Publications

 

 

 

 

Since 2005 :

 

Xie, J., Aiello, U., Clement, Y., Haidara, N., Girbig, M., Schmitzova, J., Pena, V., Müller, C. W. , Libri, D. and Porrua, O.

doi: https://doi.org/10.1101/2021.08.27.457903

Haidara, N. and Porrua, O. Modulated termination of non-coding transcription partakes in the regulation of gene expression. doi: https://doi.org/10.1101/2021.01.06.425579.

Villa, T., Barucco, M., Martin-Niclos, M.-J., Jacquier, A., and Libri, D. (2020). Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Rep 32, 107942.

Appanah, R., Lones, E.C., Aiello, U., Libri, D., and De Piccoli, G. (2020). Sen1 Is Recruited to Replication Forks via Ctf4 and Mrc1 and Promotes Genome Stability. Cell Rep 30, 2094-2105.e9.

Han, Z., Jasnovidova, O., Haidara, N., Tudek, A., Kubicek, K., Libri, D., Stefl, R., and Porrua, O. (2020). Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. EMBO J. e101548.

Porrua, O (2020). Purification and in vitro analysis of the exosome cofactors Nrd1-Nab3 and Trf4-Air2. Methods Mol Biol 2062:277-289.

Kubik, S., Bruzzone, M.J., Challal, D., Dreos, R., Mattarocci, S., Bucher, P., Libri, D., and Shore, D. (2019). Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat. Struct. Mol. Biol. 26, 744–754.

Wang, S., Han, Z., Libri, D., Porrua, O., and Strick, T.R. (2019). Single-molecule characterization of extrinsic transcription termination by Sen1 helicase. Nat Commun 10, 1545.

Candelli, T., Gros, J.*, and Libri, D*. (2018). Pervasive transcription fine-tunes replication origin activity. Elife 7.

Challal, D., Barucco, M., Kubik, S., Feuerbach, F., Candelli, T., Geoffroy, H., Benaksas, C., Shore, D., and Libri, D. (2018). General Regulatory Factors Control the Fidelity of Transcription by Restricting Non-coding and Ectopic Initiation. Mol. Cell 72, 955-969.e7.

Han, Z., Porrua, O. (2018) Helicases as transcription termination factors: Different solutions for a common problem. Transcription 9(3):152-158.

Candelli, T., Challal, D., Briand J-B, Boulay J., Porrua O., Colin J., and Libri D. (2018) High-resolution transcription maps reveal the widespread impact of roadblock termination in S. cerevisiae. EMBO J. 2018 Jan 19. pii: e97490

Luciano, P.°, El-kaoutari°, A., Challal° D., Jeon J., Candelli, T., Jourquin, F., Kim, J.*, Libri, D.*, and Geli, V.* (2017) Binding to RNA in vivo regulates Set1 function. Cell Discovery 3, 17040

Simonetti, F., Candelli,T., Leon, S., Libri, D., Rougemaille, M. (2017) Ubiquitination-dependent control of sexual differentiation in fission yeast. Elife. 2017 Aug 25;6. pii: e28046.

Leonaitė, B., Han, Z., Basquin, J., Bonneau, F., Libri, D., Porrua, O.*, and Conti, E*. (2017). Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family. EMBO J. 36, 1590–1604.

Han, Z., Libri, D., and Porrua, O. (2017). Biochemical characterization of the helicase Sen1 provides new insights into the mechanisms of non-coding transcription termination. Nucleic Acids Res. 45, 1355–1370.

Babour, A., Shen, Q., Dos-Santos, J., Murray, S., Gay, A., Challal, D., Fasken, M., Palancade, B., Corbett, A., Libri, D., Mellor, J. and Dargemont, C. (2016). The Chromatin Remodeler ISW1 Is a Quality Control Factor that Surveys Nuclear mRNP Biogenesis. Cell 167, 1201–1214.e15.

Porrua, O.*, Boudvillain, M.*, and Libri, D.* (2016). Transcription Termination: Variations on Common Themes. Trends Genet. 32, 508–522.

Libri, D. (2015). Sleeping Beauty and the Beast (of pervasive transcription). RNA 21, 678–679.

Porrua, O., and Libri, D. (2015a). Transcription termination and the control of the

transcriptome: why, where and how to stop. Nat. Rev. Mol. Cell Biol. 16, 190–202.

Porrua, O.*, and Libri, D. (2015b). Characterization of the mechanisms of transcription termination by the helicase Sen1. Methods Mol. Biol. 1259, 313–331.

Tudek, A., Candelli, T., and Libri, D. (2015). Non-coding transcription by RNA

polymerase II in yeast: Hasard or nécessité? Biochimie.

Zhang, W., Collinet, B., Graille, M., Daugeron, M.-C., Lazar, N., Libri, D., Durand, D.,

and van Tilbeurgh, H. (2015). Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex. Nucleic Acids Res. 43, 3358–3372.

Colin, J., Candelli, T., Porrua, O., Boulay, J., Zhu, C., Lacroute, F., Steinmetz, L.M.,

and Libri, D. (2014). Roadblock termination by reb1p restricts cryptic and

readthrough transcription. Mol. Cell 56, 667–680.

Tudek, A., Porrua*, O., Kabzinski, T., Lidschreiber, M., Kubicek, K., Fortova, A.,

Lacroute, F., Vanacova, S., Cramer, P., Stefl, R*. and Libri, D*. (2014). Molecular basis for the dual role of Nrd1p CID in transcription termination and non-coding RNA degradation. Mol. Cell, 55, 467-81

Porrua O, Libri D. (2013). RNA quality control in the nucleus: the Angels’ share of RNA. Biochim Biophys Acta 1829(6-7):604-11.

Mouaikel, J., Causse, S.Z., Rougemaille, M., Daubenton-Carafa, Y., Blugeon, C.,

Lemoine, S., Devaux, F., Darzacq, X., and Libri, D. (2013). High-Frequency Promoter Firing Links THO Complex Function to Heavy Chromatin Formation. Cell Rep 5, 1082-1094.

Lenstra°, T.L., Tudek°, A., Clauder, S., Xu, Z., Pachis, S.T., van Leenen, D.,

Kemmeren, P., Steinmetz, L.M., Libri*, D., and Holstege*, F.C. (2013). The Role of

Ctk1 Kinase in Termination of Small Non-Coding RNAs. PLoS One 8, e80495.

Jensen, T.H., Jacquier, A., and Libri, D. (2013). Dealing with pervasive transcription. Mol Cell 52, 473-484.

Porrua, O.*, and Libri, D.* (2013). A bacterial-like mechanism for transcription

termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol 20, 884-891.

Rougemaille, M., Braun, S., Coyle, S., Dumesic, P.A., Garcia, J.F., Isaac, R.S., Libri,

D., Narlikar, G.J., and Madhani, H.D. (2012). Ers1 links HP1 to RNAi. Proc. Natl.

Acad. Sci. U.S.A. 109, 11258–11263.

Porrua, O., Hobor, F., Boulay, J., Kubicek, K., D’Aubenton-Carafa, Y., Gudipati, R.K.,

Stefl, R., and Libri, D. (2012). In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination. EMBO J 31, 3935-3948.

Gudipati, R.K., Xu, Z., Lebreton, A., Seraphin, B., Steinmetz, L.M., Jacquier, A., and

Libri, D. (2012). Extensive degradation of RNA precursors by the exosome in wild-

type cells. Mol Cell 48, 409-421.

Rougemaille, M., and Libri, D. (2011). Control of cryptic transcription in eukaryotes. Adv Exp Med Biol 702, 122-131.

Daugeron, M.C., Lenstra, T.L., Frizzarin, M., El Yacoubi, B., Liu, X., Baudin-Baillieu,

A., Lijnzaad, P., Decourty, L., Saveanu, C., Jacquier, A., Holstege FC, de Crécy-Lagard V, van Tilbeurgh H, Libri D. (2011). Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res 39, 6148-6160.

Colin, J., Libri, D. and Porrúa, O*. (2011). Cryptic Transcription and Early Termination in the  Control of Gene Expression. Genet Res Int. 2011:653494.

Assenholt, J., Mouaikel, J., Saguez, C., Rougemaille, M., Libri, D., and Jensen, T.H.

(2011). Implication of Ccr4-Not complex function in mRNA quality control in

Saccharomyces cerevisiae. Rna 17, 1788-1794.

Libri, D. (2010). Nuclear poly(a)-binding proteins and nuclear degradation: take the mRNA and run? Mol Cell 37, 3-5.

Honorine, R., Mosrin-Huaman, C., Hervouet-Coste, N., Libri, D., and Rahmouni, A.R. (2010). Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts. Nucleic Acids Res 39, 2809-2820.

Colin, J., Libri, D., and Villa, T. (2010). Sex matters in the birth of genes. Cell Res 20, 499-501.

Villa, T., Rougemaille, M., and Libri, D. (2008). Nuclear quality control of RNA

polymerase II ribonucleoproteins in yeast: Tilting the balance to shape the

transcriptome. Biochim Biophys Acta 1779, 524-531.

Thiebaut, M., Colin, J., Neil, H., Jacquier, A., Seraphin, B., Lacroute, F., and Libri, D.

(2008). Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. Mol Cell 31, 671-682.

Schmid, M., Rougemaille, M., Libri, D., and Jensen, T.H. (2008). Chapter 10.

Estimating nuclear mRNA decay in Saccharomyces cerevisiae. Methods Enzymol

449, 205-219.

Rougemaille, M., Villa, T., Gudipati, R.K., and Libri, D. (2008). mRNA journey to the

cytoplasm: attire required. Biol Cell 100, 327-342.

Rougemaille, M., Dieppois, G., Kisseleva-Romanova, E., Gudipati, R.K., Lemoine, S., Blugeon, C., Boulay, J., Jensen, T.H., Stutz, F., Devaux, F., and Libri, D. (2008).

THO/Sub2p functions to coordinate 3′-end processing with gene-nuclear pore

association. Cell 135, 308-321.

Libri, D. (2008). Quality control: Cell and the city. Biochim Biophys Acta 1779, 523.

Hecker, A., Lopreiato, R., Graille, M., Collinet, B., Forterre, P., Libri, D., and van

Tilbeurgh, H. (2008). Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. EMBO J 27, 2340-2351.

Gudipati, R.K., Villa, T., Boulay, J., and Libri, D. (2008). Phosphorylation of the RNA

polymerase II C-terminal domain dictates transcription termination choice. Nat Struct Mol Biol 15, 786-794.

Assenholt, J., Mouaikel, J., Andersen, K.R., Brodersen, D.E., Libri, D., and Jensen,

T.H. (2008). Exonucleolysis is required for nuclear mRNA quality control in yeast

THO mutants. Rna 14, 2305-2313.

Rougemaille, M., Gudipati, R.K., Olesen, J.R., Thomsen, R., Seraphin, B., Libri, D.,

and Jensen, T.H. (2007). Dissecting mechanisms of nuclear mRNA surveillance in

THO/sub2 complex mutants. Embo J 26, 2317-2326.

Chauveau, F., Aissouni, Y., Hamm, J., Boutin, H., Libri, D., Duconge, F., and

Tavitian, B. (2007). Binding of an aptamer to the N-terminal fragment of VCAM-1.

Bioorg Med Chem Lett 17, 6119-6122.

Thiebaut, M., Kisseleva-Romanova, E., Rougemaille, M., Boulay, J., and Libri, D.

(2006). Transcription termination and nuclear degradation of cryptic unstable

transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol Cell 23,

853-864.

Pestourie, C., Cerchia, L., Gombert, K., Aissouni, Y., Boulay, J., De Franciscis, V.,

Libri, D., Tavitian, B., and Duconge, F. (2006). Comparison of different strategies to

select aptamers against a transmembrane protein target. Oligonucleotides 16, 323-335.

Kisseleva-Romanova, E., Lopreiato, R., Baudin-Baillieu, A., Rousselle, J.C., Ilan, L.,

Hofmann, K., Namane, A., Mann, C., and Libri, D. (2006). Yeast homolog of a

cancer-testis antigen defines a new transcription complex. Embo J 25, 3576-3585.

Cerchia, L., D’Alessio, A., Amabile, G., Duconge, F., Pestourie, C., Tavitian, B., Libri, D., and de Franciscis, V. (2006). An autocrine loop involving ret and glial cell-derived neurotrophic factor mediates retinoic acid-induced neuroblastoma cell differentiation. Mol Cancer Res 4, 481-488.

Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.C., Dufour, M.E., Boulay, J.,

Regnault, B., Devaux, F., Namane, A., Seraphin*, B., Libri*, D. and Jacquier* A.

(2005). Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121, 725-737. * co-corresponding authors.

Olesen, J.R., Libri, D., and Jensen, T.H. (2005). A link between transcription and

mRNP quality in Saccharomyces cerevisiae. RNA Biol 2, 45-48.