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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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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.
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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 interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways.

Jae Hoon Bahn1, Jaegyoon Ahn1, Xianzhi Lin1

  • 1Department of Integrative Biology and Physiology and the Molecular Biology Institute, Los Angeles, California, 90095.

Nature Communications
|March 10, 2015
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Summary

Adenosine deaminases acting on RNA 1 (ADAR1) binds to thousands of RNA sites beyond Alu repeats. This interaction regulates gene expression by affecting 3' UTR usage and microRNA maturation.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Adenosine deaminases acting on RNA (ADARs) mediate adenosine to inosine (A-to-I) RNA editing in metazoans.
  • ADAR1 is a key enzyme in this process, but its global RNA interactions are not fully understood.

Purpose of the Study:

  • To investigate the global interaction landscape of ADAR1 with RNA in human cells.
  • To identify novel functional targets and regulatory roles of ADAR1 beyond its known editing functions.

Main Methods:

  • Utilized individual-nucleotide resolution cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) to map ADAR1-RNA interactions genome-wide.
  • Analyzed CLIP-seq data to identify binding sites in both repetitive elements (Alu repeats) and non-repetitive regions.

Main Results:

  • Confirmed ADAR1 binding to Alu repeats, consistent with its role in RNA editing.
  • Discovered thousands of ADAR1 binding sites in non-Alu regions, implicating ADAR1 in regulating alternative 3' UTR usage and microRNA (miRNA) biogenesis.
  • Demonstrated that ADAR1 binding to 3' UTRs can block other protein binding, leading to 3' UTR lengthening.
  • Showed ADAR1 interacts with DROSHA and DGCR8, potentially enhancing mature miRNA expression by influencing primary miRNA binding.

Conclusions:

  • ADAR1 possesses broader functions than previously recognized, extending beyond canonical A-to-I editing.
  • ADAR1 plays significant roles in post-transcriptional gene regulation, including alternative 3' UTR usage and miRNA processing.
  • These newly identified functions are, at least partially, dependent on ADAR1's enzymatic editing activity.