Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs

TLDR

miRNA expression regulation remains largely undefined, although miRNAs are known to be transcribed as primary transcripts that are processed in the nucleus and cytoplasm to yield mature regulatory RNAs. The study aimed to identify the RNA polymerase that transcribes miRNAs and to characterize the full‑length structure of a human pri‑miRNA. We investigated which polymerase transcribes miRNAs and mapped the complete pri‑miR‑21 transcript, revealing it to be capped, polyadenylated, and about 3,433 nucleotides long. Our results show that human pri‑miRNAs are structurally similar to mRNAs, contain promoter and polyadenylation signals, undergo efficient nuclear processing that limits export, and that a 3′‑UTR stem‑loop only modestly suppresses linked protein expression, indicating that pri‑miRNAs can function both as miRNA precursors and as mRNAs.

Abstract

The factors regulating the expression of microRNAs (miRNAs), a ubiquitous family of approximately 22-nt noncoding regulatory RNAs, remain undefined. However, it is known that miRNAs are first transcribed as a largely unstructured precursor, termed a primary miRNA (pri-miRNA), which is sequentially processed in the nucleus, to give the approximately 65-nt pre-miRNA hairpin intermediate, and then in the cytoplasm, to give the mature miRNA. Here we have sought to identify the RNA polymerase responsible for miRNA transcription and to define the structure of a full-length human miRNA. We show that the pri-miRNA precursors for nine human miRNAs are both capped and polyadenylated and report the sequence of the full-length, approximately 3433-nt pri-miR-21 RNA. This pri-miR-21 gene sequence is flanked 5' by a promoter element able to transcribe heterologous mRNAs and 3' by a consensus polyadenylation sequence. Nuclear processing of pri-miRNAs was found to be efficient, thus largely preventing the nuclear export of full-length pri-miRNAs. Nevertheless, an intact miRNA stem-loop precursor located in the 3' UTR of a protein coding gene only moderately inhibited expression of the linked open reading frame, probably because the 3' truncated mRNA could still be exported and expressed. Together, these data show that human pri-miRNAs are not only structurally similar to mRNAs but can, in fact, function both as pri-miRNAs and mRNAs.