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The Biology of Mammalian Promoters . Erik Bongcam-Rudloff. From Single Cell to Multicellular Organism. From one dimension to 3D. The Central Dogma. Protein. mRNA. DNA. Basics of transcription. Eukaryotic DNA structure Transcription Factors Promoter. Eukaryotic DNA structure….
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The Biology of MammalianPromoters • Erik Bongcam-Rudloff
The Central Dogma Protein mRNA DNA
Basics of transcription • Eukaryotic DNA structure • Transcription Factors • Promoter
Eukaryotic DNA structure… Chromosome DNA
Model of a Polymerase II Promoter TSS Proximal Promoter Core Promoter Distal Promoter
Players Basal Transcription
DNA Transcription overview • Two types – Basal and Activated • Initiation of transcription involves the binding of the Polymerase-II holoenzyme complex • Requires a number of different proteins to start the process- termination brought about by Rho-dependent and –independent mechanisms • Product encodes for a protein
Transcription • RNA polymerase – 3 types • Supplemented by GTFs (A,B,D,E,F,H) • Pre-initiation complex formed • ….binds to the promoter • Transcription initiated
OLD Dogma • The coding part of the Genome is only 1% • We have only ~40 000 genes • The rest is junk • Most of the intergenic is repetitive sequences
The Human Genome • 1,1% exons • 24% intrones • 75% intergenic DNA
New insights • Many phenotypic traits do not depend on mutations on the proteins but on disregulation of gene expression • Different species same orchestra different compositions • ~40% of the genes are alternatvely spliced
Finding Genes • HMMs can model coding regions and splice sites simultaniously.Look for coding exons (bounded by AG / GT) • Generalized HMMs (e.g. Genscan) can glue together candidate exons. • Homology based ones (GeneWise) can map proteins to genome allowing for considerable evolutionary divergence.
Finding Promoters • Very difficult • No good tools yet
Why is promoter prediction so difficult?! • Not one single type of core promoter • Promoters are dependent on additional regulatory elements • Transcription may be activated, enhanced or repressed by regulatory proteins/protein complex • Transcriptional activators and repressors act very specifically both in terms of the cell type and time in the cell cycle • Many regulatory factors have not been characterized yet
Problems to be solved • No well defined “Core promoter” • Promoter control depends on regions both upstream and downstream of the promoter region • The transcriptional machinery is capable of recognize Promoters in contrast with present statistical data that suggest that the regulatory elements do not contain sufficient information to do so.
Strategy • Cross Species Genome Comparisons • In comparing DNA across species, the functional areas are in general more conserved than the nonfunctional areas • Classification of genes based on cell specific expression patterns
Available tools • TRANSFAC (Wingender et al.) • The Eukaryotic promoter database at SIB • HMM (Krogh): Search for CpG islands • Regulatory Sequence Analysis Tools (RSA)(mirror:http://liv.bmc.uu.se/rsa-tools • Different prediction tools on the web and our own implementation