ZHANG ZHIZHUO MAY 2010 Nucleosome Positioning & Transcription Factor Identification

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 dynamics define transcriptional enhancers. Nat Genet 42: Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biol 11:R7. Nucleosome Related TF Identification

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 REMODELING. BCH 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): , 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