PMID- 28989734
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210109
IS  - 2054-5703 (Print)
IS  - 2054-5703 (Electronic)
IS  - 2054-5703 (Linking)
VI  - 4
IP  - 9
DP  - 2017 Sep
TI  - Detecting rare asymmetrically methylated cytosines and decoding methylation 
      patterns in the honeybee genome.
PG  - 170248
LID - 10.1098/rsos.170248 [doi]
LID - 170248
AB  - Context-dependent gene expression in eukaryotes is controlled by several 
      mechanisms including cytosine methylation that primarily occurs in the CG 
      dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has 
      been found in various cell types, such as mammalian neurons, and recent results 
      suggest that these sites can repress transcription independently of CpG contexts. 
      In addition, an emerging view is that CpG hemimethylation may arise not only from 
      deregulation of cellular processes but also be a standard feature of the 
      methylome. Here, we have applied a novel approach to examine whether asymmetric 
      CpG methylation is present in a sparsely methylated genome of the honeybee, a 
      social insect with a high level of epigenetically driven phenotypic plasticity. 
      By combining strand-specific ultra-deep amplicon sequencing of illustrator genes 
      with whole-genome methylomics and bioinformatics, we show that rare 
      asymmetrically methylated CpGs can be unambiguously detected in the honeybee 
      genome. Additionally, we confirm differential methylation between two 
      phenotypically and reproductively distinct castes, queens and workers, and offer 
      new insight into the heterogeneity of brain methylation patterns. In particular, 
      we challenge the assumption that symmetrical methylation levels reflect symmetry 
      in the underlying methylation patterns and conclude that hemimethylation may 
      occur more frequently than indicated by methylation levels. Finally, we question 
      the validity of a prior study in which most of cytosine methylation in this 
      species was reported to be asymmetric.
FAU - Welsh, Laura
AU  - Welsh L
AD  - Research School of Biology, The Australian National University, Canberra, 
      Australian Capital Territory 2601, Australia.
FAU - Maleszka, Ryszard
AU  - Maleszka R
AUID- ORCID: 0000-0003-1855-555X
AD  - Research School of Biology, The Australian National University, Canberra, 
      Australian Capital Territory 2601, Australia.
FAU - Foret, Sylvain
AU  - Foret S
AD  - Research School of Biology, The Australian National University, Canberra, 
      Australian Capital Territory 2601, Australia.
LA  - eng
SI  - figshare/10.6084/m9.figshare.c.3861829
SI  - Dryad/10.5061/dryad.7nb8q
PT  - Journal Article
DEP - 20170906
PL  - England
TA  - R Soc Open Sci
JT  - Royal Society open science
JID - 101647528
PMC - PMC5627074
OTO - NOTNLM
OT  - DNA methylation
OT  - epigenomics
OT  - social insect
COIS- We have no competing interests.
EDAT- 2017/10/11 06:00
MHDA- 2017/10/11 06:01
PMCR- 2017/09/06
CRDT- 2017/10/10 06:00
PHST- 2017/03/15 00:00 [received]
PHST- 2017/08/07 00:00 [accepted]
PHST- 2017/10/10 06:00 [entrez]
PHST- 2017/10/11 06:00 [pubmed]
PHST- 2017/10/11 06:01 [medline]
PHST- 2017/09/06 00:00 [pmc-release]
AID - rsos170248 [pii]
AID - 10.1098/rsos.170248 [doi]
PST - epublish
SO  - R Soc Open Sci. 2017 Sep 6;4(9):170248. doi: 10.1098/rsos.170248. eCollection 
      2017 Sep.