MicroRNA genes are transcribed by RNA polymerase II

Abstract

MicroRNAs (miRNAs) constitute a large family of noncoding RNAs that function as guide molecules in diverse gene silencing pathways. Current efforts are focused on the regulatory function of miRNAs, while little is known about how these unusual genes themselves are regulated. Here we present the first direct evidence that miRNA genes are transcribed by RNA polymerase II (pol II). The primary miRNA transcripts (pri-miRNAs) contain cap structures as well as poly(A) tails, which are the unique properties of class II gene transcripts. The treatment of human cells with a-amanitin decreased the level of pri-miRNAs at a concentration that selectively inhibits pol II activity. Furthermore, chromatin immunoprecipitation analyses show that pol II is physically associated with a miRNA promoter. We also describe, for the first time, the detailed structure of a miRNA gene by determining the promoter and the terminator of mir-23aB27aB24-2. These data indicate that pol II is the main, if not the only, RNA polymerase for miRNA gene transcription. Our study offers a basis for understanding the structure and regulation of miRNA genes.

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

“…We speculated that pri-miRNA transcripts would be present in our poly(A) RNA-selected libraries for two reasons. First, a recent report by Kruse et al indicated that mir-1176 and mir-1177 are dependent on RNA polymerase II (RNA Pol II) transcription [30], suggesting that pri-miRNA transcripts in D. discoideum may be polyadenylated as has been demonstrated in animals and plants [4,5,49]. Secondly, the genome of D. discoideum is very AT-rich (about 78%) [26], where long stretches of As are common within transcripts and therefore most likely allow for selection of RNAs with internal poly(A)-tracts.…”

“…In animals and plants, most pri-miRNAs are transcribed by RNA polymerase II [4,5]. This may also be the case for pri-miRNAs in D. discoideum since mir-1176 and mir-1177 disappear in nuclear run-on experiments subjected to α-amanitin treatment [30].…”

“…In order to verify that the 5´-ends of the pri-miRNAs have a bona fide RNA Pol II cap structure, we isolated 7-methyl guanosine (m 7 G)-capped RNAs using variants of the eukaryotic translation initiator factor 4E (elF4E). This protein has high affinity for 5´ m 7 G capped RNA Pol II transcripts and has been used to specifically pull down mRNAs, pri-miRNAs, and non-canonical capped pre-miRNAs from mammalian cells [4,52,53]. …”

“…These small regulatory RNAs guide Argonaute effector proteins to target mRNAs via base-pairing, which in turn leads to destabilization of the target RNA and/or translational inhibition [2,3]. In both plants and animals, most miRNAs derive from stem-loop structures embedded in primary RNA (pri-RNA) transcribed by RNA polymerase II (Pol II) [4,5]. …”

MicroRNAs in glioblastoma multiforme pathogenesis and therapeutics

“…1) 4. Each pri‐miRNA folds into a stem‐loop structure via intramolecular base pairing 5 and is then cleaved by the microprocessor complex, which consists of Drosha and DGCR8.…”