presentazione standard di powerpoint...2018/07/10 · long non-coding rnas: at least 200 bp long...
TRANSCRIPT
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Rachel Schwope
EPIGENMay 24-27, 2016
Patterns of Histone Methylation and Chromatin Organization in Grapevine Leaf
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What does H3K4 methylation do?Plant of interest: Vitis vinifera
Culturally important
An economically vital organism for Italy and beyond
Scientifically intriguing
A clonal organism whose genome has not undergone meiosis – or its developmental program – in centuries.
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Chromatin – the structural and functional complex of DNA and binding proteins
ase.org.uk http://www.structuralbiology.uzh.ch/
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What does H3K4 methylation do?Chromatin is specialized to maintain genomic states
A recent ChIP-Seq meta-study identified 9 states of chromatin in Arabidopsis(Sequeira-Mendes, Plant Cell 2014)
4 types = high transcription
5 types = low transcription
(Sequeira-Mendes, Plant Cell 2014)
Intergenic andTE-rich
Promoter andCDS-rich
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What does H3K4 methylation do?What defines a Chromatin State?
(Sequeira-Mendes, Plant Cell 2014)
1) DNA methylation (CG, CHG, CHH)2) Post-translational modification of histones (H3K9ac, etc.)3) Histone variants (H3.1, H2AZ, etc.)
(www.promega.com)
From Figure 1B.
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What does H3K4 methylation do?
H3K4me3
Functions of Specific Histone Modifications at H3
H3K9me2 H3K27me3
• Recruits transcription initiation factors
• Promotes openconformation
• In Arabidopsis, bound by CMT3 DNA methylase
• In maize, increased at transposons and some genes
• Associated with Polycomb
• In maize, found in gene-dense chromatin arms, not at pericentric chromatin
Layman and Zuo, Front. Cell. Neurosci., 07 January 2015
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Chromatin Immunoprecipitation Methodology
Chromatin from fixed leaf tissue
or nuclei
ChIP with AbcamPlant Kit
Library production
(Nugen Ultralow)
Quantification and Quality
Control
125 bp PE Illumina
Sequencing
Bowtie Alignment
MACS2 Peak Call
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Peaks are generally at the 5’ ends of genes
Have a broader “shoulder” at the 3’ side of the peak
Where is H3K4me3 found in grapevine leaves?
Chromosome 2: 3,198,150..3,225,396
27 kb
>>>>>>>>>>>>> <<<<<<<<<<<< >>>>>>>>>>>>> <<<<<<<<<<<<<<<<<<
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H3K4me3 distribution across genes
As gene size increases, H3K4me3 covers a proportionally smaller amount of the gene
H3K4me3 distribution across genes
100% of gene length
Vit
isge
nes
so
rted
acc
ord
ing
to s
ize
H3K4me3 coverage over gene body
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>
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What does H3K4 methylation do?How Enriched is H3K4me3 in Grapevine leaf?
0,00
5,00
10,00
15,00
20,00
25,00
30,00
35,00
1
81
4
16
27
24
40
32
53
40
66
48
79
56
92
65
05
73
18
81
31
89
44
97
57
10
57
0
11
38
3
12
19
6
13
00
9
13
82
2
14
63
5
15
44
8
16
26
1
17
07
4
17
88
7
18
70
0
19
51
3
20
32
6
Fold
Enri
chm
en
t
Total Peaks
Enrichment of H3K4me3 peaks in grapevine leaf
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What does H3K4 methylation do?H3K4me3 Enrichment generally increases with Peak Length
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What does H3K4 methylation do?…But only correlates weakly with Transcript Accumulation
FPKM data from M. Miculan
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What does H3K4 methylation do?Peak length also correlates weakly with Transcript Accumulation
FPKM data from M. Miculan
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Where else do we find H3K4e3?Long non-coding RNAs: at least 200 bp long
• 2044 intergenic long-ncRNAs in Vitis genome (Genoscope)
• In leaf, 219 of these (11%) correlate with H3K4me3 signal
Where else do we find H3K4me3 enrichment?
<<<<<<<<<<<< <<<<<<<<Genes
lncRNA
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What does H3K4 methylation do?What are the lncRNA species co-occur with H3K4me3?
Total: 219 lncRNAs
• 15 of these encode miRNAs (mIRbase.org)
• 204 have no discernable miRNA structure
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What does H3K4 methylation do?How do Heterochromatic modifications compare?
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What does H3K4 methylation do?Where do we find H3K9me2 and H3K27me3?
LTR-Gypsy LTR-Copia RIL
K9me2
K27me3Total peaks = 12,270
Total peaks = 11,48751.8%
50.0%
26.0%
26.5%
3.3%
2.4%
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What does H3K4 methylation do?Many, but Not All Highly Repetitive TEs are Enriched
kmers
H3K27me3
H3K9me2
TEs
kmers
H3K27me3
H3K9me2
TEs
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What does H3K4 methylation do?Computational Background Test
What happens when I ask MACS2 to find peaksfrom an unenriched alignment?
Input 1
Input 2
Peak Call
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What does H3K4 methylation do?Separating Signal from Noise
kmers
H3K27me3
H3K9me2
TEs
‘Input mock’
‘True Positives’ ‘False Positives’
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What does H3K4 methylation do?What is the DNA methylation state at loci with modified histones?
H3K4me3 H3K9me2
CG CHG CHH CG CHG CHH CG CHG CHH CG CHG CHH
Genome-wide averagemethylation
M. Celii
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What does H3K4 methylation do?Vitis results support Arabidopsis data that DNA and histone methylation form feedback loop
Adapted from Stroud et al., 2013
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What does H3K4 methylation do?
Chr 4
Chr 3
Chr 2
Chr 1
CHH
CHG
CG
H3K9me2
H3K27me3
H3K4me3
Transposon Elements
Genes
M. Celii
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What does H3K4 methylation do?Looking at the Global Chromatin Environmentwith Hi-C
http://medcell.med.yale.edu
Hi-C: a method of inferring the global three-dimensional relationships from
paired-end sequence data
http://mol-biol4masters.masters.grkraj.org
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What does H3K4 methylation do?Hi-C Methodology
Adapted from Lieberman et al, 2009
In the lab:
In silico:
Integrative Genomics and Bioinformatics Core at the Salk Institute
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What does H3K4 methylation do?
Chr 8
Ch
r8
• Each chromosome shows a unique pattern of organization
A. Tocci
“Loose Structural Domain”
“Compact Structural Domain”
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What does H3K4 methylation do?
Chr 8
LSD
CSD
ChIP data corresponds with 3D structure
H3K27me3
H3K9me2
H3K4me3
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What does H3K4 methylation do?
Chr 17
Ch
r1
7
• Each chromosome shows a unique pattern of organization
A. Tocci
“Loose Structural Domain”
“Compact Structural Domain”
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What does H3K4 methylation do?
Chr 8
LSD
CSD
ChIP data corresponds with 3D structure
H3K27me3
H3K9me2
H3K4me3
Chr 17
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What does H3K4 methylation do?
Chr 4
Ch
r4
• Each chromosome shows a unique pattern of organization
A. Tocci
“Loose Structural Domain”
“Compact Structural Domain”
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What does H3K4 methylation do?
Chr 8
LSD
CSD
ChIP data corresponds with 3D structure
H3K27me3
H3K9me2
H3K4me3
Chr 4
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What does H3K4 methylation do?Chromatin Organization is Highly Stable
Biological Replicate 1 Biological Replicate 2
Chr1 2 3 4 5 6 7 8 9 10 Chr1 2 3 4 5 6 7 8 9 10
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Pinot Noir Genomic Contact Map
Easily visualize the actual locations of unassigned regions of the genome assembly
A. Tocci
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What does H3K4 methylation do?Conclusions and Future Directions
1. Much to uncover with ChIP-Seq
• H3K4me3 results = high confidence• Allele specific analysis in progress
• Other histone modifications will require finer analyses
2. Hi-C shows chromatin structure very stable
• Try varieties other than Pinot Noir – do they have the same organization?
• Use Hi-C to improve genome assembly (in progress - Aldo Tocci)
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What does H3K4 methylation do?Acknowledgements
IGAProf. Michele MorganteEmanuele de PaoliFabio MarroniAldo TocciMirko CeliiMara MiculanGabriele Magris
IGA Technology ServicesEmanuela AleoFederica MagniGiacomo Prete
Lab and AdministrationGiusi ZainaNicoletta Felice
Stefano GrassoSupported by the ERC project NOVABREED - Novel variation in plant breeding and the plant pan-genomes (Grant agreement no.: 294780)
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What does H3K4 methylation do?
Chr 1
CHH
CHG
CG
H3K9me2
H3K27me3
H3K4me3
Transposon Elements
Genes
Chr 2
Chr 3
Chr 4
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What does H3K4 methylation do?Hi-C shows H3K4me3 is located preferentially in Loose Structural Domains
2.54
12636
4.89
22098
Ave
rage
# o
f p
eak
s p
er
50
kb
win
do
w
Ave
rage
# o
f ge
nes
pe
r 5
0 k
b w
ind
ow
H3K4me3 Peaks Genes
.709
3524
2.65
11988
A. Tocci
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What does H3K4 methylation do?H3K9me2 distribution mimics that of total TEsA
vera
ge #
of
pe
aks
pe
r 5
0 k
b w
ind
ow
H3K9me2 Peaks Transposon Elements
Ave
rage
# o
f TE
s p
er 5
0 k
b w
ind
ow
18.79
12.8
1.51
6819
2.03
10068
Ratio = 1.31 Ratio = 1.46
A. Tocci
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What does H3K4 methylation do?
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What does H3K4 methylation do?Transposons with K9me2 or K27me3 have higher k-mer count
20
-mer
Km
erco
un
t
K-mer count of TEs from Chromosome 2
TEs with H3K9me2 TEs with H3K27me2 All TEs in Chr2
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http://www.biosyn.com/
Chromatin Immunoprecipitation Enriching for Antibody-associated DNA with Chromatin Immunoprecipitation
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What does H3K4 methylation do?H3K9me2 Enrichment generally increases with Peak Size
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What does H3K4 methylation do?Transposons with K9me2 or K27me3 have higher k-mer count
20
-mer
K-m
erco
un
tK-mer count of TEs in Chromosome 2
TEs with H3K27me3 TEs with H3K9me2 All TEs in Chr2
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What does H3K4 methylation do?How do heterochromatic modifications at histonesrelate to DNA methylation?
DNA transposon
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What does H3K4 methylation do?How do heterochromatic modifications at histonesrelate to DNA methylation?