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

G3 : Genes - Genomes - Genetics
Kavya KannanJian Ma

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 conservat...Continue Reading

References

Jul 20, 1987·Journal of Molecular Biology·M Gardiner-Garden, M Frommer
Sep 6, 1982·FEBS Letters·S Urieli-ShovalA Razin
May 1, 1994·Molecular and Cellular Biology·M Talerico, S M Berget
Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
Dec 16, 2000·Nature·F LykoR Jaenisch
Aug 29, 2003·Development·Natascha KunertFrank Lyko
Oct 11, 2003·Science·Charles W WhitfieldGene E Robinson
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gene Yeo, Christopher B Burge
Oct 27, 2006·Genome Research·Andrew K JonesDavid B Sattelle
Oct 31, 2006·Nature·UNKNOWN Honeybee Genome Sequencing Consortium
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Apr 18, 2009·BMC Genomics·Xing FuPhilipp Khaitovich
Jan 30, 2010·Nature·Timothy W Nilsen, Brenton R Graveley
Aug 31, 2010·Nucleic Acids Research·Kai WangJinze Liu
Dec 24, 2010·Genome Research·Bryce DainesRui Chen
Apr 6, 2011·PloS One·Tomasz E Koralewski, Konstantin V Krutovsky
Jun 24, 2011·Bioinformatics·Adam RobertsLior Pachter
Sep 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Antje JaroschRobin F A Moritz
Sep 29, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wei LiTao Jiang
Dec 14, 2011·Genes & Development·Yevgenia L KhodorMichael Rosbash
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
Oct 20, 2012·Nature Reviews. Neuroscience·Randolf Menzel
Dec 21, 2012·Nucleic Acids Research·Yang LiJian Ma
Jul 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Hongmei Li-ByarlayGene E Robinson
Jul 23, 2013·Nature Protocols·Huaiyu MiPaul D Thomas
Feb 1, 2014·BMC Genomics·Christine G ElsikUNKNOWN Honey Bee Genome Sequencing Consortium
Mar 29, 2014·Nature·James B BrownSusan E Celniker
Dec 3, 2014·Proceedings of the National Academy of Sciences of the United States of America·Clare C RittschofLisa Stubbs
Dec 24, 2015·Genome Biology·Peter H SudmantChristopher B Burge

❮ Previous
Next ❯

Citations

Jan 13, 2019·Proceedings of the National Academy of Sciences of the United States of America·Carl VellerMartin A Nowak

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
Genome Sequencing
RNASeq

Software Mentioned

IGV genome browser
MAKER2
TopHat2
MapSplice
Amel
TrueSight
Brain
PANTHER
Bowtie
GLEAN

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.