we demonstrate its expression in higher primates and presence in single nucleus RNA-seq of 15928 human cortical neurons. miRanda predicts ∼4700 miRNA recognition elements (MREs) for ∼1000 miRNAs, primarily originated within these 3’UTR-Alus. CYP20A1_Alu-LT could be a potential multi-miRNA sponge as it harbors ≥10 MREs for 140 miRNAs and has cytosolic localization. We further tested whether expression of CYP20A1_Alu-LT correlates with mRNAs harboring similar MRE targets. RNA-seq with conjoint miRNA-seq analysis was done in primary human neurons where we observed CYP20A1_Alu-LT to be downregulated during heat shock response and upregulated in HIV1-Tat treatment. 380 genes were positively correlated with its expression (significantly downregulated in heat shock and upregulated in Tat) and they harbored MREs for nine expressed miRNAs which were also enriched in CYP20A1_Alu-LT. MREs were significantly enriched in these 380 genes compared to random sets of differentially expressed genes (p = 8.134e-12). Gene ontology suggested involvement of these genes in neuronal development and hemostasis pathways thus proposing a novel component of Alu-miRNA mediated transcriptional modulation that could govern specific physiological outcomes in higher primates.

The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology

“…TE-derived RNAs may compete for regulatory molecules with host mRNAs. At least one TE-rich transcript was confirmed to function as an “miRNA sponge” participating in complex gene network regulation [ 283 ].…”

Retrotransposons as Drivers of Mammalian Brain Evolution

“…In particular, the aforementioned ADAR-dependent A-to-I RNA editing (see Section 2.3 ), which has been shown to be widely promoted by Alu inverted repeats in primate transcripts [ 82 ], is thought to be critical for brain development and functions, including their alterations in neurological and neurodegenerative disorders [ 18 , 194 , 195 ]. Exonized Alus within the 3’ UTR have regulatory potential if targeted by miRNAs, as recently shown for a primate-specific isoform of the cytochrome P450 family 20 subfamily A member 1 ( CYP20A1 ) mRNA, whose 3’UTR includes numerous miRNA-targeted Alu sequences acting as miRNA sponges with neuron-specific effects [ 196 ]. Embedded SINEs have also been shown to confer translation regulatory potential to a class of antisense lncRNAs, called SINEUPs, described both in mice and in humans.…”

Dynamic Variations of 3′UTR Length Reprogram the mRNA Regulatory Landscape

“…In this sense, only a few 3 UTR-Alu/miRNA interactions have been confirmed, among them the targeting of double minute 2/4 mRNAs (Mdm2/4) by miR-661 [166], or that of RAD1, GTSE1, NR2C1, FKBP9 and UBE2l by miR-15a-3p and miR302d-3p [116]. Other authors consider that these 3 UTR-Alus could actually work as miRNA sponges [115,167] in a way similar to that proposed for free Alus [168] or other ncRNAs [169].…”