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Protein determinants of chromosome domains
Laura Braverman
MIT PRIMES Presentation May 22, 2016
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Background
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Hi-CLoops and domains
Chromosome contact maps
High
Low
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Loops and domains2009 2012 2015
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Loops and domains2009 2012 2015
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DNA - Binding Proteins
Functional aspect
Rao et al/Cell 2014
Outside Boundary Inside
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Binding factors at boundaries
● Architectural Proteins
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Binding factors at boundaries
● Architectural Proteins
● Transcription Factors
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Chromatin Immunoprecipitation Seq (ChIP-seq)
http://slideplayer.com/slide/3385783/
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Chromatin Immunoprecipitation Seq (ChIP-seq)
Position 1 Position 2
Cell 1
Cell 2
Cell 3
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Methods and Results
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Protein Enrichment
Peak enrichment vs percentage states occupied
Rao et. al. 2014
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Percentage of loop or domain boundaries with protein
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Example:● 10 total
boundaries● 4 with green
protein● 4/10 = 40%
green protein
Percentage of loop or domain boundaries with protein
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Enrichment of proteins at loop and domain boundaries
Boundary
Enr
ichm
ent
Distance from boundary
CTCF
Outside Inside
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Architectural and transcription proteins are enriched at loop boundaries
All domains
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
All loops
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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Architectural proteins enriched at loop boundaries
CTCF
● Known to be related to 3D genome structure and loop formation
Cohesin
● RAD21 and SMC3 subunits● Forms chromatin loops in
Interphase
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Considering boundaries with a particular protein
● Only interested in boundaries with a particular protein (green)
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Considering boundaries with a particular protein
● Only interested in boundaries with a particular protein (green)
● 2 boundaries with both CTCF and the blue protein/ 4 boundaries with CTCF
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Architectural proteins CTCF, SMC3, RAD21 are co-enriched at loop boundaries
Enrichment at loops without CTCF With CTCF
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
Without CTCF
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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RNA Polymerase II is more common on boundaries without CTCF than with CTCF
Enrichment at loops without CTCF With CTCF
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
Without CTCF
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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ZNF143 is more co-enriched with CTCF than YY1
Enrichment at loops without CTCF With CTCF
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
Without CTCF
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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YY1 and RNA Polymerase II are correlated
With YY1
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
Without YY1
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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YY1 bound loci are bound by CTCF with a similar frequency but less enrichment
With YY1
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
Without YY1
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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RNA Polymerase II bound loci are bound by CTCF with a similar frequency but less enrichment
With RNA Polymerase II
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
Without RNA Polymerase II
Ave
rage
fold
enr
ichm
ent
Percent of domains bound by protein (%)
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Testable hypotheses: CTCF could be replaced with RNA Polymerase II after loops are created
Position 1 Position 1 later
Cell 1
Cell 2
Cell 3
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Conclusion
● Hypothesized classifications:○ ZNF143 = Architectural protein○ YY1 = Transcription / RNA Polymerase II associated boundary factor
● Enrichment of RNA Polymerase II is anticorrelated with CTCF● Testable hypothesis: RNA Polymerase II replaces CTCF at boundaries?
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Acknowledgements
Mirny lab:
Prof. Leonid MirnyNezar AbdennurBoryana DoyleDr. Geoff FudenbergDr. Maxim ImakaevAnton GoloborodkoThe Espresso Machine
Dr. Slava Gerovitch and Dr. Pavel Etingof for dealing with our poor adherence to deadlines
And my parents for supporting me through this journey