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Related Concept Videos

MicroRNAs01:22

MicroRNAs

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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...
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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...
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Related Experiment Video

Updated: Jun 11, 2025

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
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Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data.

Junpeng Zhang1, Lin Liu2, Xuemei Wei3

  • 1School of Engineering, Dali University, Dali, 671003, Yunnan, China. zjp@dali.edu.cn.

BMC Biology
|September 28, 2024
PubMed
Summary
This summary is machine-generated.

We developed Scan, a framework to identify sample-specific microRNA (miRNA) regulation using RNA sequencing data. Scan integrates multiple methods to improve accuracy in understanding complex diseases at a single-sample resolution.

Keywords:
Bulk RNA-sequencingHuman cancerSample correlation networkSample-specific miRNA regulationSingle-cell RNA-sequencingmRNAmiRNA

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Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • RNA sequencing is crucial for understanding microRNA (miRNA) regulation in diseases like cancer.
  • Existing computational methods identify miRNA regulation across multiple samples.
  • Heterogeneity necessitates single-sample resolution for accurate miRNA regulation inference.

Purpose of the Study:

  • To develop a framework for inferring sample-specific miRNA regulation.
  • To address the need for single-sample resolution in miRNA analysis.
  • To improve understanding of miRNA roles in individual biological samples.

Main Methods:

  • Developed the Scan framework for sample-specific miRNA regulation analysis.
  • Integrated 27 network inference methods and two strategies.
  • Applied to bulk and single-cell RNA sequencing data.
  • Incorporated prior miRNA target information.

Main Results:

  • Scan effectively infers tissue-specific or cell-specific miRNA regulation.
  • Prior information on miRNA targets enhances prediction accuracy.
  • Scan aids in constructing cell/tissue correlation networks and aggregate miRNA regulatory networks.
  • Network inference method performance is data-dependent, requiring optimal selection.

Conclusions:

  • Scan offers a valuable method for inferring sample-specific miRNA regulation from new data.
  • The framework facilitates benchmarking of network inference methods.
  • Scan deepens the understanding of miRNA regulation at the individual sample level.