Regulating gene expression
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Regulating gene expression Goal is controlling Proteins How many? Where? How active? 8 levels (two not shown are mRNA localization & prot degradation). Regulating gene expression 1) initiating transcription most important ~50% of control.

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Regulating gene expression Goal is controlling Proteins How many? Where? How active?

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Regulating gene expression goal is controlling proteins how many where how active

  • Regulating gene expression

  • Goal is

  • controlling

  • Proteins

  • How many?

  • Where?

  • How active?

  • 8 levels (two not

  • shown are mRNA

  • localization & prot

  • degradation)


Regulating gene expression goal is controlling proteins how many where how active

  • Regulating gene expression

  • 1) initiating

  • transcription

  • most important

  • ~50% of control


Regulating gene expression goal is controlling proteins how many where how active

  • Initiating transcription in Prokaryotes

  • Core RNA polymerase is promiscuous

  • sigma factors provide specificity

  • Bind promoters

  • Different sigmas bind different promoters


Regulating gene expression goal is controlling proteins how many where how active

Initiating transcription in Prokaryotes

3) Once bound, RNA polymerase

“melts”the DNA

4) rNTPs bind template

5) RNA polymerase catalyzes phosphodiester bonds, melts and unwinds template

6) sigma falls off after ~10 bases are added


Regulating gene expression goal is controlling proteins how many where how active

  • Structure of Prokaryotic promoters

    • Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter.


Regulating gene expression goal is controlling proteins how many where how active

  • Structure of Prokaryotic promoters

    • Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter.


Regulating gene expression goal is controlling proteins how many where how active

  • Structure of Prokaryotic promoters

    • Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter.

    • nrsBACD encode nickel transporters


Regulating gene expression goal is controlling proteins how many where how active

  • Structure of Prokaryotic promoters

  • Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter.

  • nrsBACD encode nickel transporters

  • nrsRS encode “two component” signal transducers

  • nrsS encodes a his kinase

  • nrsR encodes a response regulator


Regulating gene expression goal is controlling proteins how many where how active

  • Structure of Prokaryotic promoters

  • nrsRS encode “two component” signal transducers

  • nrsS encodes a his kinase

  • nrsR encodes a response regulator

    • When nrsS binds Ni it kinases nrsR


Regulating gene expression goal is controlling proteins how many where how active

  • Structure of Prokaryotic promoters

  • nrsRS encode “two component” signal transducers

  • nrsS encodes a his kinase

  • nrsR encodes a response regulator

    • When nrsS binds Ni it kinases nrsR

    • nrsR binds Ni promoter and activates

    • transcription of both operons


Regulating gene expression goal is controlling proteins how many where how active

Termination of transcription in prokaryotes

1) Sometimes go until ribosomes fall too far behind


Regulating gene expression goal is controlling proteins how many where how active

Termination of transcription in prokaryotes

1) Sometimes go until ribosomes fall too far behind

2) ~50% of E.coli genes require a termination factor called “rho”


Regulating gene expression goal is controlling proteins how many where how active

Termination of transcription in prokaryotes

1) Sometimes go until ribosomes fall too far behind

2) ~50% of E.coli genes require atermination factor called“rho”

3) rrnB first forms an RNA hairpin, followed by an 8 base sequence TATCTGTT that halts transcription


Regulating gene expression goal is controlling proteins how many where how active

Transcription in Eukaryotes

3 RNA polymerases

all are multi-subunit

complexes

5 in common

3 very similar

variable # unique ones

Now have Pols IV & V in plants

Make siRNA


Regulating gene expression goal is controlling proteins how many where how active

Transcription in Eukaryotes

RNA polymerase I: 13 subunits (5 + 3 + 5 unique)

acts exclusively in nucleolus to make 45S-rRNA precursor


Regulating gene expression goal is controlling proteins how many where how active

  • Transcription in Eukaryotes

  • Pol I: acts exclusively in nucleolus to make 45S-rRNA precursor

    • accounts for 50% of total RNA synthesis


Regulating gene expression goal is controlling proteins how many where how active

  • Transcription in Eukaryotes

  • Pol I: acts exclusively in nucleolus to make 45S-rRNA precursor

    • accounts for 50% of total RNA synthesis

    • insensitive to-aminitin


Regulating gene expression goal is controlling proteins how many where how active

  • Transcription in Eukaryotes

  • Pol I: only makes 45S-rRNA precursor

    • 50 % of total RNA synthesis

    • insensitive to-aminitin

    • Mg2+ cofactor

    • Regulated @ initiation frequency


Regulating gene expression goal is controlling proteins how many where how active

  • RNA polymerase I

  • promoter is5' to "coding sequence"

  • 2 elements

    • 1)essential core includes transcription start site

+1

-100

coding sequence

  • UCE

  • core


Regulating gene expression goal is controlling proteins how many where how active

  • RNA polymerase I

  • promoter is 5' to "coding sequence"

  • 2 elements

    • 1)essential core includes transcription start site

    • 2) UCE (Upstream Control Element) at ~ -100stimulates transcription 10-100x

+1

-100

coding sequence

  • UCE

  • core


Regulating gene expression goal is controlling proteins how many where how active

  • Initiation of transcription by Pol I

  • Order of events was determined by in vitro reconstitution

  • 1) UBF (upstream binding factor) binds UCE and core element

    • UBF is a transcription factor: DNA-binding proteins which recruit polymerases and tell them where to begin


Regulating gene expression goal is controlling proteins how many where how active

Initiation of transcription by Pol I

1) UBF binds UCE and core element

2) SL1(selectivity factor 1) bindsUBF (not DNA)

SL1 is a coactivator

proteins which

bind transcription

factors and

stimulate

transcription


Regulating gene expression goal is controlling proteins how many where how active

Initiation of transcription by Pol I

1) UBF binds UCE and core element

2) SL1(selectivity factor 1) bindsUBF(not DNA)

SL1 is a complex of

4 proteins including

TBP (TATAA-

binding protein)


Regulating gene expression goal is controlling proteins how many where how active

Initiation of transcription by Pol I

1) UBF binds UCE and core element

2) SL1(selectivity factor 1) bindsUBF (notDNA)

3) complex recruits Pol I


Regulating gene expression goal is controlling proteins how many where how active

Initiation of transcription by Pol I

1) UBF binds UCE and core element

2) SL1(selectivity factor 1) bindsUBF (not DNA)

3) complex recruits Pol I

4) Pol I transcribes until

it hits atermination site


Regulating gene expression goal is controlling proteins how many where how active

  • Processing rRNA

  • ~ 200 bases are methylated

  • Box C/D snoRNA picks sites


  • Regulating gene expression goal is controlling proteins how many where how active

    • Processing rRNA

  • ~ 200 bases are methylated

  • Box C/D snoRNA picks sites

  • One for each!


  • Regulating gene expression goal is controlling proteins how many where how active

    • Processing rRNA

  • ~ 200 bases are methylated

  • Box C/D snoRNA picks sites

  • One for each!

  • 2) Another ~ 200 are pseudo-uridylated

  • Box H/ACA snoRNAs pick sites


  • Regulating gene expression goal is controlling proteins how many where how active

    • Processing rRNA

  • ~ 400 bases are methylated or pseudo-uridylated

    • snoRNAs pick sites

    • One for each!

      2) 45S pre-rRNA is cut into 28S, 18S and 5.8S products


  • Regulating gene expression goal is controlling proteins how many where how active

    • Processing rRNA

  • ~ 200 bases are methylated

    2) 45S pre-rRNA is cut into 28S,

    18S and 5.8S products

    3) Ribosomes are assembled w/in nucleolus


  • Regulating gene expression goal is controlling proteins how many where how active

    RNA Polymerase III

    Reconstituted in vitro

    makes ribosomal 5S and tRNA

    (+ some snRNA & scRNA)


    Regulating gene expression goal is controlling proteins how many where how active

    RNA Polymerase III

    makesribosomal 5SandtRNA

    (+ some snRNA & scRNA)

    >100 different kinds of genes

    ~10% of all RNA synthesis


    Regulating gene expression goal is controlling proteins how many where how active

    RNA Polymerase III

    makesribosomal 5SandtRNA

    (+ some snRNA & scRNA)

    >100 different kinds of genes

    ~10% of all RNA synthesis

    Cofactor = Mn2+ cfMg2+


    Regulating gene expression goal is controlling proteins how many where how active

    RNA Polymerase III

    makesribosomal 5SandtRNA

    (+ some snRNA & scRNA)

    >100 different kinds of genes

    ~10% of all RNA synthesis

    Cofactor = Mn2+ cfMg2+

    sensitive to high [-aminitin]


    Regulating gene expression goal is controlling proteins how many where how active

    • RNA Polymerase III

    • makesribosomal 5SandtRNA (also some snRNA and some scRNA)

      • Has the most subunits


    Regulating gene expression goal is controlling proteins how many where how active

    • RNA Polymerase III

    • makesribosomal 5SandtRNA (also some snRNA and some scRNA)

      • Has the most subunits

      • Regulated @

      • initiation frequency


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    promoter is often w/in "coding" sequence!


    Regulating gene expression goal is controlling proteins how many where how active

    • Initiation of transcription by Pol III

    • promoter is w/in "coding" sequence!

    • 5S & tRNA promoters differ

      • 5S has single “C” box


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    1) TFIIIAbinds C box in 5S

    2) recruits TFIIIC


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    TFIIIAbinds C box

    recruits TFIIIC

    3) TFIIIB binds

    TBP & 2 others


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of Pol III transcription

    1) TFIIIA binds C box

    2) recruits TFIIIC

    3) TFIIIB binds

    4) Complex recruits Pol III


    Regulating gene expression goal is controlling proteins how many where how active

    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


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    promoter is w/in coding sequence!

    5S & tRNA promoters differ

    tRNA genes have “A”& “B”boxes


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    tRNA genes have “A”and “B”boxes

    1) TFIIIC binds B box


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    tRNA genes have “A”and “B”boxes

    1) TFIIIC binds B box

    2) recruits TFIIIB


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol III

    1) TFIIIC binds box B

    2) recruits TFIIIB

    3) complex recruits Pol III


    Regulating gene expression goal is controlling proteins how many where how active

    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


    Regulating gene expression goal is controlling proteins how many where how active

    • Processing tRNA

    • tRNA is trimmed

      • 5’ end by RNAse P

      • (contains RNA)

      • 3’ end by RNAse Z

      • Or by exonucleases


    Regulating gene expression goal is controlling proteins how many where how active

    • Processing tRNA

    • tRNA is trimmed

    • Transcript is spliced

    • Some tRNAs are

    • assembled from 2 transcripts


    Regulating gene expression goal is controlling proteins how many where how active

    • Processing tRNA

    • tRNA is trimmed

    • Transcript is spliced

    • CCA is added to 3’ end

    • By tRNA nucleotidyl

    • transferase (no template)

    • tRNA +CTP -> tRNA-C + PPitRNA-C +CTP--> tRNA-C-C + PPitRNA-C-C +ATP -> tRNA-C-C-A + PPi


    Regulating gene expression goal is controlling proteins how many where how active

    • Processing tRNA

    • tRNA is trimmed

    • Transcript is spliced

    • CCA is added to 3’ end

    • Many bases are modified

    • Significance unclear


    Regulating gene expression goal is controlling proteins how many where how active

    Processing tRNA

    tRNA is trimmed

    Transcript is spliced

    CCA is added to 3’ end

    Many bases are modified

    No cap! -> 5’ P

    (due to 5’ RNAse P cut)


    Regulating gene expression goal is controlling proteins how many where how active

    RNA Polymerase II

    makes mRNA (actually hnRNA), some snRNA and scRNA


    Regulating gene expression goal is controlling proteins how many where how active

    • RNA Polymerase II

    • makes mRNA (actually hnRNA), some snRNA and scRNA

      • >30,000 different genes


    Regulating gene expression goal is controlling proteins how many where how active

    • RNA Polymerase II

    • makes mRNA (actually hnRNA), some snRNA and scRNA

      • >30,000 different genes

      • 20-40% of total RNA synthesis


    Regulating gene expression goal is controlling proteins how many where how active

    • RNA Polymerase II

    • makes mRNA (actually hnRNA), some snRNA and scRNA

      • ~ 30,000 different genes

      • 20-40% of all RNA synthesis

      • very sensitive to -aminitin


    Regulating gene expression goal is controlling proteins how many where how active

    RNA Polymerase II

    12 subunits in yeast,

    unknown elsewhere


    Regulating gene expression goal is controlling proteins how many where how active

    • RNA Polymerase II

    • 12 subunits in yeast,

    • unknown elsewhere

    • Largest subunit (L’) has

    • CarboxyTerminal

    • Domain (CTD)

      • important role in

      • regulating pol II


    Regulating gene expression goal is controlling proteins how many where how active

    • Initiation of transcription by Pol II

    • Needs > 30 other factors to initiate transcription

      • final complex is called atranscriptosome

      • contains > 50 proteins


    Regulating gene expression goal is controlling proteins how many where how active

    • Initiation of transcription by Pol II

    • Separate basal and activated transcription

      • basal transcription is notregulated

      • driven by minimal promoter


    Regulating gene expression goal is controlling proteins how many where how active

    • Initiation of transcription by Pol II

    • Separate basaland activated transcription

      • basal transcription is not regulated

      • driven by minimal promoter

      • TATAA box at -30

    +1

    -30

    coding sequence

    • TATAA


    Regulating gene expression goal is controlling proteins how many where how active

    • Initiation of transcription by Pol II

    • Separate basal and activated transcription

      • activated transcription is regulated by proteins bound to promoter elements called enhancers and silencers

      • usually 5’ to TATAA box

    +1

    -30

    coding sequence

    • UCE

    • TATAA


    Regulating gene expression goal is controlling proteins how many where how active

    • Initiation of transcription by Pol II

    • Separate basal and activated transcription

      • activated transcription is regulated by proteins bound to promoter elements called enhancers and silencers

      • usually 5’ to TATAA box

      • Requires nucleosome repositioning

    +1

    -30

    coding sequence

    • UCE

    • TATAA


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol II

    Basal transcription

    1) TFIID (includingTBP) binds TATAA box


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription

    by Pol II

    Basal transcription

    1) TFIID binds to

    TATAA box

    2) Distorts DNA


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol II

    Basal transcription

    1) TFIID binds TATAA box

    2) TFIIA and TFIIB bind TFIID/DNA


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol II

    Basal transcription

    1) TFIID binds TATAA box

    2) TFIIA and TFIIB bind

    TFIID/DNA

    3) Complex recruits Pol II


    Regulating gene expression goal is controlling proteins how many where how active

    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


    Regulating gene expression goal is controlling proteins how many where how active

    Initiation of transcription by Pol II

    Basal transcription

    1) Once assemble initiation complex must start Pol II

    2) TFIIH kinases CTD


    Regulating gene expression goal is controlling proteins how many where how active

    • 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


    Regulating gene expression goal is controlling proteins how many where how active

    • 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


    Regulating gene expression goal is controlling proteins how many where how active

    • 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!


    Regulating gene expression goal is controlling proteins how many where how active

    • 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])


    Regulating gene expression goal is controlling proteins how many where how active

    • 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!


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