Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables

Edoardo Giacopuzzi, Massimo Gennarelli, Chiara Sacco, Alice Filippini, Jessica Mingardi, Chiara Magri, Alessandro Barbon

Research output: Contribution to journalArticle

Abstract

Background: A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing contributes to generate transcriptomic diversity and it is found altered in cancer, autoimmune and neurological disorders. Emerging evidences indicate that editing process could be influenced by genetic variations, biological and environmental variables. Results: We analyzed RNA editing levels in human blood using RNA-seq data from 459 healthy individuals and identified 2079 sites consistently edited in this tissue. As expected, analysis of gene expression revealed that ADAR is the major contributor to editing on these sites, explaining ~ 13% of observed variability. After removing ADAR effect, we found significant associations for 1122 genes, mainly involved in RNA processing. These genes were significantly enriched in genes encoding proteins interacting with ADARs, including 276 potential ADARs interactors and 9 ADARs direct partners. In addition, our analysis revealed several factors potentially influencing RNA editing in blood, including cell composition, age, Body Mass Index, smoke and alcohol consumption. Finally, we identified genetic loci associated with editing levels, including known ADAR eQTLs and a small region on chromosome 7, containing LOC730338, a lincRNA gene that appears to modulate ADARs mRNA expression. Conclusions: Our data provides a detailed picture of the most relevant RNA editing events and their variability in human blood, giving interesting insights on potential mechanisms behind this post-transcriptional modification and its regulation in this tissue.

Original languageEnglish
Article number963
JournalBMC Genomics
Volume19
Issue number1
DOIs
Publication statusPublished - Dec 27 2018

Fingerprint

RNA Editing
Genome
RNA
Messenger RNA
Genes
Long Noncoding RNA
Inosine
Chromosomes, Human, Pair 7
Genetic Loci
Nervous System Diseases
Smoke
Alcohol Drinking
Adenosine
Blood Cells
Proteins
Body Mass Index
Gene Expression
Enzymes
Neoplasms

Keywords

  • ADAR1
  • ADAR2
  • Blood
  • RNA editing
  • RNA-seq

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables. / Giacopuzzi, Edoardo; Gennarelli, Massimo; Sacco, Chiara; Filippini, Alice; Mingardi, Jessica; Magri, Chiara; Barbon, Alessandro.

In: BMC Genomics, Vol. 19, No. 1, 963, 27.12.2018.

Research output: Contribution to journalArticle

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