Related Experiment Video

Updated: Apr 5, 2026

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
07:23

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

9.0K

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

Tsung-Cheng Chang1, Mihaela Pertea2, Sungyul Lee1

  • 1Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA;

Genome Research
|August 21, 2015
PubMed

Insights

Researchers developed a novel method to map microRNA (miRNA) primary transcripts, significantly improving the understanding of miRNA gene organization and regulation in mammals. This work enhances the annotation of miRNA encoding genes.

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • MicroRNA (miRNA) expression is crucial for biological processes, but understanding its regulation is limited by incomplete primary miRNA (pri-miRNA) transcript annotation.
  • Most pri-miRNAs are long, low-abundance noncoding RNAs, poorly detected in standard RNA sequencing and transcriptome assemblies.
  • The endoribonuclease DROSHA initiates miRNA biogenesis by processing pri-miRNAs, making these transcripts challenging to study.

Purpose of the Study:

  • To develop an experimental and computational approach for genome-wide detection and mapping of pri-miRNA structures.
  • To overcome limitations in current RNA-seq data and transcriptome assemblies for pri-miRNA characterization.
  • To provide a comprehensive resource for studying mammalian miRNA gene organization and regulation.

Main Methods:

  • Utilized deep RNA sequencing in cells engineered with dominant-negative DROSHA to enhance pri-miRNA transcript coverage.
  • Developed a computational pipeline for accurate assembly and validation of pri-miRNA transcripts.
  • Applied the approach to human and mouse cell lines for large-scale pri-miRNA mapping.

Main Results:

  • Achieved significantly greater coverage of pri-miRNA transcripts compared to standard RNA-seq.
  • Generated highly accurate pri-miRNA assemblies for a substantial number of human and mouse miRNAs.
  • Identified 1291/1871 human and 888/1181 mouse pri-miRNA structures, including many outside protein-coding genes.
  • Uncovered novel regulatory mechanisms, such as links between pri-miRNAs and distant genes, alternative splicing, and polycistronic transcripts.

Conclusions:

  • The developed method dramatically expands the understanding of mammalian miRNA gene organization.
  • Provides a valuable resource for the study of miRNA regulation and its role in physiology and pathophysiology.
  • Highlights new potential regulatory mechanisms influencing miRNA expression.

More Related Videos

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis10:40

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis

Published on: April 25, 2022

3.0K
A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells06:48

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

Published on: June 16, 2022

2.5K

Related Concept Videos

MicroRNAs01:22

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...
24.7K
MicroRNAs01:22

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...
4.3K
MicroRNAs01:22

MicroRNAs

12.1K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
1.5K
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
8.5K
Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
828