Athar I Ansari (bb2749)

Biological Science

2115 Biological Sciences Building

Eukaryotic transcription and RNA processing

The transcription cycle of RNAP II consists of three consecutive steps; initiation, elongation and termination and proceeds in conjunction with RNA processing Accomplishment of each of these steps and cotranscriptional mRNA processing requires a set of accessory factors. The generally accepted view is that the factors operating at each step have distinct, essentially independent roles specific to that step. The research in my laboratory has challenged this dogma.We have observed that the initiation and termination factors are engaged in extensive crosstalk during transcription. We have shown that the general transcription factors TFIIB, TFIIH and Mediator subunits are involved in the termination step of transcription (Medler et al., 2011; Mukundan and Ansari, 2011; Mukundan and Ansari, 2013; Medler and Ansari, 2015). Similarly, termination factors have been found to influence transcription at the promoter (Al Husini et al., 2013; Al Husini et al., 2017).

The research in my lab has shown that the termination factors affect promoter-associated transcription by facilitating the recruitment of polymerase at the promoter for reinitiation and by affecting promoter directionality. The initiation factors similarly affect termination by assisting in the recruitment of termination factors towards the 3′ end of a gene. The latest research in my laboratory has shown that even transcription factors affect splicing and splicing factors, in turn, have an influence on the process of transcription (Moabbi et al., 2012; Agarwal and Ansari, 2016; Dwyer et al., manuscript under review; Dhoondia et al., manuscript in preparation).

A number of models have been proposed to explain the role of general transcription factors in termination and that of termination factors in promoter-linked transcription. One of these models is the ‘gene looping model’. According to this model, the entire terminator region of a gene physically interacts with its cognate promoter in a transcription-dependent manner resulting in the formation of a looped gene architecture. The physical proximity of the promoter and terminator regions in a gene loop provides a logical explanation for the effect of the promoter-bound factors on termination and that of the terminator-linked factors on promoter-associated transcription. Using ‘Chromosome Conformation Capture’ (CCC) approach, we have clearly demonstrated that a number of genes in yeast and higher eukaryotes have been shown to assume a looped conformation during transcription.

Furthermore, we showed that loss of gene looping adversely effects the transcription of these genes. The latest research in my laboratory has shown that the intron-mediated regulation of transcription is also through gene looping. The role of splicing in transcriptional regulation through gene looping is an emerging new area of research in my lab. Future research will also focus on elucidating the molecular basis underlying gene loop formation and the enhancement of transcription by looped gene architecture. Attempts will be made to determine the prevalence of gene looping and looping-mediated regulation of transcriptional in budding yeast as well as higher eukaryotes.

Awards and honors

• Associate editor and editorial board member of ‘Frontiers in Molecular Biosciences’, (Switzerland) (2021-present)
• Invited member of editorial board of the biochemistry and molecular biology section of ‘Biology’, (a journal of MDPI group, Switzerland) (2021-present)
• Guest editor of the special issue on the topic "The Lesser Known World of RNA Polymerases” published by ‘Frontiers in Molecular Biosciences, Switzerland (2020-2021)
• Invited member of the editorial board of the ‘AIMS Genetics’ (USA) (2017-present)
• Invited member of the editorial board of ‘Scientific Reports’, Nature group, London (2016- present)
• Invited member of the editorial board of the ‘Journal of Cytology and Molecular Biology’ (Boston) (2014-present))
• Editorial board of Journal of Biological Chemistry selected the recently accepted paper [Mukundan B and Ansari A (2011) A novel role of Mediator subunit Srb5/Med18 in termination of transcription] as ‘Paper of the week’

Grants

• Funding agency: National Institute of Health
  • Title: A new paradigm for the general transcription factor TFIIB functionality in termination and promoter directionality
  • Period of coverage: Sept. 1, 2022 to May 31, 2027
  • Amount: $1,523.584
• Funding agency: National Science Foundation
  • Title: An investigation into a novel role of Rat1 termination factor in splicing of mRNA.
  • Period of coverage: Nov. 15, 2019 to Oct. 30, 2021
  • Amount: $269, 285
• Funding agency: National Science Foundation
  • Title: Regulation of transcription by promoter-terminator interaction
  • Period of coverage: Sept. 15, 2010 to Sept. 14, 2017
  • Amount: $718, 281
• Annual Meeting Compendia of American Society of Biochemistry and Molecular Biology (2010) recognized the work from the lab (El Kaderi et al., 2009, J. Biol. Chem. 284, 25015-25025) as one of the six significant papers recently published in the Journal of Biological Chemistry on the initiation of transcription in recent years (jbc.org/site/meeting2010/dna).

• O’Brien M, and Ansari A (2022) Beyond the canonical role of TFIIB in eukaryotic transcription. Current Genetics 1-7
• Calvo O, Ansari A and Navarro F (2021) Lesser known world of RNA polymerases. Frontiers in Molecular Bioscience 8, 811413
• *Dwyer K, *Agarwal N, #Gega A and Ansari A (2021) Proximity to the promoter and terminator regions regulates transcription enhancement potential of an intron. Frontiers in Molecular Bioscience 8, 712639
• Dhoondia Z, Elewa H, Malik M, Arif Z, Pique-Regi R and Ansari A (2021) A termination-independent role of Rat1 in cotranscriptional splicing. Nucleic Acid Research (in press)
• Dwyer K, Agarwal N, Pile L and Ansari A (2021) Gene architecture facilitates intron-mediated enhancement of transcription. Frontiers in Molecular Bioscience 8, 276
• O’Brien M, and Ansari A (2021) Critical role of TFIIB in viral pathogenesis. Frontiers in Molecular Bioscience 8, 308
• Al Husini N, Medler S, Ansari A (2020) Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. Biochimica Biophysica Acta Gene Regulatory Mechanisms 1863, 194657
• Fuster PA, O'Brien MJ, Polo NG, Pereira B, Dhoondia Z, Ansari A and Calvo O (2019) RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit, Nucleic Acid Research 47, 8975-8987
• Ansari A (2019) Recent Trends in Eukaryotic Transcription: Crucial Role of Gene Architecture in Transcriptional Regulation. J Cytol Molecul Biol. 4, 2
• Alhusini N, Sharifi A, Mousavi SA, Chitsaz H and Ansari A (2017) Genomewide analysis of Clp1 function in transcription in budding yeast. Scientific Reports (Nature) 7, 6894
• Dhoondia Z, Tarockoff R, Alhusini N, Medler S, Agarwal N and Ansari A (2017) Analysis of termination of transcription using BrUTP-strand-specific transcription run-on (TRO) approach. Journal of Visualized Experiments 121: e55446
• Agarwal N and Ansari A (2016) Enhancement of transcription by a splicing-competent intron is dependent on promoter directionality. PLOS Genetics 12: e1006047
• Cloutier SC, Wang S, Ma WK, Al Husini N, Dhoondia Z, Ansari A, Pascuzzi PE and Tran EJ (2016) Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation. Molecular Cell 61, 393-404
• Medler S and Ansari A (2015) Gene looping facilitates TFIIH kinase-mediated termination of transcription. Scientific Reports (Nature) 5, 12586
• Al Husini N, Kudla P and Ansari A (2013) A role for CF1 3' end processing complex in promoter-associated transcription. PLOS Genetics 9: e1003722
• Mukundan B and Ansari A (2013) Srb5-mediated termination of transcription is dependent on gene looping. J. Biol. Chem. 288, 11384-11394
• 17. El Kaderi B, Medler S and Ansari A (2012) Analysis of interactions between genomic loci through chromosome conformation capture (3C). Current Protocols in Cell Biology 56(22.15), 1-22
• Moabbi AM, Agarwal N, El Kaderi B and Ansari A (2012) Intron-mediated transcriptional regulation is dependent on gene looping. P. Natl. Acad. Sci. USA. 109, 8505-8510
• Mukundan B and Ansari A (2011) A novel role for Mediator complex subunit Srb5/Med18 in termination of transcription. J. Biol. Chem. 286, 37053-37057
• Medler S, Al Husini N, Raghunayakula S, Mukundan B, Aldea A and Ansari A (2011) Evidence for a complex of TFIIB with poly(A) polymerase and cleavage factor I subunits required for gene looping. J. Biol. Chem. 286, 33709-33718
• El Kaderi B, Medler S, Raghunayakula S and Ansari A (2009) Gene looping is conferred by activator-dependent interactions between transcription initiation and termination machineries. J. Biol. Chem. 284, 25015-25025