05072023
Gene DNA methylation in plants: selective
pressures and sex chromosome evolution. Aline Muyle.
Most
mutations are deleterious. Epigenetics (study of changes in gene expression
that can be inherited through cell divisions but are not changes in DNA
sequence [Holliday 1987]). This is not Lamarckism (no one has observed env
induced epigenetic change so far). CG methylation epimutes over time (rate 1E-4,
should be room for selection); depleted in TSS and TTS. CHH methylated genes
(upstream) have very low expression. CHG methylation happens at gene bodies [H
is A,C,T] and is linked to medium-high expression. Gene body methylation (GBM)
is conserved across species, even 300My away, although it is variable [some
species don’t have GBM at all, or don’t change expression much when removed
(she reanalyzed the data and found the opposite); is it that important then?
others have a lot]. GBM methylation evolve slow. She has reviewed all these
topics at https://academic.oup.com/gbe/article/14/4/evac038/6550137 , she insists that papers
describing them are still highly controversial. So then she tried to measure
selection pressure on GBM, with the idea that methylated loci should be removed
from populations if GBM is removed. She used for that published methylomes of A. thaliana (n=877, leaf), described at https://pubmed.ncbi.nlm.nih.gov/33871638/, to check whether 4Ns >> 1. She
found it is (1.4, comparable to codon usage selection, “tiny effects”) for
ancestrally GBM genes [conserved in A. lyrate and C. rubella], but not for all
genes. Their hypothesis is that GDM is deleterious for most genes (mutagenic?)
and advantageous for a few ones.
She is now
working on gene imprinting, which is regulated by methylation and histone
marks, that applies to embryos but also in some adult tissues. She is comparing
dioecious and hermaphrodite plant species.
Limited water stress modulates expression of
circadian clock genes in Brachypodium distachyon roots and induces differential
response of proline-metabolism related genes– János GYÖRGYEY
Arabidopsis
is a dicot, brachy is much better for monocots. Shows a minimal circadian clock
for A. thaliana from https://cshperspectives.cshlp.org/content/8/12/a027748.full to select core clock genes. In his
experiments, core clock genes express lower in the roots than in the green
parts in most cases (GIGANTEA is the exception, also responds to drought).
ELF3/4 expression in the root is not circadian. Under drought, LHY display
lower amplitude in expression. PRR95 peaks in root and leaf are a few day hours
away.
He then
moves to the study of Pro metabolism, a regulatory hub (https://doi.org/10.1016/j.tplants.2021.07.009), is it circadian? On the shoot [Pro] seems to be circadian, it
accumulates during the day and it is consumed during the night.
Two examples of genome-wide evolutionary
response of European forest trees to past climate changes– Martin LASCOUX
Little ice
age (LIA, 1450-1850). They use a method from Vince Buffalo to look for
responses of old forests to IA, which essentially computes allele freq
covariation across generations under random drift or under selection (https://www.pnas.org/doi/abs/10.1073/pnas.1919039117). They study 3 oak forests (several
cohorts) in France after aging the sampled individuals (https://onlinelibrary.wiley.com/doi/10.1002/evl3.269). They conclude that trees respond
quickly, with polygenic responses, as the time frame is only a few generations.
