Related Experiment Video

Updated: May 13, 2026

Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification
08:46

Transcriptome-Wide Profiling of Protein-RNA Interactions by Cross-Linking and Immunoprecipitation Mediated by FLAG-Biotin Tandem Purification

Published on: May 18, 2020

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

Markus Hafner1, Klaas E A Max, Pradeep Bandaru

  • 1Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA.

RNA (New York, N.Y.)
|March 14, 2013
PubMed

Insights

Human LIN28 proteins bind specific RNA sequences, impacting mRNA stability and protein production. They also regulate let-7 miRNA levels by binding precursor molecules.

Area of Science:

  • Molecular Biology
  • Genetics
  • Developmental Biology

Background:

  • LIN28A and LIN28B are conserved RNA-binding proteins (RBPs) crucial for animal development and stem cell reprogramming.
  • Understanding LIN28 binding mechanisms and downstream effects is key to deciphering gene regulation.

Purpose of the Study:

  • To identify direct RNA targets of human LIN28 proteins.
  • To elucidate the functional consequences of LIN28 binding on target mRNA and miRNA abundance.

Main Methods:

  • Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells to map LIN28 binding sites on mRNA.
  • In vitro and in vivo assays to characterize RNA binding preferences and effects on gene expression.

Main Results:

  • Identified approximately 3000 direct mRNA targets of LIN28 proteins, with binding sites primarily in the 3' UTR and CDS.
  • LIN28 preferentially binds uridine-rich single-stranded RNA motifs, capable of disrupting RNA secondary structures.
  • LIN28 binding leads to mild mRNA stabilization and increased protein abundance for target genes.
  • LIN28 negatively regulates specific let-7 miRNA family members by binding their precursors, interfering with miRNA biogenesis.

Conclusions:

  • Human LIN28 proteins are key regulators of mRNA stability, protein production, and miRNA biogenesis.
  • LIN28's RNA-binding specificity and its impact on gene expression highlight its critical role in cellular processes.
  • The findings provide insights into LIN28-mediated post-transcriptional gene regulation and its implications in development and stem cell biology.

More Related Videos

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture10:34

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

Published on: July 22, 2016

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Related Concept Videos

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 addition of a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...
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,...
Regulated mRNA Transport02:22

Regulated mRNA Transport

In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing specific...
Regulated mRNA Transport02:22

Regulated mRNA Transport

In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing specific...