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http://cs273a.stanford.edu [Bejerano Fall10/11] 1
Thank you for the midterm feedback!
Projects will be assigned shortly.
http://cs273a.stanford.edu [Bejerano Fall10/11] 2
Lecture 12
Mid Term Feedback Feedback
Cis-Regulation
Cellular Signaling
MidTerm Feedback Feedback
General comments:•Programming requirements
–CS106A enough?
•Coverage: Depth vs. Breadth•UCSC Primer Fit•Homework vs. lectures•You’re enjoying this class :)
Let’s also reflect about doing your homework briefly.
http://cs273a.stanford.edu [Bejerano Fall10/11] 3
Big Picture Context
We are surveying the functional classes of elements encoded by the human genome.
We have previously discussed:•Repetitive sequences•Protein coding genes•Non coding RNAs
Today we’ll cover the last (known :) large class of functional elements.
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Gene Regulation
•gene (how to)•control region(when & where)
DNA
DNA binding
proteins
RNA geneProtein coding
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unicellular
multicellular
Unicellular vs. Multicellular
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Pol II Transcription
Key components:• Proteins• DNA sequence• DNA epigenetics
Protein components:• General Transcription factors• Activators• Co-activators
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Activators & Co-Activators
Protein - DNA
Protein - Protein
13
Nucleosome tail modifications
•Lysine acetylations.•Histone Acetyl-Transferases (HAT) & Histone Deacetylases (HDAC).
•Lysine and Argenine Metylations.–Modified by histone-
metyl-transferase.
•Phosphorilation.•Ubiquitination.
–H2A ubiquitination affects 10-15% of this histone in most eukaryotic cells
•ADP-ribosylation .
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Combinatorial Regulatory Code
Gene
2,000 different proteins can bind specific DNA sequences.
A regulatory region encodes 3-10 such protein binding sites.
When all are bound by proteins the regulatory region turns “on”,and the nearby gene is activated to produce protein.
Proteins
DNA
DNA
Protein binding site
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Basal factors RNAP II
Enhancer with bound protein
promoter
Enhancers: action over very large distances
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Transient Transgenic Enhancer Assay
Reporter GeneMinimal PromoterConservedElement
Construct is injected into 1 cell embryos
Taken out at embryonic day 10.5-14.5
Assayed for reporter gene activity
in situ
transgenic
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Vertebrate Enhancer Combinatorics
Sall1limbneuraltube brain
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What are Enhancers?
What do enhancers encode?
Surely a cluster of TF binding sites.
[but TFBS prediction is hard, fraught with false positives]
What else? DNA Structure related properties?
So how do we recognize enhancers?
Sequence conservation across multiple species
[weak but generic]
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Most Non-Coding Elements likely work in cis…
9Mb
“IRX1 is a member of the Iroquois homeobox gene family.
Members of this family appear to play multiple roles
during pattern formation of vertebrate embryos.”
gene deserts
regulatory jungles
Every orange tick mark is roughly 100-1,000bp long, each evolves under purifying selection, and does not code for protein.
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Many non-coding elements tested are cis-regulatory
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Vertebrate Gene Regulation
gene (how to)
control region(when & where)
DNA
proximal: in 103 letters
distal: in 106 letters
DNA binding
proteins