Transcript Regulatory Mechanisms: Inducible gene expression

Nucleosome Positioning
& Transcription Factor Identification
ZHANG ZHIZHUO
MAY 2010
Outline
 Basic Concept
 Nucleosome Positioning and Gene Regulation
 General Transcription Mechanism
 Genomic Organization of Nucleosomes
 The Organization of Nucleosomes on Genes
 Control of DNA Access
 Nucleosome Related TF Identification
 Enhancer Identification
 Integrating Histone Information to Predict TF binding sites
Basic Concept
 Histone
 Nucleosome
Basic Concept
 Histone
 Nucleosome
 Linker-DNA
 DNA between two nucleosomes
 RNA PolyII
 An enzyme catalyzes the transcription of DNA
 TBP
 TATA binding protein and a necessary component
of RNA polymerase
General Transcription Mechanism
”Bridge”
Chromatin
remodelling
General Transcription Mechanism
Genomic Organization of Nucleosomes
 Deposition of histones on DNA during DNA
replication occurs at random positions?
 Not Really!
Genomic Organization of Nucleosomes
 Highly phased or a random continuous distribution
Genomic Organization of Nucleosomes
 Highly phased or a random continuous distribution
 Facing inwards or outwards
Distance between Positioned nucleosomes
 Tend to be fixed distance
 short stretches of linker DNA
 165 bp (18 bp linker) in S. cerevisiae
 175 bp (28 bp linker) in D. melanogaste
 185 bp (38 bp linker) in humans
 ISWI complex models the spacing
 Linkers might have regulatory functions
The organization of nucleosomes on genes
 Nucleosome numbering
The organization of nucleosomes on genes
 Nucleosome numbering
 H2A.Z levels, acetylation, H3K4 methylation and
phasing
Nucleosome Positions
 Independent positioning
 Statistical Positioning
Analog to
Roulette wheel
Nucleosome-Free Region(NFR)
 Poly(dA:dT) tracts contribute to rigidity
 We thought promoter regions would be occluded by
nucleosomes except when they were activated.
 But in fact, NFRs demonstrated that open promoter
states are stable and common, even at genes that are
transcribed so infrequently.
Nucleosome-Free Region(NFR)
 Low basal levels of leaky transcription might have a
general housekeeping function
 Open architecture of the 5' NFR is necessary for the
initial 'pioneering' polymerase or whether
transcription itself establishes the NFR from the
closed state (after the last transcription)
Transcription start site selection by nucleosomes?
 Most promoters seem to lack core promoter elements,
including a TATA box, the TFIIB recognition element
(BRE), INR, downstream promoter element (DPE) or motif
ten element (MTE)
Control of DNA Access
 DNA accessibility without catalysis
 thermal fluctuation
 energetically less favourable towards the midpoint of the
nucleosome
 Binding of one factor might stabilize a partially disassembled
state
Control of DNA Access
 DNA accessibility without catalysis
 DNA accessibility and remodelling complexes
Control of DNA Access
 DNA accessibility without catalysis
 DNA accessibility and remodelling complexes
 Nucleosome eviction
Nucleosome Related TF
Identification
Nucleosome dynamics define transcriptional
enhancers. Nat Genet 42:343-347.
Genome-wide prediction of transcription factor
binding sites using an integrated model. Genome
Biol 11:R7.
Nucleosome Dynamics Define Transcriptional
Enhancers
 Monomethylated H3K4 (H3K4me) : enhancers,
 Trimethylated H3K4 (H3K4me3) :TSS,
 Dimethylated H3K4 (H3K4me2) : both the TSS and
enhancers
H3K4me2 are destabilized at AR
binding site, but better positioning at
flanking loci.
FOXA1 as pioneer factor to stabilize
the nucleosomes.
Motif Analysis in the Paired Nucleosome Regions
 Identify Nucleosome
Motif Analysis in the Paired Nucleosome Regions
 Identify Nucleosome
 Identify Enhancer Region
Motif Analysis in the Paired Nucleosome Regions
 Identify Nucleosome
 Identify Enhancer Region
 Motif Analysis in Enhancer Region
Genome-wide prediction of transcription factor
binding sites using an integrated model
 Eight chromatin marks (H3, H3K4me1, H3K4me2,
H3K4me3, H3K9me3, H3K36me3, H3K20me3, and
H3K27me3)
Genome-wide prediction of transcription factor
binding sites using an integrated model
Future work
 Finding candidate nucleosome organizing factors
 Better understand nucleosome positioning
Reference
 I) NUCLEOSOME POSITIONING.II) NUCLEOSOME
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REMODELING. BCH 6415. http://www.med.ufl.edu/biochem/tyang/
http://www.uio.no/studier/emner/matnat/molbio/MBV4230/
Nucleosome dynamics define transcriptional enhancers, Nature
genetics 42 (4): 343-7, 2010 Apr
Nucleosome positioning and gene regulation: advances through
genomics, Nature reviews. Genetics 10 (3): 161-72, 2009 Mar
Inducible gene expression: diverse regulatory mechanisms, Nature
reviews. Genetics , 2010 Apr 27
Genome-wide prediction of transcription factor binding sites using an
integrated model, Genome biology 11 (1): R7, 2010 Jan 22
http://en.wikipedia.org/wiki/Histone