Transcript Features of Hybrids

Weizmann
Institute of
Science
Transcriptome rewiring in hybrids
and polyploids
Or
What hybrids can teach us on
biodiversity
How species are formed?
Genetic barrier
Hybridization
Species 1
Progenitor Isolation
Accumulation
of mutations
&
Natural selection
Homoploid
Hybrid
Dead end
Polyploid
Species *2
Genome
doubling
Introgression
Features of Hybrids:
The benefits
Heterotic features
Broader range of adaptation
Novel traits
The troubles
Embryonic lethality
Adult inferiority
Hybrid necrosis
Sterility (chromosome pairing or
nuclear-cytoplasmic interactions)
Hybrid (homoploid) species
Allopolyploid species
AA X BB
(2x) (2x)
AB
AABB
(4x)
Studying interspecific hybrids and allopolyploids in
Two model systems
Merging of wheat genomes
Merging of yeast genomes
(sensu stricto, n=16)
P1
P2
+
S. Paradoxux
S. cerevisiae
F1
Ae. sharonensis
(genome SlSl)
Amphiploid
(SlSlAmAm)
T. monococcum
(genome AmAm)
Collaboration with Naama Barkai’s lab
Today’s question: What goes on at the
molecular level during
speciation/hybridization/
polyploidization ?
What drives divergence in gene expression
and how is gene expression rewired in
hybrids/polyploids
The yeast system
Sensu Stricto (5-20 Mya)
P1
P2
+
S. Paradoxux
S. cerevisiae
F1
Growth vigor in the cerevisiae x paradoxus hybrid
Max slope
0.06
0.05
0.04
S. paradoxus
hybrid
S. cerevisiae
0.03
0.02
0.01
How is gene expression rewired ?
Are new patterns of expression related to heterosis?
GENE EXPRESSION EVOLUTION AND REWIRING IN
HYBRIDS AND ALLOPOLYPLOIDS
Accumulation of
mutations
Cis or trans?
Species 1
merging
Novel patterns of
gene expression
Hybridization
Homoploid
Hybrid
Progenitor Isolation
Dead end
Polyploid
Species 2
Genome
doubling
Genetic barrier
Only Cis divergence
c-p= cis+trans
cerevisiae
cis=ch-ph
c/p = ch/ph
Hybrid
c
Progenitor
Speciation
ch
Hybridization
paradoxus
p
Allelic differences are maintained in the hybrid
ph
Only trans divergence
c>p
cerevisiae
ch = ph
Hybrid
c
Progenitor
Speciation
ch
Hybridization
paradoxus
p
Allelic differences are abolished in the hybrid
ph
Two-species array
S. cerevisiae
S. paradoxus
TGCTCGTCGGGTAGCTAATAGCTAGTGAGATAGGTCCAGCACCATGTCACG
TGCCCGTCGTGTAGCTACTGCGTAGAGATGTACGTGCAGTACCATCTCACG
*** ***** ******* *
*** ** ** ** *** ***** *****
Select 12 homoeoallele-specific 60mers oligos for 4400 genes
Tirosh et al. 2009 Science
Analyze allele expression in parental
versus hybrid background
P
H
P-H
Cis Only
Trans Only
Cis+Trans
Tirosh et al. 2009 Science
Genome-wide analysis of cis-trans effects
Alterations in cis factors
are the prominent cause
of divergence in gene
expression
Responsiveness to the
environment is determined
essentially by alterations in
trans factors
What is the origin of the Trans effect?
Divergence in gene
expression, related
to trans effects, is not
related to divergence
in transcription
factors or chromatin
remodeler
(expression or seq.)
but rather to
environment
signalers
Genes with both Cis and trans effects-Impact on over/under expression
Same-direction mutations
Enhancing
Opposite direction mutations
Compensating
Prominence of genes with both cis and trans effects among
overexpressed and underexpressed genes
Two types of
over/under
expression
in the hybrid:
-One type,
affecting only
one allele, mostly
due to novel cistrans interactions
-One type
affecting both
alleles
Novel expression patterns can be achieved
“overnight” in hybrids through novel
cis/trans, or trans interactions
Compensatory mutations and Hybridspecific trans effect explain
overexpression in hybrids
In the hybrid (under rich medium)
respiration genes are preferentially
overexpressed, maybe causing heterosis.
Thanks to:
Naama
Barkai
Naama Barkai
Itay Tirosh
Itay Tirosh
Michal
Keinan-
Dena
Leshkowitz
Sharon Reikhav
Cathy MelamedBessudo
Naomi AviviRagolsky
Khalil Kashkush
Moshe Feldman
Evolutionary history of wheat
Divergence from
a common
progenitor
Formation of wild
allotetraploid
wheat
2n=2x=14
(~4 MYA)
2n=4x=28
(~0.5 MYA)
PP
AA
BB
DD
BBAA
Domestication of
allotetraploid
wheat
2n=4x=28
(~10,500 Cal BP)
BBAA
Formation of
bread wheat
2n=6x=42
(~9,500 Cal BP)
BBAADD
Aegilops tauschii
DD
F1
BAD
S1
Triticum durum
BBAADD
BBAA
Heterosis
and
Hybrid
necrosis
TQ113
F1
S1
TTR16
Novel genetic and epigenetic variation released upon
hybridization and polyploidization
Gene silencing/activation
Changes in DNA methylation
Transposons activation
DNA elimination
The small RNAs hypothesis-A mechanism related to all of the above
Deep sequencing of small RNA w/Illumina/Solexa system:
-- Isolation of small RNAs
--Amplification
--Quality control (trimming “primers” from all tags, NNs, junk..)
--Bioinformatic analysis (alignment, annotation, normalization..)
#reads
327063
130015
102323
68524
62126
42354
25798
Signatures
TCGCTTGGTGCAGATCGGGACTCGTATGCCGTC
TGACAGAAGAGAGTGAGCACTCGTATGCCGTCT
GGCGGATGTAGCCAAGTGGATCGTATGCCGTCT
GGGCCTGTAGCTCAGAGGATCGTATGCCGTCTT
TTGACAGAAGAGAGTGAGCACTCGTATGCCGTC
TGAGAAGGTAGATCATAATAGCTCGTATGCCGT
GCGTCTGTAGTCCAACGGTTCGTATGCCGTCTT
MiR168
Analysis of small RNA data
Total reads
Reads after QC
# signatures >30
reads
Parent 1
Denome DD
3,064,285
1,202,651
4292
Parent 2
Genome BBA A
5,633,938
1,576,108
7967
F1 hybrid
S1 polyploid
total
6,421,516
1,689,159
6756
3,458,759
1,561,663
2772
18,578,498
6,029,581
21,787
Annotation: Hits in
Micro-RNAs
siRNAs corresponding
to repeats, transposons
Genes, tRNAs rRNA..
Transposons make up about 80% of the wheat genome
and therefore present a major hazard to genome stability
Adapted from Kronmiller and Wise, Plant Physiol. Vol. 146(1): 45-59, 2008
85% of small RNAs corresponding to transposons are
down-regulated in the polyploid
n=1113
100%
90%
percent(cumulative)
(cumulative)
percent
80%
70%
60%
hybrid
polyploid
50%
40%
30%
20%
10%
-16
-14
-12
-10
-8
-6
-4
0%
-2 -1 0
1 2
4
6
Log2(#log2(reads/MPV)
reads / # reads in MPV)
<MPV
hybrid
39%
polyploid 85%
~MPV
42%
12%
>MPV
19%
3%
8
10
12
Wis2-1A retrotransposon activation correlates with
down-regulation of siRNAs
Transcriptional activation
of Wis2-1 in S1
Kashkush et al. Nat Genet 2003
Down-regulation
of Wis2-1 siRNAs in S1
Keinan-Eichler et al. Unpublished
Total small RNA count for Wis2-1A:
TTR16 TQ113 MPV F1
S1
756
528
642
475
0
Northern (Wis probe)
•Small RNAs are highly responsive to
Polyploidization
•They can be induced -- miRNAs or
Repressed --siRNAs
•The suppression of siRNAs
correlates with transposons
activation
Extensive genetic and epigenetic
rewiring occurs in hybrid and
polyploids through novel cis-trans
interactions that alter the activity of
genes, repeats and small RNAs.
Phenotypic consequences range
from heterotic effects to genetic
incompatibilities.
Release of transposon silencing
might lead to hybrid dysgenesis
Thanks to:
Naama
Barkai
Naama Barkai
Itay Tirosh
Itay Tirosh
Michal
Keinan-
Dena
Leshkowitz
Sharon Reikhav
Cathy MelamedBessudo
Naomi AviviRagolsky
Khalil Kashkush
Moshe Feldman