Umberto Aiello

All Publications

• Sen1 is a key regulator of transcription-driven conflicts. Molecular cell Aiello, U., Challal, D., Wentzinger, G., Lengronne, A., Appanah, R., Pasero, P., Palancade, B., Libri, D. 2022

  Abstract

  Cellular homeostasis requires the coordination of several machineries concurrently engaged in the DNA. Wide-spread transcription can interfere with other processes, and transcription-replication conflicts (TRCs) threaten genome stability. The conserved Sen1 helicase not only terminates non-coding transcription but also interacts with the replisome and reportedly resolves genotoxic R-loops. Sen1 prevents genomic instability, but how this relates to its molecular functions remains unclear. We generated high-resolution, genome-wide maps of transcription-dependent conflicts and R-loops using a Sen1 mutant that has lost interaction with the replisome but is termination proficient. We show that, under physiological conditions, Sen1 removes RNA polymerase II at TRCs within genes and the rDNA and at sites of transcription-transcription conflicts, thus qualifying as a "key regulator of conflicts." We demonstrate that genomic stability is affected by Sen1 mutation only when in addition to its role at the replisome, the termination of non-coding transcription or R-loop removal are additionally compromised.

  View details for DOI 10.1016/j.molcel.2022.06.021

  View details for PubMedID 35839782

• Sen1: the varied virtues of a multifaceted helicase. Journal of molecular biology Aiello, U., Porrua, O., Libri, D. 2024: 168808

  Abstract

  Several machineries concurrently work on the DNA, but among them RNA Polymerases (RNAPs) are the most widespread and active users. The homeostasis of such a busy genomic environment relies on the existence of mechanisms that allow to limit transcription to a functional level, both in terms of extent and rate. Sen1 is a central player in this sense: using its translocase activity this protein has evolved the specific function of dislodging RNAPs from the DNA template, thus ending the transcription cycle. Over the years, studies have shown that Sen1 uses this same mechanism in a multitude of situations, allowing termination of all three eukaryotic RNAPs in different contexts. In virtue of its helicase activity, Sen1 has also been proposed to have a prominent function in the resolution of co-transcriptional genotoxic R-loops, which can cause the stalling of replication forks. In this review, we provide a synopsis of past and recent findings on the functions of Sen1 in yeast and of its human homologue Senataxin (SETX).

  View details for DOI 10.1016/j.jmb.2024.168808

  View details for PubMedID 39357815

• RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart. The EMBO journal Heuzé, J., Kemiha, S., Barthe, A., Vilarrubias, A. T., Aouadi, E., Aiello, U., Libri, D., Lin, Y. L., Lengronne, A., Poli, J., Pasero, P. 2023: e113104

  Abstract

  R-loops represent a major source of replication stress, but the mechanism by which these structures impede fork progression remains unclear. To address this question, we monitored fork progression, arrest, and restart in Saccharomyces cerevisiae cells lacking RNase H1 and H2, two enzymes responsible for degrading RNA:DNA hybrids. We found that while RNase H-deficient cells could replicate their chromosomes normally under unchallenged growth conditions, their replication was impaired when exposed to hydroxyurea (HU) or methyl methanesulfonate (MMS). Treated cells exhibited increased levels of RNA:DNA hybrids at stalled forks and were unable to generate RPA-coated single-stranded (ssDNA), an important postreplicative intermediate in resuming replication. Similar impairments in nascent DNA resection and ssDNA formation at HU-arrested forks were observed in human cells lacking RNase H2. However, fork resection was fully restored by addition of triptolide, an inhibitor of transcription that induces RNA polymerase degradation. Taken together, these data indicate that RNA:DNA hybrids not only act as barriers to replication forks, but also interfere with postreplicative fork repair mechanisms if not promptly degraded by RNase H.

  View details for DOI 10.15252/embj.2022113104

  View details for PubMedID 37855233

• DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes. Molecular cell Patel, H. P., Coppola, S., Pomp, W., Aiello, U., Brouwer, I., Libri, D., Lenstra, T. L. 2023; 83 (10): 1573-1587.e8

  Abstract

  DNA supercoiling has emerged as a major contributor to gene regulation in bacteria, but how DNA supercoiling impacts transcription dynamics in eukaryotes is unclear. Here, using single-molecule dual-color nascent transcription imaging in budding yeast, we show that transcriptional bursting of divergent and tandem GAL genes is coupled. Temporal coupling of neighboring genes requires rapid release of DNA supercoils by topoisomerases. When DNA supercoils accumulate, transcription of one gene inhibits transcription at its adjacent genes. Transcription inhibition of the GAL genes results from destabilized binding of the transcription factor Gal4. Moreover, wild-type yeast minimizes supercoiling-mediated inhibition by maintaining sufficient levels of topoisomerases. Overall, we discover fundamental differences in transcriptional control by DNA supercoiling between bacteria and yeast and show that rapid supercoiling release in eukaryotes ensures proper gene expression of neighboring genes.

  View details for DOI 10.1016/j.molcel.2023.04.015

  View details for PubMedID 37207624

• An integrated model for termination of RNA polymerase III transcription. Science advances Xie, J., Aiello, U., Clement, Y., Haidara, N., Girbig, M., Schmitzova, J., Pena, V., Müller, C. W., Libri, D., Porrua, O. 2022; 8 (28): eabm9875

  Abstract

  RNA polymerase III (RNAPIII) synthesizes essential and abundant noncoding RNAs such as transfer RNAs. Controlling RNAPIII span of activity by accurate and efficient termination is a challenging necessity to ensure robust gene expression and to prevent conflicts with other DNA-associated machineries. The mechanism of RNAPIII termination is believed to be simpler than that of other eukaryotic RNA polymerases, solely relying on the recognition of a T-tract in the nontemplate strand. Here, we combine high-resolution genome-wide analyses and in vitro transcription termination assays to revisit the mechanism of RNAPIII transcription termination in budding yeast. We show that T-tracts are necessary but not always sufficient for termination and that secondary structures of the nascent RNAs are important auxiliary cis-acting elements. Moreover, we show that the helicase Sen1 plays a key role in a fail-safe termination pathway. Our results provide a comprehensive model illustrating how multiple mechanisms cooperate to ensure efficient RNAPIII transcription termination.

  View details for DOI 10.1126/sciadv.abm9875

  View details for PubMedID 35857496

• Sen1 Is Recruited to Replication Forks via Ctf4 and Mrc1 and Promotes Genome Stability CELL REPORTS Appanah, R., Lones, E., Aiello, U., Libri, D., De Piccoli, G. 2020; 30 (7): 2094-2105

  Abstract

  DNA replication and RNA transcription compete for the same substrate during S phase. Cells have evolved several mechanisms to minimize such conflicts. Here, we identify the mechanism by which the transcription termination helicase Sen1 associates with replisomes. We show that the N terminus of Sen1 is both sufficient and necessary for replisome association and that it binds to the replisome via the components Ctf4 and Mrc1. We generated a separation of function mutant, sen1-3, which abolishes replisome binding without affecting transcription termination. We observe that the sen1-3 mutants show increased genome instability and recombination levels. Moreover, sen1-3 is synthetically defective with mutations in genes involved in RNA metabolism and the S phase checkpoint. RNH1 overexpression suppresses defects in the former, but not the latter. These findings illustrate how Sen1 plays a key function at replication forks during DNA replication to promote fork progression and chromosome stability.

  View details for DOI 10.1016/j.celrep.2020.01.087

  View details for Web of Science ID 000514824500005

  View details for PubMedID 32075754

  View details for PubMedCentralID PMC7034062