Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera

Abstract

RNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee ( Apis mellifera ) is an important model organism for studying the molecular underpinnings of behavioral plasticity and social behavior, and recent RNA-seq studies of honey bees have revealed AS patterns and their regulation by DNA methylation. However, tissue-specific AS patterns have not been fully explored. In this paper, we characterized AS patterns in two different honey bee tissue types, and also explored their conservation and regulation. We used the RNA-seq data from brain and fat body to improve the existing models of honey bee genes and identified tissue-specific AS patterns. We found that AS genes show high conservation between honey bee and Drosophila melanogaster . We also confirmed and extended previous findings of a correlation between gene body DNA methylation and AS patterns, providing further support for the role of DNA methylation in regulating AS. In addition, our analysis suggests distinct functional roles for tissue-specific alternatively spliced genes. Taken together, our work provides new insights into the conservation and dynamics of AS patterns across different tissue types.

DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

“…In support of the hypothesis that gene body methylation in honey bees modulates transcription, the RNA interference‐mediated knockdown of the DNA methyltransferase 3 ( Dnmt3 ) gene, which codes for the enzyme responsible for de novo DNA methylation, affected 14% of the honey bee worker transcriptome (Li‐Byarlay et al, 2013). RNA splicing was also affected, corroborating previous in silico predictions that associated DNA methylation with alternative splicing (Bonasio et al, 2012; Cingolani et al, 2013; Flores et al, 2012; Foret et al, 2012; Glastad et al, 2016; Herb et al, 2012; Kannan et al, 2019; Lyko et al, 2010). Even more spectacularly, the knockdown of Dnmt3 in young female larvae resulted in adults with a queen‐like phenotype, mimicking the transcriptional programme induced by a royal jelly diet (Kucharski et al, 2008).…”

DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

“…In support of the hypothesis that gene body methylation of honey bees modulates transcription, the RNA interference-mediated knockdown of the DNA methyltransferase 3 (Dnmt3) gene, which codes for the enzyme responsible for de novo DNA methylation, affected 14% of the honey bee worker transcriptome (9). RNA splicing was also affected, corroborating previous in-silico predictions that associated DNA methylation with alternative splicing (6,7,13,15,(26)(27)(28)(29). Even more spectacularly, the knockdown of Dnmt3 in young female larvae resulted in adults with a queen-like phenotype, mimicking the transcriptional program induced by a royal jelly diet (16).…”

Transcriptional expression of m6A and m5C RNA methyltransferase genes in the brain and fat body of honey bee adult workers

“…Concerning the differences we found in the expression of m 6 A and m 5 C methyltransferases between honey bee tissues, we speculate that they may reflect in the regulation of tissue-specific splicing variants previously found in the brain and fat body ( Kannan et al, 2019 ), and/or several differentially expressed coding-genes and miRNA from workers performing different behaviors ( Whitfield et al, 2003 ; Behura and Whitfield, 2010 ).…”