RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.

TitleRNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.
Publication TypeJournal Article
Year of Publication2013
AuthorsLi-Byarlay, H, Li, Y, Stroud, H, Feng, S, Newman, TC, Kaneda, M, Hou, KK, Worley, KC, Elsik, CG, Wickline, SA, Jacobsen, SE, Ma, J, Robinson, GE
JournalProc Natl Acad Sci U S A
Volume110
Issue31
Pagination12750-5
Date Published2013 Jul 30
ISSN1091-6490
KeywordsAlternative Splicing, Animals, Bees, Behavior, Animal, DNA (Cytosine-5-)-Methyltransferase, DNA Methylation, Gene Knockdown Techniques, Insect Proteins, RNA Interference, Social Behavior
Abstract

Studies of DNA methylation from fungi, plants, and animals indicate that gene body methylation is ancient and highly conserved in eukaryotic genomes, but its role has not been clearly defined. It has been postulated that regulation of alternative splicing of transcripts was an original function of DNA methylation, but a direct experimental test of the effect of methylation on alternative slicing at the whole genome level has never been performed. To do this, we developed a unique method to administer RNA interference (RNAi) in a high-throughput and noninvasive manner and then used it to knock down the expression of DNA methyl-transferase 3 (dnmt3), which is required for de novo DNA methylation. We chose the honey bee (Apis mellifera) for this test because it has recently emerged as an important model organism for studying the effects of DNA methylation on development and social behavior, and DNA methylation in honey bees is predominantly on gene bodies. Here we show that dnmt3 RNAi decreased global genomic methylation level as expected and in addition caused widespread and diverse changes in alternative splicing in fat tissue. Four different types of splicing events were affected by dnmt3 gene knockdown, and change in two types, exon skipping and intron retention, was directly related to decreased methylation. These results demonstrate that one function of gene body DNA methylation is to regulate alternative splicing.

DOI10.1073/pnas.1310735110
Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID23852726
PubMed Central IDPMC3732956
Grant List1DP1OD006416 / OD / NIH HHS / United States
1R21HG006464 / HG / NHGRI NIH HHS / United States
GM60398 / GM / NIGMS NIH HHS / United States
R01 AR056223 / AR / NIAMS NIH HHS / United States
R01 HL073646 / HL / NHLBI NIH HHS / United States
R01 HL073646 / HL / NHLBI NIH HHS / United States
R37 GM060398 / GM / NIGMS NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
/ / Howard Hughes Medical Institute / United States