lec 7.2 - initiation w/ RNA pol I and RNA pol III

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13 Terms

1
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external binding/promoter

upstream protein binding

  • upstream of start site/outside of transcribed genes

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internal binding/promoter

downstream protein binding

  • downstream of start site/inside of transcribed genes

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how does RNA polymerase recognize where to start transcription?

depends on the RNA polymerase used

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RNA pol I

  • what does it transcribe?

  • describe promoter

  • transcribes rRNAs, 18S and 26S

  • promoter consists of

    • core sequence (-45 to +20) - spans the start site

    • upstream control element (UCE) (G + C rich)(-180 to -107)

      • additional regulatory element that influences efficiency and regulation of RNA polymerase I transcription

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transcription by RNA pol I requires what two factors?

  • where does each bind?

  • UBF (UCE binding factor)

  • SL1 that binds to core of promoter

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role of UBF (upstream binding factor)

  • maintains open chromatin structure (loosens it up)

  • prevents histone H1 protein binding, which binds to DNA btwn histones → allows genes to remain accessible

  • stimulates SL1

  • responsible for RNA pol initiation from promoter

<ul><li><p>maintains open chromatin structure (loosens it up)</p></li><li><p>prevents histone H1 protein binding, which binds to DNA btwn histones → allows genes to remain accessible</p></li><li><p>stimulates SL1</p></li><li><p>responsible for RNA pol initiation from promoter</p></li></ul>
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what is SL1?

  • 4 protein structure

  • contains TBP (TATA binding protein)

  • responsible for RNA polymerase recruitment and proper alignment

<ul><li><p>4 protein structure</p></li><li><p>contains TBP (TATA binding protein) </p></li><li><p>responsible for RNA polymerase recruitment and proper alignment</p></li></ul>
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RNA pol III

  • describe it

  • describe promoters

  • transcribes genes for snRNAs, tRNAs and 5S rRNA

    • uses 2 types of promoters

promoter types:

  • class I and II – are internal promoters (type1), recognition sequences downstream of start site

    • 5s rRNA and tRNA

  • class III – is external promoter (type 2), recognition sequences

    upstream of start site

    • snRNA

<ul><li><p>transcribes genes for snRNAs, tRNAs and 5S rRNA</p><ul><li><p>uses 2 types of promoters</p></li></ul></li></ul><p>promoter types:</p><ul><li><p>class I and II – are internal promoters (type1), recognition sequences downstream of start site</p><ul><li><p>5s rRNA and tRNA </p></li></ul></li><li><p>class III – is external promoter (type 2), recognition sequences</p><p>upstream of start site</p><ul><li><p>snRNA</p></li></ul></li></ul>
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explain RNA pol III - class I internal promoter initiation for tRNA

  • Assembly factors are TFIIIA, TFIIIB, TFIIIC

  • two TFIIICs bind to box A and B (one per box) - internal binding (within gene)

    • help in positioning RNA polymerase III complex for accurate initiation

  • TFIIIB binds to start point and TBP subunit that binds to pol III - external binding

    • is composed of various subunits, including the TATA-box binding protein (TBP)

      • TBP subunit of TFIIIB interacts w RNA pol III complex + aids in accurate positioning of pol III at transcription start site for initiation of tRNA synthesis

<ul><li><p>Assembly factors are TFIIIA, TFIIIB, TFIIIC</p></li><li><p>two TFIIICs bind to box A and B (one per box) - <strong>internal binding (within gene)</strong></p><ul><li><p>help in positioning RNA polymerase III complex for accurate initiation</p></li></ul></li><li><p>TFIIIB binds to start point and TBP subunit that binds to pol III - <strong>external binding</strong></p><ul><li><p>is composed of various subunits, including the TATA-box binding protein (TBP)</p><ul><li><p>TBP subunit of TFIIIB interacts w RNA pol III complex + aids in accurate positioning of pol III at transcription start site for initiation of tRNA synthesis</p></li></ul></li></ul></li></ul>
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explain RNA pol III - class I internal promoter initiation for 5s rRNA

  • TFIIIA and TFIIIC – internal binding

    • TFIIIA binds to box A and helps TFIIIC bind to box C

    • TFIIIA also binds to 5S rRNA transcript and acts as a chaperone and gene regulator

  • then TFIIIB can bind to start site with TBP which binds to RNA pol II to start transcription - external binding

<ul><li><p>TFIIIA and TFIIIC – <strong>internal binding</strong></p><ul><li><p>TFIIIA binds to box A and helps TFIIIC bind to box C </p></li><li><p>TFIIIA also binds to 5S rRNA transcript and acts as a chaperone and gene regulator</p></li></ul></li><li><p>then TFIIIB can bind to start site with TBP which binds to RNA pol II to start transcription - <strong>external binding</strong></p></li></ul>
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where does TFIIIB always bind?

upstream of start site (in both tRNA and 5s rRNA transcription)

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RNA pol III - external promoter functions

  • class III

  • used for snRNA transcription

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RNA pol III - class III external promoter - snRNA

  • uses TATA box and help from enhancers:

    • Oct (8 base sequence)

    • PSE (proximal sequence element)

      • act as enhancers that help in regulation and initiation of snRNA transcription by RNA pol III

  • all the elements are upstream of the start site (box A and box B) in order:

    • Oct, PSE, TATA