centro biotecnologie avanzate

LABORATORY OF: RNA Technology 1
CONTACT PERSON: Dr.Roberto Gherzi (IST)
Phone +39 010 5737580 E-mail: roberto.gherzi@istge.it

Description of Laboratory and Expertise:

In the last few years Roberto Gherzi’s group has been working on control of mRNA turnover contributing to the identification and the functional characterization of the human exosome, and to the discovery that some proteins are able to recruit the decay enzymes to labile mRNAs encoding transcription factors, oncogenes, cytokines. Signalling pathways affect the recruitment process and, influencing the mRNA half-life of critical regulatory factors, modulate gene expression at a post-transcriptional level.

Abstract of Activities:

Molecular mechanisms that regulate gene expression at a post-transcriptional level through activation of signaling pathways. In the last few years the focus of the research work was on the control of mRNA degradation in respons to proliferative and differentiative stimuli in mammalian cells. The recent discovery that a single strand RNA-binding protein interacts with the terminal loop of a subset of miRNAs and regulates their processing opens an exciting new area, the stimulus-specific control of miRNA maturation and biosynthesis.

Detailed Research Activities:

Our aims are:
To get insights on molecular basis of the miRNA-specific maturative process.
To investigate how activation of signaling pathways impacts on miRNA-specific maturative process.
To employ biologically relevant model systems in which the regulation of expression and maturation of miRNAs can be investigated. Specifically, we identified the following cellular models: i) C2C12 myoblasts: this murine myoblast cell line undergoes terminal differentiation into myotubes upon either serum withdrawal or activation of the MAPKp38 signaling cascade. ii) murine microglia cell lines (N9 and BV-2). The treatment of these cells with the bacterial wall lipopolysaccharide (LPS) induces pronounced changes in the expression of inflammatory cytokines and chemokines in a way that depends on activation of MAPp38, MAP JNK, and NFkB signaling.
To understand the control of miRNA expression and maturation during the course of lymphoproliferative diseases.

Ongoing collaborations:

Jens S. Andersen, Ph.D., is Director of the Center for Experimental Bioinformatics (CEBI). His Laboratory has a vast expertise on methods for protein identification, isolation of multi-protein complexes, searching of mass spectrometric data in sequence databases including genomic databases, use of mass spectrometry for the large scale analysis of protein function (functional proteomics). Dr. Andersen is involved in a large-scale network for functional characterization of RNA binding proteins at the structural level.

Ching-Yi Chen, Ph.D., leads a group at the Biochemistry and Biophysics Department of UAB (Birmingham, AL). His main interest is to decipher the mechanism and regulation of mammalian mRNA turnover. He developed an inducible reporter-based strategy to investigate the contribution of disinct enzymathic components to mRNA decay.

Witold Filipowicz, Ph.D., is group leader at the Friedrich Miescher Institute (Basel, CH). His main interest is to investigate the biochemistry and function of RNA interference and microRNAs. Dr Filipowicz is a frontrunner in understanding the mechanism and a biological function of RNAi and miRNAs and on the role for the miRNA apparatus in transcriptional gene silencing in mammals.

Andres Ramos, Ph.D., leads a Structural Biology group at MRC (London). His main scientific interest is the molecular recognition in post-transcriptional regulation. His present work takes advantage of a range of structural and biophysical tools to study the role of protein-RNA interactions in mRNA decay, 3'mRNA editing and viral regulation.

M. Geoff Rosenfeld, M.D., is HHMI investigator at the University of California at San Diego (CA). In the last two decades his laboratory applied genetic, biochemical, and molecular biological approaches to understand precisely the molecular mechanisms that control gene transcription, and its modulation, by signal transduction pathways during organogenesis.

Most recent and significant publications:

Chen C.Y.*, Gherzi R.*, Andersen J.S., Gaietta G., Jürchott K., Royer H.D., Mann M. and Karin M. Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA stabilization during T-cell activations Genes Dev. 2000 May 15;14(10):1236-48.

Chen C.Y.*, Gherzi R.*, Ong S.E., Chan E.L., Raijmakers R., Pruijn G.J., Stoecklin G., Moroni C., Mann M., and Karin M. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs.Cell. 2001 Nov 16;107(4):451-64.

Briata, P., Ilengo, C., Corte, G., Moroni, C. M.G., Chen, C.-Y., and Gherzi, R The Wnt/beta-catenin-->Pitx2 pathway controls the turnover of Pitx2 and other unstable mRNAs Mol Cell. 2003 Nov;12(5):1201-11.

Gherzi, R., LeeK.Y., Briata, P., Wegmüller, D., Moroni, C., Karin, M., and ChenC.-Y. A. A KH domain RNA binding protein, KSRP, promotes ARE-directed mRNA turnover by recruiting the degradation machinery.Mol Cell. 2004 Jun 4;14(5):571-83.

Schmidlin, M., Lu, M., Leuenberger, S.A., Stoecklin, G., Mallaun, M., Gross, B., Gherzi, R., Hess, D., Hemmings, B.A., and Moroni, C. The ARE-dependent mRNA-destabilizing activity of BRF1 is regulated by proteins EMBO J. 2004 Dec 8;23(24):4760-9. Epub 2004 Nov 11

Briata, P., Forcales, S.V., Ponassi, M., Corte, G., Chen, C.-Y., Karin, M., Puri, P.L., and Gherzi, R. p38-dependent phosphorylation of the mRNA decay-promoting factor KSRP controls the stability of select myogenic transcripts.Mol Cell. 2005 Dec 22;20(6):891-903.

Chou, C.F., Mulky, A., Maitra, S., Lin, W.J., Gherzi, R., Kappes, J., and Chen, C.Y. Tethering KSRP, a decay-promoting AU-rich element-binding protein, to mRNAs elicits mRNA decay.
Mol Cell Biol. 2006 May;26(10):3695-706.

Gherzi R, Trabucchi M, Ponassi M, Ruggiero T, Corte G, Moroni C, Chen CY, Khabar KS, Andersen JS, and Briata P. The RNA-binding protein KSRP promotes decay of beta-catenin mRNA and is inactivated by PI3K-AKT signaling.PLoS Biol. 2006 Dec;5(1):e5.

Garcia-Mayoral, M.F., Hollingworth, D., Masino, L., Diaz-Moreno, I., Kelly, G., Gherzi, R., Chou, C.F., Chen, C.Y., and Ramos, A. The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation.Structure. 2007 Apr;15(4):485-98.

Ruggiero, T., Trabucchi, M., Ponassi, M., Corte, G., Chen, C.-Y., Al-Haj, L., Khabar, K.S., Briata, P., and Gherzi R. Identification of a set of KSRP target transcripts upregulated by PI3K-AKT signaling.BMC Mol Biol. 2007 Apr 16;8:28-40