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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 the pre-miRNA...
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 ends...
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 ends...

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Related Experiment Video

Updated: May 8, 2026

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis
10:40

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis

Published on: April 25, 2022

Reconstructing dynamic microRNA-regulated interaction networks.

Marcel H Schulz1, Kusum V Pandit, Christian L Lino Cardenas

  • 1Ray and Stephanie Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

Proceedings of the National Academy of Sciences of the United States of America
|August 30, 2013
PubMed
Summary
This summary is machine-generated.

We developed mirDREM, a novel method to uncover dynamic gene regulation by microRNAs (miRNAs) and transcription factors. This approach identified key regulatory miRNAs during lung development and revealed links to idiopathic pulmonary fibrosis.

Keywords:
network modelingsystems biology

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Genome-wide Analysis of HDAC Inhibitor-mediated Modulation of microRNAs and mRNAs in B Cells Induced to Undergo Class-switch DNA Recombination and Plasma Cell Differentiation

Published on: September 20, 2017

Area of Science:

  • Molecular Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Gene expression regulation by microRNAs (miRNAs) is crucial but dynamic processes are difficult to capture.
  • Existing methods for miRNA target identification often neglect temporal dynamics, missing key regulatory interactions.
  • Understanding dynamic gene regulation is essential for deciphering complex biological processes and diseases.

Purpose of the Study:

  • To develop a novel computational method, MIRna Dynamic Regulatory Events Miner (mirDREM), for reconstructing dynamic gene regulatory networks.
  • To apply mirDREM to analyze temporal gene expression data during mouse lung development.
  • To identify novel miRNA-mediated regulatory mechanisms in lung development and their potential links to idiopathic pulmonary fibrosis.

Main Methods:

  • Developed mirDREM, a probabilistic model utilizing input-output hidden Markov models to infer dynamic regulatory networks.
  • Measured time-series miRNA and mRNA expression data during postnatal mouse lung development.
  • Integrated sequence information with temporal expression data for network reconstruction.

Main Results:

  • The reconstructed dynamic network accurately identified known regulatory miRNAs and transcription factors involved in lung development.
  • mirDREM predicted novel miRNAs and their specific roles in distinct developmental phases, with experimental validation.
  • Identified significant links between lung development miRNAs and those dysregulated in idiopathic pulmonary fibrosis, validated through proliferation assays.

Conclusions:

  • mirDREM is an effective tool for dissecting dynamic gene regulatory networks, particularly miRNA-mediated regulation.
  • The study provides novel insights into the temporal control of gene expression during lung development.
  • Findings suggest a potential link between lung differentiation pathways and idiopathic pulmonary fibrosis pathogenesis, opening new avenues for research.