Download Transcriptional Regulation III

CS173
Lecture 9: Transcriptional regulation III
MW 11:00-12:15 in Beckman B302
Prof: Gill Bejerano
TAs: Jim Notwell & Harendra Guturu
http://cs173.stanford.edu [BejeranoWinter12/13]
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Announcements
• Halfway feedback end of class today
• Undergrads: CURIS in summer
http://cs173.stanford.edu [BejeranoWinter12/13]
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ATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATA
TATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTC
TAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTC
TGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACT
CTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATG
AATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAA
GCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAAT
TTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAA
CTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGG
TTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAATTGGTGAACATATTGATTATTGTGACTTCTCGGTTTTACCTTTAGCTATTGAT
TGATATGCTTTGCGCCGTCAAAGTTTTGAACGATGAGATTTCAAGTCTTAAAGCTATATCAGAGGGCTAAGCATGTGTATTCTGAAT
TTAAGAGTCTTGAAGGCTGTGAAATTAATGACTACAGCGAGCTTTACTGCCGACGAAGACTTTTTCAAGCAATTTGGTGCCTTGATG
CGAGTCTCAAGCTTCTTGCGATAAACTTTACGAATGTTCTTGTCCAGAGATTGACAAAATTTGTTCCATTGCTTTGTCAAATGGATC
ATGGTTCCCGTTTGACCGGAGCTGGCTGGGGTGGTTGTACTGTTCACTTGGTTCCAGGGGGCCCAAATGGCAACATAGAAAAGGTAA
GAAGCCCTTGCCAATGAGTTCTACAAGGTCAAGTACCCTAAGATCACTGATGCTGAGCTAGAAAATGCTATCATCGTCTCTAAACCA
ATTGGGCAGCTGTCTATATGAATTAGTCAAGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAA
TTAGCATCACAAAATACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGA
ATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTT
ATACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTTGCGAAGTT
TGGCAAGTTGCCAACTGACGAGATGCAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGT
TCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATAC
ATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGTTCT
GCAAGTTGCCAACTGACGAGATGCAGTTTCCTACGCATAATAAGAATAGGAGGGAATATCAAGCCAGACAATCTATCATTACATTTA
CGGCTCTTCAAAAAGATTGAACTCTCGCCAACTTATGGAATCTTCCAATGAGACCTTTGCGCCAAATAATGTGGATTTGGAAAAAGA
ATAAGTCATCTCAGAGTAATATAACTACCGAAGTTTATGAGGCATCGAGCTTTGAAGAAAAAGTAAGCTCAGAAAAACCTCAATACA
TCATTCTGGAAGAAAATCTATTATGAATATGTGGTCGTTGACAAATCAATCTTGGGTGTTTCTATTCTGGATTCATTTATGTACAAC
GGACTTGAAGCCCGTCGAAAAAGAAAGGCGGGTTTGGTCCTGGTACAATTATTGTTACTTCTGGCTTGCTGAATGTTTCAATATCAA
CTTGGCAAATTGCAGCTACAGGTCTACAACTGGGTCTAAATTGGTGGCAGTGTTGGATAACAATTTGGATTGGGTACGGTTTCGTTG
GCTTTTGTTGTTTTGGCCTCTAGAGTTGGATCTGCTTATCATTTGTCATTCCCTATATCATCTAGAGCATCATTCGGTATTTTCTTC
TTTATGGCCCGTTATTAACAGAGTCGTCATGGCCATCGTTTGGTATAGTGTCCAAGCTTATATTGCGGCAACTCCCGTATCATTAAT
TGAAATCTATCTTTGGAAAAGATTTACAATGATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGTTCT
GCAAGTTGCCAACTGACGAGATGCAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTT
AATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATACCT
TCTTGACATGATATGACTACCATTTTGTTATTGTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTT
AATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGA
TTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTA
CTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTT
TACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTT
ACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAA
http://cs173.stanford.edu [BejeranoWinter12/13]
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AATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGT
Transcription Regulation
http://cs173.stanford.edu [BejeranoWinter12/13]
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Gene Regulation
Some proteins and non
coding RNAs go “back”
to bind DNA near
genes, turning these
genes on and off.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Transcription Activation
Terminology:
• RNA polymerase
• Transcription Factor
• Transcription Factor Binding Site
• Promoter
• Enhancer
• Gene Regulatory Domain
TF
DNA
http://cs173.stanford.edu [BejeranoWinter12/13]
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Transcriptional Repression
• Transcription factors can bind key genomic
sites, preventing/repelling the binding of
– The RNA polymerase machinery
– Activating transcription factors
• DNA can be bent into 3D shape preventing
enhancer – promoter interactions.
• Activator and co-activator proteins can be
modified into inactive states.
Activation and repression counter-act to provide
the cell the needed levels of output from the
same stretch of DNA under the many cellular
conditions all served by (identical copies of) the
same genome.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Locus Control Region
http://cs173.stanford.edu [BejeranoWinter12/13]
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Nucleosomes, Histones, Transcription
Chromatin / Proteins
Genome packaging
provides a critical layer
of gene regulation.
DNA / Proteins
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Chromosome Centromere
Centromere:
region of DNA typically found
near the middle of a
chromosome where two
identical sister chromatids
come in contact. It is
involved in cell division
http://cs173.stanford.edu [BejeranoWinter12/13]
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Heterochromatin & Euchromatin
Heterochromatin:
Tightly coiled chromosome
material; believed to be
mostly genetically inactive.
Euchromatin:
Where temporal opening and
closing of chromatin
(“nucleosome positioning”)
and transcription takes place.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Insulators
Insulators are DNA sequences that when
placed between target gene and enhancer
prevent enhancer from acting on the gene.
•Known insulators contain binding sites for a
specific DNA binding protein (CTCF) that is
involved in DNA 3D conformation.
•However, CTCF fulfills additional roles
besides insulation. I.e, the presence of a
CTCF site does not ensure that a genomic
region acts as an insulator.
TSS1
TSS2
Insulator
http://cs173.stanford.edu [BejeranoWinter12/13]
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Signal Transduction
Everything we discussed so far happens within the cell.
But cells talk to each other, copiously.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Enhancers as Integrators
IF the cell is
part of a certain tissue
AND
receives a certain signal
THEN turn Gene ON
Gene
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Gene Regulation
Chromatin / Proteins
Extracellular signals
DNA / Proteins
http://cs173.stanford.edu [BejeranoWinter12/13]
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Histone Tails, Histone Marks
DNA is wrapped around nucleosomes.
Nucleosomes are made of histones.
Histones have free tails.
Residues in the tails are modified in specific patterns
in conjunction with specific gene regulation activity.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Histone Mark Correlation Examples
Active gene promoters are marked by H3K4me3
Silenced gene promoters are marked by H3K27me3
p300, a protein component of many active enhancers
acetylates H3k27Ac.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Measuring these different states
Note that the DNA itself doesn’t change. We sequence different portions of it that
are currently in different states (bound by a TF, wrapped around a nucleosome etc.)
http://cs173.stanford.edu [BejeranoWinter12/13]
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Epigenomics: study all these marks genomewide
Translate observations
into current genome state.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Obtain a network of all active genes & DNA
Now what?
(to be revisited)
“Ridicilogram”
http://cs173.stanford.edu [BejeranoWinter12/13]
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Histone Code Hypothesis
Histone modifications serve to recruit other proteins by
specific recognition of the modified histone via protein
domains specialized for such purposes, rather than through
simply stabilizing or destabilizing the interaction between
histone and the underlying DNA.
histone
modification:
writer
eraser
…
reader
http://cs173.stanford.edu [BejeranoWinter12/13]
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Cis-Regulatory Components
Low level (“atoms”):
• Promoter motifs (TATA box, etc)
• Transcription factor binding sites (TFBS)
Mid Level:
• Promoter
• Enhancers
• Repressors/silencers
• Insulators/boundary elements
• Locus control regions
High Level:
• Epigenomic domains / signatures
• Gene expression domains
• Gene regulatory networks
http://cs173.stanford.edu [BejeranoWinter12/13]
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Epigenomics is not Epigenetics
Epigenetics is the study of heritable changes in gene expression or
cellular phenotype, caused by mechanisms other than changes in the
underlying DNA sequence
There are objections to the use of the term epigenetic to describe
chemical modification of histone, since it remains unknown whether or
not these modifications are heritable.
http://cs173.stanford.edu [BejeranoWinter12/13]
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Almost done with genome content & function
We’ve talked about transcripts and their regulation.
We’re still ignore at least half the genome…
http://cs173.stanford.edu [BejeranoWinter12/13]
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To be continued
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Halfway Feedback
Thank you!
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