Identification and characterization of the variants of metastasis-associated protein 1 generated following alternative splicing

The structure of the core NuRD repression complex provides insights into its interaction with chromatin

The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.

Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins

Alternative splicing (AS) plays a critical role in cell fate transitions, development, and disease. Recent studies have shown that AS also influences pluripotency and somatic cell reprogramming. We profiled transcriptome-wide AS changes that occur during reprogramming of fibroblasts to pluripotency. This analysis revealed distinct phases of AS, including a splicing program that is unique to transgene-independent induced pluripotent stem cells (iPSCs). Changes in the expression of AS factors Zcchc24, Esrp1, Mbnl1/2, and Rbm47 were demonstrated to contribute to phase-specific AS. RNA-binding motif enrichment analysis near alternatively spliced exons provided further insight into the combinatorial regulation of AS during reprogramming by different RNA-binding proteins. Ectopic expression of Esrp1 enhanced reprogramming, in part by modulating the AS of the epithelial specific transcription factor Grhl1. These data represent a comprehensive temporal analysis of the dynamic regulation of AS during the acquisition of pluripotency.

Connecting the dots: chromatin and alternative splicing in EMT

Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.

Structure and function insights into the NuRD chromatin remodeling complex

Transcription regulation through chromatin compaction and decompaction is regulated through various chromatin-remodeling complexes such as nucleosome remodeling and histone deacetylation (NuRD) complex. NuRD is a 1 MDa multi-subunit protein complex which comprises many different subunits, among which histone deacetylases HDAC1/2, ATP-dependent remodeling enzymes CHD3/4, histone chaperones RbAp46/48, CpG-binding proteins MBD2/3, the GATAD2a (p66α) and/or GATAD2b (p66β) and specific DNA-binding proteins MTA1/2/3. Here, we review the currently known crystal and NMR structures of these subunits, the functional data and their relevance for biomedical research considering the implication of NuRD subunits in cancer and various other diseases. The complexity of this macromolecular assembly, and its poorly understood mode of interaction with the nucleosome, the repeating unit of chromatin, illustrate that this complex is a major challenge for structure-function relationship studies which will be tackled best by an integrated biology approach.

Towards an understanding of the structure and function of MTA1

Gene expression is controlled through the recruitment of large coregulator complexes to specific gene loci to regulate chromatin structure by modifying epigenetic marks on DNA and histones. Metastasis-associated protein 1 (MTA1) is an essential component of the nucleosome remodelling and deacetylase (NuRD) complex that acts as a scaffold protein to assemble enzymatic activity and nucleosome targeting proteins. MTA1 consists of four characterised domains, a number of interaction motifs, and regions that are predicted to be intrinsically disordered. The ELM2-SANT domain is one of the best-characterised regions of MTA1, which recruits histone deacetylase 1 (HDAC1) and activates the enzyme in the presence of inositol phosphate. MTA1 is highly upregulated in several types of aggressive tumours and is therefore a possible target for cancer therapy. In this review, we summarise the structure and function of the four domains of MTA1 and discuss the possible functions of less well-characterised regions of the protein.

Metastasis tumor-associated protein-2 knockdown suppresses the proliferation and invasion of human glioma cells in vitro and in vivo

Metastasis tumor-associated protein 2 (MTA2) is a member of the MTA family that is closely associated with tumor progression and metastasis. However, the role of MTA2 in glioma cells remains unclear. The expression of MTA2 was measured using immunohistochemistry and western blotting in the human brain tumor tissue array and human glioma cell lines. The impact of MTA2 knockdown on GBM8401 and Hs683 cell growth was evaluated by MTT assay and flow cytometry. Cell migration and invasion were analyzed by cell-migration assay and Matrigel invasion assay. In addition, we used subcutaneous tumor models to study the effect of MTA2 on the growth of glioma cells in vivo. We found that MTA2 protein and mRNA expression are higher in GBM8401 and Hs683 cells than in other glioma cells (M059 J, M059 K and U-87 MG), and glioma tumor tissue correlated significantly with tumor grade (P < 0.001). Knockdown of MTA2 expression significantly inhibited cell growth, cell migration and invasion, and induced G0/G1 phase arrest in human GBM8401 and Hs683 cells in vitro. Moreover, in vivo studies using subcutaneous xenografts in mice models indicate that MTA2 knockdown significantly inhibited tumorigenicity. These results indicate that MTA2 plays an important oncogenic role in the development and progression of gliomas.

Expression of metastasis-associated protein 2 (MTA2) might predict proliferation in non-small cell lung cancer

Metastatic tumor antigen 2 (MTA2) is a member of the MTA family that is closely associated with tumor progression and metastasis. In this study, the expression profile of MTA2 in 223 cases of non-small cell lung cancer (NSCLC) tissues and two lung cancer cell lines was investigated. Interestingly, we found MTA2, which was believed to have nuclear distribution only, was distributed in both nucleus and cytoplasm in normal and cancer cells. Nuclear MTA2 expression was detected in 148 cases of NSCLC (66.4%), and was correlated with advanced TNM stages (p=0.023), tumor size (p=0.036), and lymph node metastasis (p=0.004). Besides, the Ki-67 proliferation index was significantly higher in nuclear MTA2-positive tumors than in nuclear MTA2-negative tumors (r=0.538, p=0.006). However, there was no significant difference in cytoplasmic MTA2 status by age, gender, tumor stage, histology, grade, lymph node metastasis, and Ki-67 proliferation index. Univariate analysis revealed nuclear MTA2 expression was correlated with poor overall survival (p=0.035), whereas there was a nonsignificant trend in the same direction for cytoplasmic MTA2 (p=0.134). Multivariate Cox regression analysis revealed the overexpression of nuclear and cytoplasmic MTA2 not to be independent factors predictive of poor disease outcome. Our data suggested that MTA2 might play roles in both the nucleus and cytoplasm in the progression of NSCLC.

Expression profile of MTA1 in adult mouse tissues

MTA1, as a constituent of the nucleosome-remodeling and -deacetylation complex (NuRD), is thought to modulate transcription by influencing the status of chromatin remodeling. Despite its strong correlation with the metastatic potential of several cancer cell lines and tissues, MTA1 can also regulate divergent cellular pathways by modifying the acetylation status of crucial target genes. However, its fundamental physiological functions have not been characterized. To further address the possible physiological role of this protein in mammals, the authors examined the expression pattern of mouse MTA1 in a variety of adult mouse tissues by a combination of techniques, including semi-quantitative RT-PCR, Western blotting and immunohistochemistry. Positive signals were observed on variety of tissues/cells in multiple systems including nervous, cardiovascular, respiratory, digestive, immune, endocrine, urinary, reproductive and sensory organ systems. MTA1 was localized in both the cytoplasm and the nuclei, and was accumulated in the nuclei. In mature mice, MTA1 expression was seen in cell types that constantly undergo proliferation or self-renewal, such as testis and cell types not constantly engaged in proliferation or self-renewal, such as brain, liver and kidney. This differential expression suggests that this protein serves distinct functions in murine organs.

Identification of Metastasis Associated Antigen 1 (MTA1) by Serological Screening of Prostate Cancer cDNA Libraries

Over the past 10 years the serological analysis of recombinant cDNA expression libraries (SEREX) has proved to be an effective method for the identification of tumour antigens. In the present study, two prostate cancer libraries were constructed and screened using autologous sera. Fifty five genes were isolated, including 46 known genes and 9 previously uncharacterised genes. Among the known genes, a metastasis-associated gene, MTA1, previously identified by differential cDNA hybridisation, was preferentially expressed in a panel of malignant tissues compared with normal tissues, as analysed by reverse transcriptase-polymerase chain reaction (RT-PCR). MTA1 transcripts were observed to be over-expressed in normal human testes as well as various cancer tissues when compared to the panel of normal tissues. MTA1 antigen reacted with 2 of 13 allogeneic prostate cancer patient sera tested, but no sera reactivity was observed to any of the normal adult sera tested. Furthermore, a similar distribution and expression level of MTA-1 was observed in murine tissues and cancer cell lines. Based on these findings and previous reports on the literature on this gene, MTA-1 can be considered not only as a “biomarker” of aggressive disease but also as a potential therapeutic target.

MTA family of coregulators in nuclear receptor biology and pathology

Nuclear receptors (NRs) rely on coregulators (coactivators and corepressors) to modulate the transcription of target genes. By interacting with nucleosome remodeling complexes, NR coactivators potentiate transcription, whereas corepressors inhibit transcription of the target genes. Metastasis-associated proteins (MTA) represent an emerging family of novel NR coregulators. In general, MTA family members form independent nucleosome remodeling and deacetylation (NuRD) complexes and repress the transcription of different genes by recruiting histone deacetylases onto their target genes. However, MTA1 also acts as a coactivator in a promoter-context dependent manner. Recent findings that repression of estrogen receptor transactivation functions by MTA1, MTA1s, and MTA2 and regulation of MTA3 by estrogen signaling have indicated the significance of these proteins in NR signaling. Here, we highlight the action of MTA proteins on NR signaling and their roles in pathophysiological conditions.

The zinc finger and C-terminal domains of MTA proteins are required for FOG-2-mediated transcriptional repression via the NuRD complex

FOG-2 is a transcriptional co-regulator that is required for cardiac morphogenesis as mice deficient in this factor die during mid-gestation of cardiac malformations. FOG-2 interacts with GATA4 to attenuate GATA4-dependent gene expression. The first 12 amino acids of FOG-2 (the FOG Repression Motif) are necessary to mediate this repression. To determine the mechanism by which the FOG Repression Motif functions, we identified 7 polypeptides from rat cardiac nuclear extracts that co-purified with a GST-FOG-2 fusion protein. All proteins identified are members of the NuRD nucleosome remodeling complex. Using in vitro binding and co-immunoprecipitation assays, we demonstrate that Metastasis-Associated proteins (MTA)-1, 2 and 3 and Retinoblastoma binding proteins RbAp46 and RbAp48 interact with FOG-2, but not with a mutant form of FOG-2 that is unable to repress transcription. Furthermore, we define a novel domain located in the C-terminal portion of MTA-1 that mediates the FOG-2/MTA-1 interaction. We also demonstrate that knockdown of MTA protein expression dramatically impairs the ability of FOG-2 to repress GATA4 activity. Finally, we show that the zinc finger domain of MTA-1 is required for FOG-2-mediated transcriptional repression and that this domain interacts with RbAp46 and RbAp48 subunits of the NuRD complex. Together, these results demonstrate the importance of FOG-2/MTA/RbAp interactions for FOG-2-mediated transcriptional repression and further define the molecular interactions between the FOG Repression Motif and the NuRD complex.

Metastasis tumor antigens, an emerging family of multifaceted master coregulators

Regulation of fundamental genetic processes demands dynamic participation of transcription factors, their coregulators, and multiprotein chromatin remodeling activities at target genes. One family of chromatin modifiers that is ubiquitously expressed is the metastasis tumor antigens (MTA), which are integral parts of nucleosome remodeling and histone deacetylation (NuRD) complexes. MTA family members exist in distinct NuRD complexes, and functional redundancy is lacking among MTA family members. MTA proteins regulate divergent cellular pathways, including hormonal action, epithelial-to-mesenchymal transitions, differentiation, protein stability and development, and cell fate programs by modifying the acetylation status of crucial target genes. Intriguingly, at least one member of this family, MTA1, itself undergoes acetylation and acts as a coactivator in certain contexts. We discuss the roles of the MTA family of chromatin modifiers, with an emphasis on their physiologic functions.