Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream...

12
1 Biol321 Molecular Genetics Handout 9

Transcript of Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream...

Page 1: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

1

Biol321 Molecular Genetics

Handout 9

Page 2: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

2

Yeast RNA polymerase II subunits

PTSPSYS CTD

Epitope tagging

Page 3: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

3

Prokaryotic RNA polymerase

Eukaryotic RNA polymerase

RNAP from T. aquaticus

Page 4: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

4

Initiation of transcription by RNA

polymerase II

UCE

-200 -150 -100 -50 +1 +50 +100 +150 +200

-45 +20

-25 InrUps tream Elements

Core promoter

RNA Pol I

RNA Pol II

RNA Pol III

RNA polymerase promoters

Page 5: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

5

Initiation at RNA Pol. II promoter

Initiator sequenceYYCARR

-25 box = TATA boxTATAWAW

-25 InrUps tream Elements

RNA Pol II

TFIID: (~800kD, larger than RNA pol II at ~600kD)

TBP

TAFs(9 to14)

TBP = TATA binding protein

TAF = TBP associated factors

TATAAATATAAA

mRNA

Building the preinitiation complex (PIC)

Page 6: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

6

TBP bends DNA ~80o and forces open the minor groove

Page 7: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

7

-200 -150 -100 -50 +1 +50 +100 +150 +200

-25 InrUps tream elements

RNA Pol II

Initiation at RNA Pol. II promoter

TF TF TF

- + +

TAF

TBPA B

F

EH

Stimulation of transcription by activator binding to an enhancer

Page 8: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

8

The Mediator Complex Links Activation Domains to RNA Pol II

Activation of transcriptionBy transcription factors (TFs),

activator, and coactivator proteins

Page 9: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

9

Initiation at RNA Pol. I promoter

Core Promoter

Upstream Control Element

(CP)

Initiation at RNA Pol. I promoter

(CP)

RNAP I

UB

FU

BF

UB

FU

BF

SL1TIF-IATIF-IC

OnUBF UBF Binds (as a dimer) CP and UCE

SL1 SL1 (in humans) ≡ TIF-IB in mouseTIF-IATIF-IC Recruitment of RNA Pol. I

RNAP I RNA Pol. I

Page 10: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

10

RNA polymerase III promoters

Initiation at RNA Pol. III promoter

TFIIIC Binds box A and box C

Binds to TFIIIC

Recruitment of RNA Pol. III

RNAP III RNA Pol. III

TFIIIA

TFIIIB

Recruit TFIIIB

TFIIIC TFIIICTFIIIA

TFIIIB

RNAP III

On

Page 11: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

11

Page 12: Biol321 Molecular Genetics - WordPress.com · 7-200 -150 -100 -50 +1 +50 +100 +150 +200 Upstream elements -25 Inr RNA Pol II Initiation at RNA Pol. II promoter TF TF TF-+ + TAF A

12

Regulatory

Holoenzymes with different promoter-binding specificity

SigmaFactor Promoters Recognized Promoter Consensus

-35 Region -10 Region70 (rpoD) Most genes TTGACAT TATAAT32 (rpoH) Genes induced by heat shock TCTCNCCCTTGAA CCCCATNTA

-24 Region -12 Region54 (rpoN) Genes for nitrogen metabolism and CTGGNA TTGCAother functions


Escherichia coli DNA Polymerase IV (Pol IV), but Not Pol ...Pol I, Pol II, Pol IV, and Pol V. Pol I, like Pol III, contributes to DNA replication, particularly on the lagging strand

Escherichia coli DNA Polymerase IV (Pol IV), but Not Pol ...Pol I, Pol II, Pol IV, and Pol V. Pol I, like Pol III, contributes to DNA replication, particularly on the lagging strand

VIETNAM Forest Sector Development Project · forest sector development project (ida-39530 ida-50700 tf-50865 tf-54122 tf-54523 tf-54524 tf-53397)

VIETNAM Forest Sector Development Project · forest sector development project (ida-39530 ida-50700 tf-50865 tf-54122 tf-54523 tf-54524 tf-53397)

Widespread Backtracking by RNA Pol II Is a Major Effector ... · (A) Transcription rates were calculated using Bru-seq data shown in Fig. 3A (left panel) or pol II ChIP-seq data shown

Widespread Backtracking by RNA Pol II Is a Major Effector ... · (A) Transcription rates were calculated using Bru-seq data shown in Fig. 3A (left panel) or pol II ChIP-seq data shown

Edwin van der Pol November 19th, 2019 · Extracellular vesicles (EVs) cells release vesicles: biological nanoparticles with receptors, DNA, RNA specialized functions clinically relevant

Edwin van der Pol November 19th, 2019 · Extracellular vesicles (EVs) cells release vesicles: biological nanoparticles with receptors, DNA, RNA specialized functions clinically relevant

Double-Stranded RNA Virus Gag-Pol Fusion Protein

Double-Stranded RNA Virus Gag-Pol Fusion Protein

Crystal structure of the 14-subunit RNA polymerase I · 2020-03-06 · The crystal structure of Pol I reveals several striking new features compared to other RNA polymerases (Fig.

Crystal structure of the 14-subunit RNA polymerase I · 2020-03-06 · The crystal structure of Pol I reveals several striking new features compared to other RNA polymerases (Fig.

CAGE, RAMPAGE, & RNA Pol II - GEP Community Servercommunity.gep.wustl.edu/.../Module_TSS3_Advanced.docx · Web viewThe Celniker TSS predictions were based on the analysis of experimental

CAGE, RAMPAGE, & RNA Pol II - GEP Community Servercommunity.gep.wustl.edu/.../Module_TSS3_Advanced.docx · Web viewThe Celniker TSS predictions were based on the analysis of experimental

Single Cell RNA-seq Data Clustering using TF-IDF based …Keywords: Single cell RNA-Seq; clustering; TF-IDF Introduction The recent advances in single cell RNA sequencing (scRNA-Seq)

Single Cell RNA-seq Data Clustering using TF-IDF based …Keywords: Single cell RNA-Seq; clustering; TF-IDF Introduction The recent advances in single cell RNA sequencing (scRNA-Seq)

BIFURCATIONS OF THE FORCED VAN DER POL OSCILLATOR* · 2018. 11. 16. · BIFURCATIONS OF THE FORCED VAN DER POL OSCILLATOR 499 segment CB, such that, for («, F) £ Bsc , X{0>tF) has

BIFURCATIONS OF THE FORCED VAN DER POL OSCILLATOR* · 2018. 11. 16. · BIFURCATIONS OF THE FORCED VAN DER POL OSCILLATOR 499 segment CB, such that, for («, F) £ Bsc , X{0>tF) has

TF 0031 DIN TF 0705 DIN TF 0967 DIN TF 0813 DIN TF 0747 ...imgusr.tradekey.com/images/uploadedimages/...TF 0705 BED TF 0733 BED TF 0753 BED TF 1020 BED TF 1090 BED TF 0724 BED (Single)

TF 0031 DIN TF 0705 DIN TF 0967 DIN TF 0813 DIN TF 0747 ...imgusr.tradekey.com/images/uploadedimages/...TF 0705 BED TF 0733 BED TF 0753 BED TF 1020 BED TF 1090 BED TF 0724 BED (Single)

Regulating transcription Telling RNA pol to copy a DNA sequence Transcription factors bind promoters & control initiation of transcription 1/signal gene.

Regulating transcription Telling RNA pol to copy a DNA sequence Transcription factors bind promoters & control initiation of transcription 1/signal gene.

RNA Protein DNA Replication TranscriptionTranslation Polymerase Monomers DNA Pol III (and I) dNTPs Direction of synthesis 5’ to 3’ TemplatessDNA Product.

RNA Protein DNA Replication TranscriptionTranslation Polymerase Monomers DNA Pol III (and I) dNTPs Direction of synthesis 5’ to 3’ TemplatessDNA Product.

Targeting RNA-Polymerase I in Both Chemosensitive and ... · genesis, and targeting this process with RNA polymerase I (Pol I) inhibitors has shown some efficacy. We examined the

Targeting RNA-Polymerase I in Both Chemosensitive and ... · genesis, and targeting this process with RNA polymerase I (Pol I) inhibitors has shown some efficacy. We examined the

DNA Synthesis 3' 5' SSB 5' Leading Strand 5' DNA Pol I 3' DNA Ligase Lagging Strand Helicase Gyrase 3' 5' DNA Pol III Primase RNA primers DNA template.

DNA Synthesis 3' 5' SSB 5' Leading Strand 5' DNA Pol I 3' DNA Ligase Lagging Strand Helicase Gyrase 3' 5' DNA Pol III Primase RNA primers DNA template.

Alteration of BRCA1 expression affects alcohol-induced transcription of RNA Pol III-dependent genes

Alteration of BRCA1 expression affects alcohol-induced transcription of RNA Pol III-dependent genes

Biology 331 Virology II. Class IV and V Viruses RNA/RNA Pol (1 error/50,000 bases)

Biology 331 Virology II. Class IV and V Viruses RNA/RNA Pol (1 error/50,000 bases)

Genome-wide mapping of RNA Pol-II promoter usage in mouse ...

Genome-wide mapping of RNA Pol-II promoter usage in mouse ...

(TF-QA1,TF-QC1,TF-QC3,TF-QS5)en.led595.com/DownLoad/TF-Q serial control card smart settings... · (TF-QA1,TF-QC1,TF-QC3,TF-QS5) Controlcardmustbeconnectedwithcomputer Afterinstalledthesoftware“PowerLED”pleaseopenthesoftware.

(TF-QA1,TF-QC1,TF-QC3,TF-QS5)en.led595.com/DownLoad/TF-Q serial control card smart settings... · (TF-QA1,TF-QC1,TF-QC3,TF-QS5) Controlcardmustbeconnectedwithcomputer Afterinstalledthesoftware“PowerLED”pleaseopenthesoftware.

Transcriptional repression by FACT is linked to regulation ...€¦ · At these so-called bidirectional promoters, RNA Pol II initiates transcription and undergoes promoter-proximal

Transcriptional repression by FACT is linked to regulation ...€¦ · At these so-called bidirectional promoters, RNA Pol II initiates transcription and undergoes promoter-proximal

Recap eukaryotes have 3 nuclear RNA polymerases, which transcribe unique sets of genes RNA pol II transcribes protein coding genes and must respond to.

Recap eukaryotes have 3 nuclear RNA polymerases, which transcribe unique sets of genes RNA pol II transcribes protein coding genes and must respond to.