Ernest Martinez

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Dr. Ernest Martinez

Assistant Professor of Biochemistry
Ph.D. University of Lausanne (Switzerland), 1989.
Post-Doctoral Fellow of the Swiss National Science Foundation, The Rockefeller University, 1990-1992.
Post-Doctoral Associate, The Rockefeller University, 1992-1995.
Biomedical Research Fellow of The Charles Revson & Norman and Rosita Winston Foundation, The Rockefeller University, 1995-1996.
Research Associate, The Rockefeller University, 1996-2000.
CAREER Award - U.S. National Science Foundation, 2005-2010.


Phone : (951) 827-2031
Fax : (951) 827-4434
e-mail :


My research interest is in the characterization of the factors and molecular mechanisms involved in the regulation of gene transcription by RNA polymerase II, with emphasis on the transcriptional control of mammalian cell proliferation, and differentiation. Research in the lab currently focuses on 3 interrelated projects (see below and Fig.1):
(i) Structure, function, and regulation of the human STAGA complex, a chromatin-modifying coactivator complex.
(ii) Transcription regulation by the oncoproteins and cell cycle regulators c-Myc and E2F1.
(iii) Role of chromatin structure, TAFIIs, and novel cofactors in core promoter selectivity.
A combination of cellular, molecular biological and biochemical techniques are used, including the reconstitution of transcription regulatory processes in vitro with purified native and recombinant factors and chromatin-assembled physiological target genes.

I. Structure, function, and regulation of the human STAGA coactivator complex.
In eukaryotes, genomic DNA is packaged by histones into nucleosomes, the basic repeating units of chromatin that further fold into higher order chromatin structures and generally inhibit sequence-specific protein-DNA interactions. Eukaryotic cells have evolved two major enzymatic mechanisms to modify chromatin structure (and to alleviate its repressive nature): (i) ATP-dependent nucleosome remodeling by multiprotein complexes that use the energy of ATP hydrolysis to alter the association of core histones with DNA and (ii) covalent modifications of core histones, including acetylation by histone acetyltransferases (HATs), that regulate core histone interactions with either DNA, adjacent nucleosomes and/or other regulatory proteins. In yeast, GCN5, the prototypical HAT, has a transcription coactivator function as part of the SAGA (SPT-ADA-GCN5 Acetyltransferase) complex. Mammalian cells have two distinct GCN5 homologues (PCAF and GCN5) that form part of at least three different SAGA-like complexes (PCAF, TFTC and STAGA). The composition, structure, and roles of these mammalian HAT complexes are still poorly characterized. We are concentrating on the characterization of the human STAGA (SPT3-TAFII31-GCN5-L Acetylase) complex. My previous studies have shown that STAGA contains TAFIIs (TBP-Associated Factors) and is thus related to TFIID, but lacks a TATA-binding protein (TBP). STAGA also contains homologues of most yeast SAGA coactivator components, including an ataxia telangiectasia mutated (ATM)-related protein TRRAP that was originally identified through its interaction with c-Myc and E2F1 and which contributes to cellular transformation by c-Myc in vitro. Accordingly, STAGA functions as a transcription coactivator for an artificial (Gal4-VP16) activator in vitro on a chromatin-assembled promoter. Interestingly, STAGA also interacts with splicing and UV-damaged DNA-binding factors in vivo, suggesting a role in transcription-coupled pre-mRNA splicing and DNA repair within chromatin. Important questions that remain to be addressed include the exact molecular mechanisms of STAGA function in transcription, the role of the different STAGA protein subunits and of STAGA interactions with splicing and DNA repair factors, the identification of physiological target genes and activators, and whether STAGA activities are regulated within the cell. Furthermore, in collaboration with the group of Dr. Stephan Wilkens (in our Department) we are interested in the three dimensional structure and dynamics of the complex.

II. Transcription regulation by the oncoproteins and cell cycle regulators c-Myc and E2F1.
Regulated c-myc gene expression is critical for controlled cell proliferation. Mutations that affect the expression levels and/or the amino acid sequence of the c-Myc protein are among the most commonly found in human cancers. Biological functions of c-Myc include transformation, immortalization, blockage of cell differentiation and induction of apoptosis. Furthermore, c-Myc is required for efficient progression through the cell cycle. In general these biological activities of c-Myc are thought to result from its transcriptional regulatory functions. Indeed, the c-Myc protein has an N-terminal transcription activation domain that is required for its cell transformation function and exhibits sequence-specific DNA binding when dimerized through its HLH-Zip domain with its partner Max. DNA binding is mediated through the basic region, which recognizes the core E-box sequence CACGTG. However, the physiological target genes and coactivators of c-Myc still remain largely unknown. Similarly, E2F1 has a DNA-binding/dimerization partner (DP1) and is a sequence-specific transcription activator that stimulates both cell cycle progression (G1 t o S transition) and apoptosis. Although, several target genes for E2F1 are known, the coactivators and molecular mechanisms of E2F1-mediated transcription activation are still poorly characterized. Our approach to understand how Myc and E2F1 activities contribute at the molecular level to growth promotion, transformation, and apoptosis is to examine the nature, function and regulation of their direct molecular targets at the gene/promoter level.

III. Role of chromatin structure, TAFIIs, and novel cofactors in core promoter selectivity.
The class II basal transcription machinery comprises RNA polymerase II (pol II) and accessory general transcription factors (GTFs), i.e., TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, that are ubiquitous and interact with the core promoter region surrounding the transcription start site(s) of all class II genes (Fig.1). It has been known for quite some time that optimal induction of gene-selective transcription by distal enhancers requires, in some cases, specific core promoter sequences/structures. Indeed, important core promoter elements like the TATA box and/or the initiator element are not present in all genes. Since TBP/TFIID binding to the TATA box is the first step in pre-initiation complex assembly that is required for the recruitment of all the other GTFs and pol II, an unsolved question is: how is TFIID/TBP stably and functionally recruited to TATA-less promoters or to core promoter sequences and TATA boxes that are "masked" by nucleosomes or by other core promoter-bound proteins like E2F factors? We already know that TBP-associated factors (TAFIIs) can interact with core promoter sequences (initiator and downstream sequences) and are essential for basal transcription from TATA-less promoters. Consistent with this, TAFIIs are important for cell cycle progression in vivo and most mammalian cell cycle-regulated promoters are TATA-less. However, TAF-promoter interactions are not sufficient for functional TFIID recruitment to TATA-less promoters that require novel partially purified TAF- and Initiator-dependent Cofactors (TICs). We are interested in the identification of TICs and other cofactors and molecular mechanisms involved in TAFII-dependent transcription from initiator-dependent TATA-less promoters and from E2F-dependent cell cycle-regulated TATA-less genes.

We are interested in the role(s) of (i) chromatin-modifying coactivators and epigenetic regulators such as GCN5 histone acetyltransferase complexes and (ii) oncogenic transcription factors such as the c-MYC oncoprotein in self-renewal, proliferation, and/or differentiation of stem cells, and in identifying potential important differences in the expression, structure, and/or function of theses factors in normal stem cells versus cancer cells.


See publications on PubMed

Faiola, F., Liu, X., Lo, S.-Y., Pan, S., Zhang, K., Lymar, E., Farina, A. and Martinez , E. (2005) Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol. Cell. Biol., 25, 10220-10234.

Zhang, K., Faiola, F. and Martinez, E. (2005) Six lysine residues on c-Myc are direct substrates for acetylation by p300. Biochem. Biophys. Res. Commun., 336, 274-280.

Farina, A., Faiola, F. and Martinez , E. (2004) Reconstitution of an E box-binding Myc:Max complex with recombinant full-length proteins expressed in Escherichia coli. Protein Express. Purif., 34, 215-222.

Liu, X., Tesfai, J., Evrard, Y.A., Dent, S.Y.R., and Martinez, E. (2003) c-Myc transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity for transcription activation. J. Biol. Chem., 278, 20405-20412.

Martinez , E. (2002) Multi-protein complexes in eukaryotic gene transcription. Plant Mol. Biol., 50, 925-947 .

Martinez, E., Palhan, V., Tjernberg, A., Lymar, E.S., Gamper, A.M., Kundu, T.K., Chait, B.T. and Roeder, R.G. (2001) Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol. Cell. Biol., 21, 6782-6795.

Teichman, M., Wang, Z., Martinez, E., Tjernberg, A., Zhang, D., Vollmer, F., Chait, B.T. and Roeder, R.G. (1999) Human TATA-binding protein-related factor-2 (hTRF2) stably associates with hTFIIA in HeLa cells. Proc. Natl. Acad. Sci. USA, 96, 13720-13725.

Gu, W., Malik, S., Ito, M., Yuan, C.-X., Fondell, J.D., Zhang, X.L., Martinez , E., Qin, J. and Roeder, R.G. (1999) A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Mol. Cell, 3, 97-108.

Martinez , E., Kundu, T.K., Fu, J. and Roeder, R.G. (1998) A human SPT3-TAFII31-GCN5-L acetylase complex distinct from TFIID. J. Biol. Chem., 273, 23781-23785.

Martinez , E., Ge, H., Tao, Y., Yuan, C.-X., Palhan, V. and Roeder, R.G. (1998) Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex. Mol. Cell. Biol., 18, 6571-6583.

Tao, Y., Guermah, M., Martinez , E., Oelgeschläger, T., Hasegawa, S., Takada, R., Yamamoto, T., Horikoshi, M. and Roeder, R.G. (1997) Specific interactions and potential functions of human TAFII100. J. Biol. Chem., 272, 6714-6721.

Ge, H., Martinez , E., Chiang, C.-M. and Roeder, R.G. (1996) Activator-Dependent Transcription by Mammalian RNA Polymerase II: In Vitro Reconstitution with General Transcription Factors and Cofactors. In Methods in Enzymology (Edited by Sankar Adhya), Academic Press Inc.,Vol.274, 57-71.

Martinez, E., Zhou, Q., L'Etoile, N., Oelgeschläger, T., Berk, A.J. and Roeder, R.G. (1995) Core promoter-specific function of a mutant transcription factor TFIID defective in TATA box-binding. Proc. Natl. Acad. Sci. USA, 92, 11864-11868.

Martinez, E., Chiang, C.-M., Ge, H. and Roeder, R.G. (1994) TATA-binding protein-associated factor(s) in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter. EMBO J., 13, 3115-3126.

Martinez, E., Lagna, G. and Roeder, R.G. (1994) Overlapping transcription by RNA polymerases II and III of the Xenopus TFIIIA gene in somatic cells. J. Biol. Chem., 269, 25692-25698.

Martinez, E., Dusserre, Y., Wahli, W. and Mermod, N. (1991) Synergistic transcriptional activation by CTF/NF-I and the estrogen receptor involves stabilized interactions with a limiting target factor. Mol. Cell. Biol., 11, 2937-2945.

Wahli, W. and Martinez, E. (1991) Superfamily of steroid nuclear receptors : positive and negative regulators of gene expression. FASEB J., 5, 2243-2249.

Martinez, E. and Wahli, W. (1991) Characterization of hormone response elements. In Nuclear Hormone Receptors (Edited by M. G. Parker), Academic Press Limited, New York, London, pp 125-153.

Martinez, E., Givel, F. and Wahli, W. (1991) A common ancestor DNA motif for invertebrate and vertebrate hormone response elements. EMBO J., 10, 263-268.

Martinez, E. and Wahli, W. (1989) Cooperative binding of estrogen receptor to imperfect estrogen-responsive DNA elements correlates with their synergistic hormone-dependent enhancer activity. EMBO J., 8, 3781-3791.

Martinez, E., Givel, F. and Wahli, W. (1987) The estrogen-responsive element as an inducible enhancer : DNA sequence requirements and conversion to a glucocorticoid-responsive element. EMBO J., 6, 3719-3727.

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