Review
The c-Myc target gene network

https://doi.org/10.1016/j.semcancer.2006.07.014Get rights and content

Abstract

For more than a decade, numerous studies have suggested that the c-Myc oncogenic protein is likely to broadly influence the composition of the transcriptome. However, the evidence required to support this notion was made available only recently, much to the anticipation of an eagerly awaiting field. In the past 5 years, many high-throughput screens based on microarray gene expression profiling, serial analysis of gene expression (SAGE), chromatin immunoprecipitation (ChIP) followed by genomic array analysis, and Myc-methylase chimeric proteins have generated a wealth of information regarding Myc responsive and target genes. From these studies, the c-Myc target gene network is estimated to comprise about 15% of all genes from flies to humans. Both genomic and functional analyses of c-Myc targets suggest that while c-Myc behaves as a global regulator of transcription, groups of genes involved in cell cycle regulation, metabolism, ribosome biogenesis, protein synthesis, and mitochondrial function are over-represented in the c-Myc target gene network. c-Myc also consistently represses genes involved in cell growth arrest and cell adhesion. The overexpression of c-Myc predisposes cells to apoptosis under nutrient or growth factor deprivation conditions, although the critical sets of genes involved remain elusive. Despite tremendous advances, the downstream target genes that distinguish between physiologic and tumorigenic functions of c-Myc remain to be delineated.

Introduction

The c-MYC proto-oncogene is one of the most frequently activated oncogenes and is estimated to be involved in 20% of all human cancers, affecting about 100,000 US cancer deaths per year (http://www.myccancergene.org) [1], [2]. It is therefore critical that the function of c-MYC is well delineated. Despite its initial ambiguous functional definition as an oncoprotein implicated in DNA replication, RNA splicing or transcription, c-Myc has emerged foremost as a transcription factor. In particular, the discoveries that c-Myc contains an N-terminal transactivation domain and requires the bHLH (basic helix–loop–helix) partner protein Max to bind specific DNA sequences solidified its role in transcription (Fig. 1) [1], [3], [4], [5], [6], [7], [8]. In fact, recent estimates suggest that c-Myc could regulate as many as 15% of genes in genomes from flies to humans. c-Myc regulates transcription through several mechanisms, including recruitment of histone acetylases, chromatin modulating proteins, basal transcriptional factors and DNA methyltransferase [9], [10], [11], [12], [13], [14], [15], [16]. Hence, c-Myc targets can be classified into distinct subgroups whose regulation may involve some or all mechanisms through which c-Myc affects transcription. Moreover, the cis-regulatory modules for these subgroups are likely to contain binding sites for other specific transcription factors that cooperate with c-Myc, such that a module containing binding sites for c-Myc and transcription factor X may regulate the subgroup Xi of target genes. For example, one may envision that there are c-Myc target genes (such as “housekeeping” genes) whose histones are pre-acetylated via the binding of transcription factor X prior to c-Myc binding. The association of c-Myc with the promoters of these targets would then recruit additional factors to enhance rates of transcription. In contrast, a hypothetical subset of c-Myc target genes may exist that require c-Myc to bind first and initiate histone acetylation before other transcription factors proceed to execute the final steps of transcriptional activation. These targets would thus require c-Myc in order to allow for any transcription to occur.

In addition to transactivation, the mechanisms of c-Myc-mediated trans-repression are beginning to be defined. The identification of the Mad family of proteins (Mad1/Mad2/Mxi1, Mad3, and Mad4) has allowed further insight into the dynamics of protein interactions that regulate c-Myc's function. When bound to Max, Mad family members bind consensus enhancer box (E-box) sequences and compete for binding with c-Myc/Max heterodimers. Mad/Max dimers repress transcription by recruiting the chromatin-modifying co-repressor complex containing Sin3, N-CoR, and the class I histone deacetylases HDAC1 and 2 to the promoters of target genes. Recruitment of this complex results in deacetylation of histone tails and a closed chromatin conformation, thus preventing the transcriptional activation that occurs through E-boxes [17], [18]. In contrast to Max, which is ubiquitously expressed, the Mad/Mnt proteins are induced during terminal differentiation [19]. Consistent with these findings, chromatin immunoprecipitation experiments revealed a switch from c-Myc/Max binding to Mad/Max binding during cellular differentiation [20], [21]. Recent studies combining ChIP and CpG island microarrays have demonstrated that Max bound to targets that were activated and repressed by c-Myc [22]. Moreover, a functional Myc:Max interaction was shown to be essential for repression of gene targets. These findings suggest that Max may in fact play a more universal role in transcriptional regulation than previously thought.

Through direct interaction with the transcriptional activator Miz-1, Myc binds to and interferes with Miz-1 mediated transactivation thereby causing trans-repression of specific Miz-1 target genes [23], [24], [25], [26]. One study demonstrated that c-Myc/Max dimers bind the p15INK4B promoter (at the INR initiator element, which recruits the basal transcriptional machinery to TATA-lacking promoters) and repress transcription by disrupting the association of Miz1 with the p300 coactivator [26]. Another report found that c-Myc is recruited to the p21 promoter by Miz1. This interaction prevented p21 induction by p53, resulting in the initiation of apoptosis over cell cycle arrest [27]. Recently, c-Myc has been shown to serve as a molecular bridge between Miz-1 bound to the p21 promoter and the DNA methylase Dnmt3a to mediate methylation and transcriptional silencing of p21 [16]. Another possible mechanism of trans-repression may involve the interaction of c-Myc with CAAT box binding proteins, such as NF-Y. This appears to be the case with the transcriptional repression of PDGFR-β and perhaps of collagen genes [28], [29], [30], [31]. Taken together, these studies provide evidence that c-Myc can inhibit transcription by directly interfering with other factors that activate gene expression.

With transcriptional regulation as its acknowledged function, the search for physiological and pathological c-Myc target genes has intensified over the past decade [3], [4], [5], [6], [7], [32], [33], [34], [35], [36]. Searches for target genes have involved hypothesis-driven, low-throughput studies of candidate c-Myc target genes as well as medium-throughput studies to define a larger repertoire of c-Myc responsive genes through subtraction cloning methods. More recently, the field has rapidly adopted high-throughput microarray technologies for the discovery of c-Myc responsive genes [11], [22], [37], [38], [39], [40], [41], [42]. Despite impressive advances, major milestones still must be met to achieve a complete understanding of c-Myc responsive genes and how they relate to tumorigenesis.

Section snippets

Identification of c-Myc target genes

To understand the network of target genes regulated by c-Myc, it is crucial to determine whether c-Myc responsive genes are directly bound by c-Myc or whether the responsive genes are secondary events that require the activities of the direct target genes (i.e., indirect targets). Direct targets are defined as genes that are bound by c-Myc and respond to changes in c-Myc levels or c-Myc activity.

Until factors that alter the activity of c-Myc protein are better defined, most current models to

Myc target genes

What is the functional significance of a given c-Myc target gene? Only a fraction of genes appear to be universally regulated by c-Myc independent of cell type or species [64]. c-Myc responsive genes that appear recurrently in different cell types, systems and species can be identified from the c-Myc target gene database (http://www.myccancergene.org). In addition, the use of ChIP has further identified direct c-Myc targets among the genes that appear to respond to c-Myc regardless of the cell

Functions of c-Myc target genes

Although c-Myc is thought to influence up to about 15% of genes [10], [58], [69] and despite the functional range of specific genes altered, c-Myc consistently affects specific classes of genes that involve metabolism, protein biosynthesis, cell cycle regulation, cell adhesion and the cytoskeleton. The deregulated expression of c-Myc also induces genes that contribute to apoptosis under nutrient or growth factor deprivation; however, c-Myc target genes involved in apoptosis remain to be fully

An integrated database of Myc responsive genes

Given the diverse cell types and experimental systems used to study Myc target genes, how does the field begin to achieve a comprehensive accounting of Myc responsive target genes? To begin to glean a collective view of Myc responsive transcriptomes, we have launched a publicly accessible Myc target gene database (http://www.myccancergene.org) [64]. The database is searchable and provides the ability to prioritize the putative target genes according to the level of experimental evidence

The c-Myc transcriptional regulatory network

By studying the structure and behavior of transcriptional networks, biologists are beginning to understand the complex processes that control gene expression. The goal of this type of analysis is to better understand how relationships between molecules (in this case a transcription factor and its target genes) control cellular behavior (for example, the process of transformation). For a full appreciation of target genes, the wiring of the c-Myc target gene network will need to be delineated in

Conclusion and outlook

The intense interest in c-Myc function through the identification of its target genes has rallied the c-Myc research community to generate vast amounts of information over the last several years. Although thousands of c-Myc responsive genes have been identified and a general picture emerges for c-Myc function in regulating cell cycle progression, metabolism, ribosome biogenesis, and cell adhesion, the set of c-Myc target genes that distinguishes physiologic c-Myc function from pathologic,

Acknowledgements

We apologize for omissions due to space limitation. We thank J. Mendell and members of the Dang Laboratory for their comments. Our original work is supported by NCI grants CA51497 and CA57341. CVD is Johns Hopkins Family Professor in Oncology Research.

References (132)

  • S.R. Eberhardy et al.

    c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism

    J Biol Chem

    (2001)
  • K.I. Zeller et al.

    Characterization of nucleophosmin (B23) as a Myc target by scanning chromatin immunoprecipitation

    J Biol Chem

    (2001)
  • S. Cawley et al.

    Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

    Cell

    (2004)
  • K. Kozar et al.

    Mouse development and cell proliferation in the absence of D-cyclins

    Cell

    (2004)
  • C. de la Cova et al.

    Drosophila myc regulates organ size by inducing cell competition

    Cell

    (2004)
  • E. Moreno et al.

    dMyc transforms cells into super-competitors

    Cell

    (2004)
  • J. Secombe et al.

    Myc: a weapon of mass destruction

    Cell

    (2004)
  • R.C. Osthus et al.

    Deregulation of glucose transporter 1 and glycolytic gene expression by c-Myc

    J Biol Chem

    (2000)
  • C.E. Nesbit et al.

    MYC oncogenes and human neoplastic disease

    Oncogene

    (1999)
  • C.V. Dang

    c-Myc target genes involved in cell growth, apoptosis, and metabolism

    Mol Cell Biol

    (1999)
  • S. Pelengaris et al.

    c-MYC: more than just a matter of life and death

    Nat Rev Cancer

    (2002)
  • M.D. Cole et al.

    The Myc oncoprotein: a critical evaluation of transactivation and target gene regulation

    Oncogene

    (1999)
  • R.N. Eisenman

    Deconstructing myc

    Genes Dev

    (2001)
  • C. Grandori et al.

    The Myc/Max/Mad network and the transcriptional control of cell behavior

    Annu Rev Cell Dev Biol

    (2000)
  • T.A. Baudino et al.

    The Max network gone mad

    Mol Cell Biol

    (2001)
  • A. Orian et al.

    Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network

    Genes Dev

    (2003)
  • P.C. Fernandez et al.

    Genomic targets of the human c-Myc protein

    Genes Dev

    (2003)
  • S.W. Cheng et al.

    c-MYC interacts with INI1/hSNF5 and requires the SWI/SNF complex for transactivation function

    Nat Genet

    (1999)
  • S. Kanazawa et al.

    c-Myc recruits P-TEFb for transcription, cellular proliferation and apoptosis

    Oncogene

    (2003)
  • C. Brenner et al.

    Myc represses transcription through recruitment of DNA methyltransferase corepressor

    EMBO J

    (2005)
  • L. Alland et al.

    Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression [see comments]

    Nature

    (1997)
  • D.E. Ayer et al.

    A switch from Myc:Max to Mad:Max heterocomplexes accompanies monocyte/macrophage differentiation

    Genes Dev

    (1993)
  • C. Bouchard et al.

    Regulation of cyclin D2 gene expression by the Myc/Max/Mad network: Myc-dependent TRRAP recruitment and histone acetylation at the cyclin D2 promoter

    Genes Dev

    (2001)
  • D. Xu et al.

    Switch from Myc/Max to Mad1/Max binding and decrease in histone acetylation at the telomerase reverse transcriptase promoter during differentiation of HL60 cells

    Proc Natl Acad Sci USA

    (2001)
  • S. Wu et al.

    Myc represses differentiation-induced p21CIP1 expression via Miz-1-dependent interaction with the p21 core promoter

    Oncogene

    (2003)
  • J. Seoane et al.

    TGFbeta influences Myc, Miz-1 and Smad to control the CDK inhibitor p15INK4b

    Nat Cell Biol

    (2001)
  • P. Staller et al.

    Repression of p15INK4b expression by Myc through association with Miz-1

    Nat Cell Biol

    (2001)
  • J. Seoane et al.

    Myc suppression of the p21(Cip1) Cdk inhibitor influences the outcome of the p53 response to DNA damage

    Nature

    (2002)
  • D. Barsyte-Lovejoy et al.

    c-Myc represses the proximal promoters of GADD45a and GADD153 by a post-RNA polymerase II recruitment mechanism

    Oncogene

    (2004)
  • D.Y. Mao et al.

    Promoter-binding and repression of PDGFRB by c-Myc are separable activities

    Nucleic Acids Res

    (2004)
  • H. Izumi et al.

    Mechanism for the transcriptional repression by c-Myc on PDGF beta-receptor

    J Cell Sci

    (2001)
  • B.S. Yang et al.

    Transcriptional suppression of cellular gene expression by c-Myc

    Mol Cell Biol

    (1991)
  • J.H. Patel et al.

    Analysis of genomic targets reveals complex functions of MYC

    Nat Rev Cancer

    (2004)
  • D.L. Levens

    Reconstructing MYC

    Genes Dev

    (2003)
  • D. Levens

    Disentangling the MYC web

    Proc Natl Acad Sci USA

    (2002)
  • L.M. Boxer et al.

    Translocations involving c-myc and c-myc function

    Oncogene

    (2001)
  • G.F. Claassen et al.

    Myc-mediated transformation: the repression connection

    Oncogene

    (1999)
  • H.A. Coller et al.

    Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion

    Proc Natl Acad Sci USA

    (2000)
  • Q.M. Guo et al.

    Identification of c-myc responsive genes using rat cDNA microarray

    Cancer Res

    (2000)
  • M. Schuhmacher et al.

    The transcriptional program of a human B cell line in response to Myc

    Nucleic Acids Res

    (2001)
  • Cited by (0)

    View full text