Centro Andaluz de Biología Molecular y Medicina Regenerativa
Ana G. Rondón

Email: ana.rondon@cabimer.es


Main Research Lines:

  1. Causes and consequences of R-loops formation during transcription elongation.
  2. Understanding the mechanisms governing RNAPII transcription termination.

1.  Causes and consequences of R-loops formation during transcription elongation.

The initial step in genome expression is the synthesis of an RNA transcribing the information contained into the template DNA molecule. Transcription could be conceptually divided in three phases: initiation, when the RNA polymerase (RNAP) is recruited to the promoter; elongation, when RNAP is actively synthesising the transcript and termination, when RNAP disengages from the template. During transcription the nascent RNA is processed and assembled into an exportable ribonucleoparticle. Defects in mRNA processing increases the RNA ability to thread back into the template DNA forming an RNA:DNA hybrid that leaves the non-template strand as ssDNA, a structure generally termed R-loop. R-loop formation is an important source of transcription associated genome instability as it affects fundamental processes like transcription and replication. Although it has a detrimental effect during elongation, R-loops are required for accurate termination at multiple human genes. My research focus in understanding how R-loops affect transcription at the elongation and the termination phases.

2. Understanding the mechanisms governing RNAPII transcription termination.

RNAPII transcription termination is coupled to RNA 3’ end processing.  In the yeast Saccharomyces cerevisiae two alternative transcription termination mechanisms operate: the polyA dependent and the NNS dependent pathways. In the first case, termination relies on recognition and cleavage at the polyadenylation signal in the transcript generating an stable mRNA on one side and an unprotected 5’ end at the RNA still attached to the RNAPII. Degradation of this RNA by Rat1 exonuclease triggers RNAPII disengagement by an still unknown mechanism. In the NNS dependent pathway, Nrd1 and Nab3 binding to nascent RNA causes RNAPII termination. NNS (Nrd1-Nab3-Sen1) complex recruits the exosome to the transcript that is degraded in the case of non-coding RNAs, or trimmed to the mature form in the case of snoRNAs. The signals present in the RNA together with the phosphorylation state of the RNAPII CTD determine the termination mechanism employed. We are interested in identifying new factors involved in RNAPII termination especially at the polyA dependent pathway.

Garcia-Rubio M.L. Aguilera P, Lafunete-Barquero j., Ruiz JF, Simon MN, Geli V, Rondón AG#, Aguilera A#. Yra1-bound RNA-DNA hybrids cause orientation-independent transcription-replication collisions and telomere instability.  Genes Dev. 2018 1;32(13-14):965-977 doi: 10.1101/gad.311274.117.

García-Pichardo D,  Cañas JC, García-Rubio ML., Gómez-González B., Rondón AG, Aguilera A. Histone Mutants Separate R Loop formation from Genome Instability Induction. Mol. Cell vol.66. 2013. pág.:597-609. doi 10.1016/j.molcel.2017.05.014.

Castellano-Pozo M., Santos-Pereira, JM., Rondón, AG., Barroso, S., Andújar, E., Pérez-Alegre M., Garcia-Muse T. y Aguilera A. R-loops are linked to histone H3 Ser10 phosphorylation and chromatin condensation. Mol. Cell vol.52. 2013. pág.:583-590. doi: 10.1016/j.molcel.2013.10.006.

Luna R., Rondón, AG. y Aguilera A. New clues to understand the role of THO and other functionally related factors in mRNP biogenesis. Biochim. Biophys. Acta- Gene Regulatory Mechanism vol.1819. 2012. pág.:514-520. (♯corresponding).  doi: 10.1016/j.bbagrm.2011.11.012.

Tous C#, Rondón AG#, García-Rubio M, González-Aguilera C, Luna R, Aguilera A.  A novel assay identifies transcript elongation roles for the Nup84 complex and RNA processing factors. EMBO J. vol.30. 2011. pág.:1953-1964. doi: 10.1038/emboj.2011.109.       

Mischo HE, Gómez-González B, Grzechnik P, Rondón AG, Wei W, Steinmetz L, Aguilera A, Proudfoot NJ. Yeast Sen1 helicase protects the genome from transcription-associated instability Mol. Cell vol.41. 2011. pág.:21-32.

Rondón AG#, Jimeno S y Aguilera A. The interface between transcription and mRNP export: from THO to THSC/TREX-2. Biochim. Biophys. Acta- Gene Regulatory Mechanism vol.1799. 2010. pág.:533-538.. doi: 10.1016/j.bbagrm.2010.06.002..

Rondón AG, Mischo HE, Kawauchi J, Proudfoot NJ.. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae Mol. Cell. vol.36.  2009  pág.:88-89. doi: 10.1016/j.molcel.2009.07.028.

Kawauchi J., Mischo H., Braglia P., Rondón AG, Proudfoot NJ. Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev. vol.22. 2008. pág.:1082-1092. doi: 10.1101/gad.463408.

Rondón AG, Gallardo M, García-Rubio M, Aguilera A. Molecular evidence indicating that the yeast PAF complex is required for transcription elongation. EMBO Rep. 2004 5:47-53.

Rondón AG, Jimeno S, García-Rubio M, Aguilera A. Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation. J Biol Chem. 2003;278(40):39037-43.

Rondón AG, García-Rubio M, González-Barrera S, Aguilera A. Molecular evidence for a positive role of Spt4 in transcription elongation. EMBO J. 2003;22(3):612-20.

Jimeno S, Rondón AG, Luna R, Aguilera A. The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability. EMBO J. 2002;21(13):3526-35.

Strässer K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondón AG, Aguilera A, Struhl K, Reed R, Hurt E. TREX is a conserved complex coupling transcription with messenger RNA export. Nature. 2002;417(6886):304-8.

Chávez S, Beilharz T, Rondón AG, Erdjument-Bromage H, Tempst P, Svejstrup JQ, Lithgow T, Aguilera A. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J. 2000;19(21):5824-34.