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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...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Small interfering RNAs (siRNA)02:30

Small interfering RNAs (siRNA)

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: Jun 4, 2026

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay
12:49

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

Isoform-level microRNA-155 target prediction using RNA-seq.

Nan Deng1, Adriane Puetter, Kun Zhang

  • 1Department of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.

Nucleic Acids Research
|February 15, 2011
PubMed
Summary

This study introduces an isoform-level approach for microRNA target prediction, improving accuracy by analyzing RNA sequencing data. The method effectively identifies novel microRNA targets, including those on non-dominant isoforms, advancing computational biology.

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Related Experiment Videos

Last Updated: Jun 4, 2026

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay
12:49

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library
08:40

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Published on: April 6, 2012

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
09:29

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

Area of Science:

  • Computational biology
  • Genomics
  • Molecular biology

Background:

  • MicroRNA target prediction is challenging, with current methods primarily focusing on gene-level analysis.
  • RNA sequencing data offers new opportunities for microRNA target prediction at the isoform level.

Purpose of the Study:

  • To develop and validate an isoform-level computational approach for microRNA target prediction.
  • To identify novel microRNA targets and their targeting regions, including those on non-dominant isoforms.

Main Methods:

  • Utilized an iterative expectation maximization (EM) algorithm for isoform-level transcriptome quantification.
  • Employed joint evidence from isoform-level down-regulation and seed enrichment for microRNA-155 target prediction.
  • Validated predictions using in vitro 3'-UTR assays and augmented splicing databases with exon-exon junction evidence.

Main Results:

  • The EM algorithm demonstrated effective transcriptome quantification in simulation studies.
  • Successfully predicted 51 novel microRNA-155 isoform targets, validated by in vitro assays.
  • Identified and quantified 1572 novel cell line-specific isoforms.

Conclusions:

  • Isoform-level analysis is crucial for accurate microRNA target prediction, revealing targets missed by gene-level approaches.
  • The developed computational method advances the field of microRNA target prediction by incorporating isoform-specific information.
  • This study pioneers isoform-level microRNA target prediction, offering a more comprehensive understanding of microRNA function.