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Eukaryotic RNA Polymerases

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...

Eukaryotic RNA Polymerases

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

MicroRNAs

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...

Transcription Initiation

Transcription Initiation

Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...

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Updated: Jul 18, 2026

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

RNA polymerase III transcribes human microRNAs.

Glen M Borchert¹, William Lanier, Beverly L Davidson

¹Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA.

Nature Structural & Molecular Biology

|November 14, 2006

Summary

MicroRNA (miRNA) expression typically uses RNA polymerase II (Pol II). This study reveals that some human miRNAs, particularly in the C19MC cluster, are transcribed by RNA polymerase III (Pol III), challenging previous assumptions.

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Area of Science:

Molecular Biology
Genomics
Epigenetics

Background:

Mammalian microRNA (miRNA) biogenesis is generally understood to be dependent on RNA polymerase II (Pol II).
The transcriptional requirements for a significant number of miRNAs have not been fully elucidated.
The human chromosome 19 miRNA cluster (C19MC) contains miRNAs interspersed within Alu repetitive elements.

Purpose of the Study:

To investigate the transcriptional machinery responsible for the expression of miRNAs within the human C19MC.
To determine whether RNA polymerase III (Pol III) is involved in the transcription of C19MC miRNAs, given their association with Alu elements.

Main Methods:

Genomic analysis of miRNA sequences within the C19MC.
Chromatin immunoprecipitation assays to identify associated polymerases.
Cell-free transcription assays to assess polymerase activity.

Main Results:

Alu elements upstream of C19MC miRNAs contain sequences critical for Pol III activity.
Chromatin immunoprecipitation and transcription assays demonstrated that Pol III, not Pol II, is associated with C19MC miRNA genomic regions and drives their transcription.
Approximately 50 additional human miRNAs were identified within repetitive elements, including Alu sequences.

Conclusions:

The findings indicate that Pol III is the primary polymerase for transcribing certain human miRNAs, particularly those in the C19MC.
This expands the known mechanisms of miRNA gene regulation and identifies a novel role for Pol III in miRNA biogenesis.
A significant portion of human miRNAs may originate from repetitive elements, utilizing Pol III for their expression.