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Eukaryotic Transcription- Elongation & Termination

Eukaryotic Transcription- Elongation & Termination

Dr.V.Malathi

The promoters of  RNA polymerase I

The promoters recognized by RNA polymerase I consists of

  •  a core element  :  It  surrounds the transcription start site , and
  • an upstream promoter element  :  This  is about 100 bp farther upstream.
  • RNA polymerase  binds to promoter containing a core promoter element and an upstream control element (UCE). The Tata Binding Protein ( TBP), which is part of a larger complex called SL1, helps RNA polymerase I to recognize the core promoter

The promoters of RNA polymerase III

  • The RNA polymerase III promoters are of two types namely  Type I and Type II . These  promoters  lie wholly within the genes. 
  • The type II promoter of the Xenopus laevis 5S RNA gene consists of an internal control region (ICR). This is  subdivided into A box (+50 to +60), intermediate element (IE, +67 to +72), and C box (+80 to +90).
  • The type II  promoter of the X. laevis tRNALeugene consists of an A box (+8 to +19) and a B box (+52 to +62).
  • The type III promoter of the Homo sapiens U6 snRNA gene consists of a distal sequence element (DSE, −215 to −240)  and a core promoter composed of a proximal sequence element (PSE, −65 to −48) and a TATA box (−32 to −25). 

Elongation

  • RNA Polymerase  clears or “escapes” the promoter region and leaves most of the transcription initiation proteins behind.

  • RNA Polymerases travel along the template DNA strand in the 3′ to 5′ direction .The synthesis of new RNA strands takes place in the 5′ to 3′ direction. i.e.,  new nucleotides are added to the 3′ end of the growing RNA strand.

  • RNA Polymerases unwind the double stranded DNA ahead of them and rewinds the unwound DNA behind them.
  • RNA strand synthesis occurs in a transcription bubble of about 25 unwound DNA base pairs.
  • About 8 nucleotides of newly-synthesized RNA remain base paired to the template DNA. The rest of the RNA molecules falls off the template  and this  allows the DNA behind it to rewind.

Termination

  • The termination of transcription is different for the three different eukaryotic RNA polymerases.
  • RNA Polymerase I contain a specific sequence of base pairs -11 bp long in humans  :  18 bp in mice .  This sequence is recognized by a termination protein called TTF-1 (Transcription Termination Factor for RNA Polymerase I.).  This protein binds the DNA at its recognition sequence and blocks further transcription, causing the RNA Polymerase I to detach from the template DNA strand and  releases the newly-synthesized RNA.
  • RNA Polymerse II lack any specific signals or sequences that direct RNA Polymerase II to terminate at specific locations. The transcript is cleaved at an internal site before RNA Polymerase II finishes transcribing. The cleavage site occurs between an upstream AAUAAA sequence and a downstream GU-rich sequence separated by about 40-60 nucleotides in the emerging RNA.
  •  The upstream portion of the transcript is released .
  • The remainder of the transcript is digested by a 5′-exonuclease (called Xrn2 in humans) while it is still being transcribed by the RNA Polymerase II. When the 5′-exonulease “catches up” to RNA Polymerase II by digesting away all the overhanging RNA, it  disengage the polymerase from its DNA template strand, finally terminating transcription.
  • A protein called CPSF in humans binds the AAUAAA sequence and a protein called CstF in humans binds the GU-rich sequence. CPSF cleaves the nascent pre-mRNA at a site 10-30 nucleotides downstream from the AAUAAA site. The Poly(A) Polymerase enzyme  catalyze the addition of a 3′ poly-A tail on the pre-mRNA .
  • The RNAs transcribed by RNA Polymerase III have a short stretch of four to seven U’s at their 3′ end. This somehow triggers RNA Polymerase III to both release the nascent RNA and disengage from the template DNA strand.

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