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MW  11:00-12:15 in Beckman B302Prof: Gill BejeranoTAs: Jim Notwell & Harendra Guturu

CS173

Lecture 9: Transcriptional regulation III

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Announcements• Halfway feedback end of class today• Undergrads: CURIS in summer

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TTATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATACATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCAGTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCCGTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACTAGCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGATAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTGTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAATTCTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGATTTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAATTGGTGAACATATTGATTATTGTGACTTCTCGGTTTTACCTTTAGCTATTGATTTTGATATGCTTTGCGCCGTCAAAGTTTTGAACGATGAGATTTCAAGTCTTAAAGCTATATCAGAGGGCTAAGCATGTGTATTCTGAATCTTTAAGAGTCTTGAAGGCTGTGAAATTAATGACTACAGCGAGCTTTACTGCCGACGAAGACTTTTTCAAGCAATTTGGTGCCTTGATGAACGAGTCTCAAGCTTCTTGCGATAAACTTTACGAATGTTCTTGTCCAGAGATTGACAAAATTTGTTCCATTGCTTTGTCAAATGGATCATATGGTTCCCGTTTGACCGGAGCTGGCTGGGGTGGTTGTACTGTTCACTTGGTTCCAGGGGGCCCAAATGGCAACATAGAAAAGGTAAAAGAAGCCCTTGCCAATGAGTTCTACAAGGTCAAGTACCCTAAGATCACTGATGCTGAGCTAGAAAATGCTATCATCGTCTCTAAACCAGCATTGGGCAGCTGTCTATATGAATTAGTCAAGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAACTTTAGCATCACAAAATACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTTTCCTACGCATAATAAGAATAGGAGGGAATATCAAGCCAGACAATCTATCATTACATTTAAGCGGCTCTTCAAAAAGATTGAACTCTCGCCAACTTATGGAATCTTCCAATGAGACCTTTGCGCCAAATAATGTGGATTTGGAAAAAGAGTATAAGTCATCTCAGAGTAATATAACTACCGAAGTTTATGAGGCATCGAGCTTTGAAGAAAAAGTAAGCTCAGAAAAACCTCAATACAGCTCATTCTGGAAGAAAATCTATTATGAATATGTGGTCGTTGACAAATCAATCTTGGGTGTTTCTATTCTGGATTCATTTATGTACAACCAGGACTTGAAGCCCGTCGAAAAAGAAAGGCGGGTTTGGTCCTGGTACAATTATTGTTACTTCTGGCTTGCTGAATGTTTCAATATCAACACTTGGCAAATTGCAGCTACAGGTCTACAACTGGGTCTAAATTGGTGGCAGTGTTGGATAACAATTTGGATTGGGTACGGTTTCGTTGGTGCTTTTGTTGTTTTGGCCTCTAGAGTTGGATCTGCTTATCATTTGTCATTCCCTATATCATCTAGAGCATCATTCGGTATTTTCTTCTCTTTATGGCCCGTTATTAACAGAGTCGTCATGGCCATCGTTTGGTATAGTGTCCAAGCTTATATTGCGGCAACTCCCGTATCATTAATGCTGAAATCTATCTTTGGAAAAGATTTACAATGATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGTTCTTGGCAAGTTGCCAACTGACGAGATGCAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGATACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATAAAG

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Transcription Regulation

Gene Regulation

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Some proteins and non coding RNAs go “back” to bind DNA near genes, turning these genes on and off.

Transcription Activation

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Terminology:• RNA polymerase• Transcription Factor• Transcription Factor Binding Site• Promoter• Enhancer• Gene Regulatory Domain

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TF

DNA

Transcriptional Repression

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• 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.

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Locus Control Region

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Nucleosomes, Histones, Transcription

Chromatin / Proteins

DNA / Proteins

Genome packaging provides a critical layer of gene regulation.

Chromosome Centromere

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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

Heterochromatin & Euchromatin

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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.

Insulators

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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.

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TSS1 TSS2

Insulator

Signal TransductionEverything we discussed so far happens within the cell.But cells talk to each other, copiously.

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Enhancers as Integrators

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Gene

IF the cell ispart of a certain tissueANDreceives a certain signal

THEN turn Gene ON

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Gene RegulationChromatin / Proteins

DNA / Proteins

Extracellular signals

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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.

Histone Mark Correlation ExamplesActive gene promoters are marked by H3K4me3Silenced gene promoters are marked by H3K27me3p300, a protein component of many active enhancers acetylates H3k27Ac.

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Measuring these different states

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Note that the DNA itself doesn’t change. We sequence different portions of it thatare currently in different states (bound by a TF, wrapped around a nucleosome etc.)

Epigenomics: study all these marks genomewide

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Translate observationsinto current genome state.

Obtain a network of all active genes & DNA

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Now what?(to be revisited)

“Ridicilogram”

Histone Code HypothesisHistone 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.

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histonemodification:

writer

reader

eraser…

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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 regionsHigh Level:• Epigenomic domains / signatures• Gene expression domains• Gene regulatory networks

Epigenomics is not EpigeneticsEpigenetics 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.

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Almost done with genome content & functionWe’ve talked about transcripts and their regulation.We’re still ignore at least half the genome…

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To be continued

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Halfway Feedback

Thank you!