Initiation of transcription by Pol I

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Initiation of transcription by Pol I 1) UBF binds UCE and core element 2) SL1 (selectivity factor 1) binds UBF (not DNA) 3) complex recruits Pol I 4) Pol I transcribes until it hits a termination site

Initiation of Pol III transcription 1) TFIIIA binds C box 2) recruits TFIIIC 3) TFIIIB binds 4) Complex recruits Pol III 5) Pol III goes until hits > 4 T's

Initiation of transcription by Pol III 1) TFIIIC binds box B 2) recruits TFIIIB 3) complex recruits Pol III 4) Pol III runs until hits > 4 Ts

Initiation of transcription by Pol II Basal transcription 1) TFIID binds TATAA box 2) TFIIA and TFIIB bind to TFIID/DNA 3) Complex recruits Pol II 4) Still must recruit TFIIE & TFIIH to form initiation complex

Initiation of transcription by Pol II Basal transcription 1) Once assemble initiation complex must start Pol II 2) TFIIH kinases CTD

Initiation of transcription by Pol II Basal transcription 1) Once assemble initiation complex must start Pol II 2) TFIIH kinases CTD negative charge gets it started 3) Exchange initiation for elongation factors

Initiation of transcription by Pol II Basal transcription 1) Once assemble initiation complex must start Pol II 2) Kinase CTD negative charge gets it started 3) Exchange initiation for elongation factors 4) Continues until hits terminator

Initiation of transcription by Pol II Basal transcription 1) Once assemble initiation complex must start Pol II 2) Kinase CTD negative charge gets it started 3) RNA pol II is paused on many promoters!

Initiation of transcription by Pol II Basal transcription 1) Once assemble initiation complex must start Pol II 2) Kinase CTD negative charge gets it started 3) RNA pol II is paused on many promoters! even of genes that aren’t expressed! (low [mRNA])

Initiation of transcription by Pol II RNA pol II is paused on many promoters! even of genes that aren’t expressed! (low [mRNA]) Early elongation is also regulated!

Initiation of transcription by Pol II RNA pol II is paused on many promoters! even of genes that aren’t expressed! (low [mRNA]) Early elongation is also regulated! PTEFb kinases CTD to stimulate processivity & processing

Initiation of transcription by Pol II RNA pol II is paused on many promoters! even of genes that aren’t expressed! (low [mRNA]) Early elongation is also regulated! PTEFb kinases CTD to stimulate processivity & processing Many genes have short transcripts

Initiation of transcription by Pol II RNA pol II is paused on many promoters! even of genes that aren’t expressed! (low [mRNA]) Early elongation is also regulated! PTEFb kinases CTD to stimulate processivity & processing Many genes have short transcripts Yet another new level of control!

Transcription Template strand determines next base Positioned by H-bonds until RNA polymerase links 5’ P to 3’ OH in front

Transcription Template strand determines next base Positioned by H-bonds until RNA polymerase links 5’ P to 3’ OH in front Energy comes from hydrolysis of 2 Pi

NTP enters E site & rotates into A site Transcription NTP enters E site & rotates into A site

NTP enters E site & rotates into A site Transcription NTP enters E site & rotates into A site Specificity comes from trigger loop

Specificity comes from trigger loop Transcription Specificity comes from trigger loop Mobile motif that swings into position & triggers catalysis

Specificity comes from trigger loop Transcription Specificity comes from trigger loop Mobile motif that swings into position & triggers catalysis Release of PPi Triggers translocation

Transcription Proofreading: when it makes a mistake it removes ~ 5 bases & tries again

Activated transcription by Pol II Studied by mutating promoters for reporter genes

Activated transcription by Pol II Studied by mutating promoters for reporter genes Requires transcription factors and changes in chromatin

Activated transcription by Pol II enhancers are sequences 5’ to TATAA transcriptional activators bind them have distinct DNA binding and activation domains

Activated transcription by Pol II enhancers are sequences 5’ to TATAA transcriptional activators bind them have distinct DNA binding and activation domains activation domain interacts with mediator helps assemble initiation complex on TATAA

Activated transcription by Pol II enhancers are sequences 5’ to TATAA transcriptional activators bind them have distinct DNA binding and activation domains activation domain interacts with mediator helps assemble initiation complex on TATAA Recently identified “activating RNA”: bind enhancers & mediator

Activated transcription by Pol II Other lncRNA “promote transcriptional poising” in yeast http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001715 lncRNA displaces glucose-responsive repressors & co- repressors from genes for galactose catabolism

Activated transcription by Pol II Other lncRNA “promote transcriptional poising” in yeast http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001715 lncRNA displaces glucose-responsive repressors & co- repressors from genes for galactose catabolism Speeds induction of GAL genes