Related Experiment Video

Updated: Nov 23, 2025

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells
06:48

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

Published on: June 16, 2022

2.2K

Bulges control pri-miRNA processing in a position and strand-dependent manner

Shaohua Li1, Thi Nhu-Y Le1, Trung Duc Nguyen1

  • 1Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China.

RNA Biology
|December 31, 2020
PubMed

Insights

Bulges in primary microRNA (pri-miRNA) structures are crucial for accurate processing by the Microprocessor complex. Specific bulges, like midB, enhance microRNA (miRNA) production by orienting DROSHA, improving gene expression regulation.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • MicroRNAs (miRNAs) regulate gene expression and are implicated in various human diseases.
  • The biogenesis of miRNAs depends on the processing of primary miRNA (pri-miRNA) transcripts by the Microprocessor complex, comprising DROSHA and DGCR8.
  • Understanding pri-miRNA processing is key to deciphering miRNA biogenesis and its regulatory roles.

Purpose of the Study:

  • To investigate the role of bulges within pri-miRNA secondary structures in the processing activity of the Microprocessor complex.
  • To determine how bulges influence the efficiency and accuracy of pri-miRNA cleavage.
  • To elucidate the mechanism by which specific bulges, such as midB, affect DROSHA orientation and subsequent miRNA production.

Main Methods:

  • Analysis of high-throughput pri-miRNA processing assays.
  • Examination of pri-miRNA secondary structures.
  • Investigating the positional and strand-dependent effects of bulges on Microprocessor activity.
  • Characterizing the function of conserved bulges (midB) in DROSHA orientation.

Main Results:

  • Bulges at various positions within pri-miRNAs significantly control both the efficiency and accuracy of Microprocessor-mediated cleavage.
  • These bulges exert their effects on the Microprocessor complex, specifically interacting with the catalytic subunit DROSHA.
  • The function of bulges is dependent on their position and the strand of the pri-miRNA.
  • Enriched and conserved bulges, termed midB, were found to correct DROSHA orientation on pri-miRNAs, leading to enhanced miRNA production.

Conclusions:

  • Bulges within pri-miRNA structures are critical regulatory elements in miRNA biogenesis.
  • The position and sequence context of bulges dictate their impact on DROSHA-DGCR8 processing.
  • The midB bulge represents a novel mechanism for enhancing miRNA production by optimizing DROSHA engagement.
  • These findings provide a deeper understanding of pri-miRNA processing and highlight potential targets for miRNA biogenesis regulation.
Keywords:
BulgesDGCR8DROSHAMicroprocessormiRNA biogenesis

More Related Videos

mirMachine: A One-Stop Shop for Plant miRNA Annotation06:16

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

2.8K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

6.9K

Related Concept Videos

pre-mRNA Processing02:01

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
55.8K
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...
7.7K
Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
13.0K
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...
23.3K
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...
3.4K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
11.3K