ADAR regulates RNA editing, transcript stability, and gene expression.
Bottom Line: To study the role of ADAR proteins in RNA editing and gene regulation, we sequenced and compared the DNA and RNA of human B cells.The results uncovered over 60,000 A-to-G editing sites and several thousand genes whose expression levels are influenced by ADARs.Our results also reveal that ADAR regulates transcript stability and gene expression through interaction with HuR (ELAVL1).
Affiliation: Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA. Electronic address: firstname.lastname@example.org.Show MeSH
Mentions: The results from ADAR knockdown and RNA-IP suggest that although ADARs mediate A-to-G editing, they do not mediate other types of RDDs. The levels of other types of differences were largely unaffected by ADAR knockdown, and the transcripts that showed those differences were not bound by ADAR. This prompted us to compare the genomic features surrounding the A-to-G editing sites and other types of RDDs. First, the sequence contexts of A-to-G and non-A-to-G sites are different. The base 5′ adjacent to the adenosine in A-to-G sites is depleted of guanosine (G) and the base 3′ to A-to-G editing sites is enriched for G (Figure 5A), consistent with previous reports (Lehmann and Bass, 2000). This sequence feature is specific to A-to-G editing because it is not present in random adenosines within nonedited Alu repeats (data not shown). This sequence motif was also not found for any of the RDDs. We identified sequence motifs for G-to-A and T-to-C sites, and they differed from the motif around the A-to-G sites (Figure 5A). Second, the A-to-G sites were more clustered than the non-A-to-G sites (67% of A-to-G sites were found within 25 nt of each other, compared with 14% of non-A-to-G RDDs). Third, most of the A-to-G sites were within or near inverted repeats, which form dsRNA and are preferentially recognized and bound by ADAR enzymes. Nearly 45% of the A-to-G sites resided within inverted repeats and another 30% were found near inverted repeats (<1 kb). In contrast, very few (0.9%) of the non-A-to-G sites were found in inverted repeats. Lastly, A-to-G sites and RDD sites were found in different regions of genes. A-to-G sites were found mostly in the 3′ UTRs, whereas RDDs were found mainly in the 5′ UTRs and in coding exons. Only 4% of the A-to-G sites (compared with 35% of RDDs) were in coding exons (Figure 5B). The differences between A-to-G editing sites and the other types of RDDs suggest that they are mediated by different mechanisms. Biochemically, this is expected since some of the RDDs are transversion events that cannot be explained simply by deamination.
Affiliation: Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA. Electronic address: email@example.com.