Download Introduction Aim TE presence/absence variant discovery Abundant

Population scale analysis
of transposable element mobilization
Tim Stuart1, Steven R. Eichten2, Jonathan Cahn1, Justin Borevitz2, Ryan Lister1
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia (1), The Australian National University (2)
Aim
R2
R1
+
-
D
-5
-10
coverage
TE variants
0
n=4452
n=740
Old
n=2108
1
0
0
200
400
600
TE ranks over SNP-SNP median rank
61% of TE variants
are not in linkage
disequilibrium
with surrounding
SNPs
1
10
0
ur
fe
ic
se
nt
at
t
en
es
om
en
G
TE
12
1
TE variants associated with
DNA methylation changes
TE mC correlation
Young
Mid
Old
Density
2
1
0
-1
0
1 -1
0
1 -1
0
1
Pearson correlation values (r2)
Presence of TE variants is associated
with increased DNA methylation
>50%
DNA methylation level is
positively correlated with TE age
-2kb
mC/C
Insertion point
FPKM x 104
14
2
Accessions with
TE present
FPKM
>25 x 105
16
3
TE abs
pr ent
es
en
t
Low
4
*
TE
FPKM
20
18
r2
0
TE
Genic
Intergenic
Pseudogene
TE insertion sites
Pericentromeric regions
Chromosome arms
RNA-seq
AT AtR
2G LP
15 18
04
AT
0
2G
15
04
2
High
5
a
TE bs
pr ent
es
en
t
TE
pr
TE ese
ab nt
TE se
pr nt
TE ese
ab nt
se
nt
0
AT2G01360
22
FPKM x 105
FPKM x 105
10
Accessions with TE absent
20
QPT
AT2G01350
TE
*
Activated gene
(PPR protein)
AT Q
2G PT
01
35
AT
0
2G
01
36
0
*
Accessions with
TE present Accessions with TE absent
ATAtR
2G LP
15 18
04
0
AT
2G
15
04
2
Col-0
TE absent
Bl-1
TE present
Col-0
TE absent
Accessions with
TE present
RNA-seq
Genes
Genes
AT5TE47175
chr2:165010-169070
QPT
AT2G01360
AT2G01350
chr2:6507400-6512770
AtRLP18
AT2G15040 AT2TE26610 AT2G15042
pr
TE insertion in gene upstream region
AT3TE29460
Mid
es
Differential gene expression linked to TE variants
TE insertion in gene exon
Young
TE Superfamily
0%
+2kb
https://github.com/ListerLab/TEPID
ab
tepid-map
TE
TE
Mapped split reads
R2
0
2
43.7 kb
Mapped read pairs
TE absence identification
5
Insertion point
ATCGCTAGCAGCATCAGCATCATTGCTGTAC
Superfamily enrichments for TE variants
Distal genomic DNA sequence
TE
TE-SNP linkage
Old
chr2:9225478
R2
+
-
0
H
TE insertion identification
YAHA
Split read alignments
ATCGCTAGCAGCATCAGCATCATTGCTGTAC
tepid-refine
R1
10
+2kb
-2kb
Read alignments
R1
20
Enrichment (%)
bowtie2
Unmapped and
clipped reads
(single end)
+
-
discordant read
split read
Young
48.9 kb
predicted TE insertion point
Paired-end short reads
30
Count r2 values (x103)
tepid-discover
Genomic features
DNA
DNA/En−Spm
DNA/Harbinger
DNA/HAT
DNA/Mariner
DNA/MuDR
DNA/Pogo
DNA/Tc1
LINE
LINE/L1
LTR/Copia
LTR/Gypsy
RathE1_cons
RathE2_cons
RathE3_cons
RC/Helitron
SINE
Unassigned
FASTQ
Abundant novel genetic diversity
chr1:18816503
TE presence/absence variant discovery
To identify TE presence/absence variants in a population of wild
Arabidopsis accessions, and examine the effects of these TE
variants upon genome and cellular function
U Ss
ps ite
tre
5’ am
U
I n TR
tro
Ex n
on
D 3
ow ’ U
ns TR
tre
am
Ps
eu T
do E
ge
ne
Transposable element (TE) activity is silenced through DNA methylation
A large fraction of genetic differences between individuals is due to TE
presence/absence variants
It is challenging to identify TE presence/absence variants from short
read DNA sequencing data
% with TE variant
Introduction
0
Dual
Fertilization
Anther
Petal
Central cell
Stigma
Carpel
Sepal
Arabidopsis flower
Ovule
0
20 40 60 80 100
%TEs absent other lines
Egg
4
p <1x10-4
n = 937
2
0
0
20 40 60 80 100
%TEs absent other lines
20 40 60 80 100
%TEs absent other lines
Endosperm hypo CG−DMR
p <1x10
n = 953
4
-4
0
20 40 60 80 100
%TEs absent other lines
Sperm-demethylated TEs are often
absent from non-Col-0 accessions
and are responsible for more unique
TE insertions in the population
2
1
-0
ol
C
r
Le
C
C
x
-0
ol
C
ol
C
-0
vi
x
x
r
Le
rx
50
vi
ol
Le0
rx
C
vi
x
vi
100
C
3
0
2
0
4
mCG
mCHH
150
Le
1
0
Sperm cell hypo CHH−DMR
Frequency x103
Sperm cells
Vegetative cell
p = 0.1034
n = 407
3
2
* *
200
0
−50
−100
Absence of a TE in the maternal
genome leads to demethylation
of the paternal copy in the
embryo
--
-♂
♀-
Parental genome containing TE
Embryo mC levels for sperm
mCHH-demethylated TEs
∆ mC/C relative to Col−0 x Col−0 (%)
Seed
Pollen
0
Frequency x103
Vegetative cell nucleus
p = 0.0926
n = 109
5
Cvi, n=777
Ler, n=592
p > 0.02
p < 1.4 x 10-10
C
Embryo
2
Embryo hyper CHH−DMR
Frequency x103
Frequency x103
Sperm cell hyper CG−DMR
Whole seed 21−24 nt smRNA abundance
Microspore
Sperm cell
Microspore
Sperm cell
Embryo
Endosperm
All TEs
Endosperm
Transposition frequencies
* *
6
Unique TE insertions
Frequency that differentially methylated TEs
are absent from non-Col-0 genomes
∆ smRNA relative to Col-0 x Col-0 (%)
Parental differences in genomic TE content associated with DNA demethylation in hybrid progeny
40
Cvi x Col-0 Col-0 x Cvi
20
**
*
mCG
mCHG
mCHH
**
0
−20
−40
-♂
♀-
Parental genome containing TE
References
Population DNA sequencing, RNA-seq and WGBS data: Schmitz, R. J. et al. Patterns of
population epigenomic diversity. Nature 495, 193–198 (2013).
Whole seed smRNA data, embryo DNA methylation data: Pignatta, D. et al. Natural epigenetic
polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. eLife 3, e03198 (2014).
Pollen differentially methylated regions: Calarco, J. P. et al. Reprogramming of DNA Methylation
in Pollen Guides Epigenetic Inheritance via Small RNA. Cell 151, 194–205 (2012).
Embryo and endosperm differentially methylated regions: Hsieh, T. F. et al. Genome-Wide
Demethylation of Arabidopsis Endosperm. Science 324, 1451–1454 (2009).
DNase I hypersensitivity data: Sullivan, A. M. et al. Mapping and dynamics of regulatory DNA and
transcription factor networks in A. thaliana. Cell 8, 2015–2030 (2014).
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more
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