Abortive initiation

Molecular Mechanism of Transcription Initiation

1. Abortive Initiation

2. Outline Introduction Why abortive transcripts are formed Steps Involved Fate of product formed Conclusion

3. Introduction Repetitive synthesis and release of short nascent RNAs by RNA polymerase. accompanies steady-state transcription ~95% of the total RNA contains ribo -oligonucleotide products usually ranging between 2-15 nts in length.

4. Transcriptional initiation involves three steps- Formation of closed ‘preinitiation’ complex, formation the open complex transitions from initiation to elongation - promoter escape. .

5. Dr. M. Thomm et al .

6. Closed Complex Open complex RNAP starts synthesizing of RNA Abortive Initiation Synthesis of 2-15 nt transcript Stressed intermediate DNA Scrunching Promotor Clearance Reinitiation Enters Elongation

7. DNA Scrunching The polymerase remains stationary and downstream DNA passed through its active site Leads to unwinding and compaction of the DNA. Stressed intermediate . Stress is relieved either by aborting transcription or by promoter clearance .

8. Promotor Clearance Once transcript grows longer than 12 nts , TFIIB is displaced RNAP leaves the promotor Productive initiation starts

9. RNAP bound with TFIIB provides checkpoint for transition Structural transition of RNAP on escape Re-closure of upstream transcription bubble TFIIE and TFIIH mediates escape and then elongation

10. Importance of the process Dissociation of sigma factors and transcription factors Promoter clearance Proper orientation of DNA and RNA Polymerase complex for entering the elongation stage.

11. Abortive vs Productive Initiation depends on Initially transcribed sequence Tight binding of sigma factor to core enzyme. The affinity of bacterial RNA polymerase for the promoter (Promotor s trength) Presence of GreA /B factors

12. Fate of Abortive Transcripts Very short lived, usually d egraded quickly Functions not known Abortive transcription events stall polymerases Might be involved in antisense mediated regulation

13. Conclusion Conserved phenomenon Promotor escaping based on DNA Scrunching mechanism Transition from initiation to elongation phase Short lived transcripts Unknown biological functions

14. References . Achillefs N. Kapanidis , Emmanuel Margeat , Sam On Ho, Ekaterine Kortkhonjia , Shimon Weiss, and Richard H. Ebright ; Initial Transcription By Rna Polymerase Proceeds Through A Dna -scrunching Mechanism; Science. 2006 ; 314(5802): 1139–1143. Goldman, SR, Ebright RH, Nickels BE.  2009.  Direct detection of abortive RNA transcripts in vivo. Science. 324:927-8. Joseph T Wade1 and Kevin Struhl; The transition from transcriptional initiation to elongation; Current Opinion in Genetics & Development 2008, 18:130–136. Lilian M. Hsu; Monitoring abortive initiation; Methods, 2008; 1046-2023.

15.      6. Sooncheol Lee, Huong Minh Nguyen and Changwon Kang; Tiny abortive initiation transcripts exert antitermination activity on an RNA hairpin-dependent intrinsic terminator; Nucleic Acids Research, 2010, Vol. 38, No. 18. 7. Sabyasachi Baboo and Peter R Cook,; Dark matter” worlds of unstable RNA and protein; Nucleus 5:4, 281–286; July/August 2014 8. Taft RJ et al (2009) Tiny RNAs associated with transcription start sites in animals. Nat Genet 41: 572–578.

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