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Biomedical subjects

Paul A Wade

Publications and source records attributed to Paul A Wade.

At least 19 recordsLinked to original sources
PubMed2006

MBD family proteins: reading the epigenetic code.

Methylation of DNA in mammalian cells serves to demarcate functionally specialized regions of the genome and is strongly associated with transcriptional repression. A highly conserved family of DNA-binding proteins characterized by a common sequence motif is widely believed to convert the information represented by methylation patterns into the appropriate functional state. This family, the MBD family, has been characterized at both the biochemical and genetic levels. A key issue, given their highly similar DNA-binding surfaces, is whether the individual MBD proteins bind differentially to distinct regions within the genome and, if so, by what mechanism. Somewhat surprisingly, some MBD family members, such as MeCP2, have considerable selectivity for specific sequences. Other family members, such as MBD2, appear to bind with somewhat relaxed specificity to methylated DNA. Recent genetic and molecular experiments have shed considerable light on these and other issues relevant to the chromosomal biology of this interesting protein family.

Animals↗
PubMed2006

Nuclear Akt associates with PKC-phosphorylated Ebp1, preventing DNA fragmentation by inhibition of caspase-activated DNase.

Akt promotes cell survival through phosphorylation. The physiological functions of cytoplasmic Akt have been well defined, but little is known about the nuclear counterpart. Employing a cell-free apoptotic assay and NGF-treated PC12 nuclear extracts, we purified Ebp1 as a factor, which contributes to inhibition of DNA fragmentation by CAD. Depletion of Ebp1 from nuclear extracts or knockdown of Ebp1 in PC12 cells abolishes the protective effects of nerve growth factor, whereas overexpression of Ebp1 prevents apoptosis. Ebp1 (S360A), which cannot be phosphorylated by PKC, barely binds Akt or inhibits DNA fragmentation, whereas Ebp1 S360D, which mimics phosphorylation, strongly binds Akt and suppresses apoptosis. Further, phosphorylated nuclear but not cytoplasmic Akt interacts with Ebp1 and enhances its antiapoptotic action independent of Akt kinase activity. Moreover, knocking down of Akt diminishes the antiapoptotic effect of Ebp1 in the nucleus. Thus, nuclear Akt might contribute to suppressing apoptosis through interaction with Ebp1.

Adaptor Proteins, Signal Transducing↗
PubMed2005

Nucleophosmin/B23, a nuclear PI(3,4,5)P(3) receptor, mediates the antiapoptotic actions of NGF by inhibiting CAD.

Phosphatidylinositol 3,4,5-triphosphate [PI(3,4,5)P(3)] is an essential second messenger implicated in various cellular processes. Cytoplasmic PI(3,4,5)P(3) has been well characterized, but little is known about the physiological role of nuclear PI(3,4,5)P(3). Here, we describe a nuclear PI(3,4,5)P(3) receptor, nucleophosmin (NPM)/B23, that mediates the antiapoptotic effects of NGF by inhibiting DNA fragmentation activity of caspase-activated DNase (CAD). Employing PI(3,4,5)P(3) column and NGF-treated PC12 nuclear extracts, we identified B23 as a nuclear PI(3,4,5)P(3) binding protein. Purification from nuclear extract demonstrates that B23 contributes to DNA fragmentation inhibitory activity. Depletion of B23 from nuclear extracts or knockdown B23 in PC12 cells abolishes NGF-provoked protective effect, whereas overexpression of B23 in PC12 cells prevents apoptosis. Further, hydrolyzing PI(3,4,5)P(3) with PTEN or SHIP abrogates its antiapoptotic activity. Moreover, B23 mutants that can not associate with PI(3,4,5)P(3) fail to prevent DNA fragmentation. Thus, the nuclear B23-PI(3,4,5)P(3) complex regulates the antiapoptotic activity of NGF in the nucleus.

Animals↗
PubMed2004

MTA3 and the Mi-2/NuRD complex regulate cell fate during B lymphocyte differentiation.

The transcriptional repressor BCL-6 regulates B lymphocyte cell fate during the germinal center reaction by preventing terminal differentiation of B lymphocytes into plasma cells until appropriate signals are received. Here, we report a cofactor, MTA3, a cell type-specific subunit of the corepressor complex Mi-2/NuRD, for BCL-6-dependent cell fate determination. MTA3 is expressed in the same pattern in germinal centers as BCL-6. BCL-6 physically interacts with Mi-2/NuRD and this interaction is sensitive to BCL-6 acetylation status. Depletion of MTA3 by RNAi impairs BCL-6-dependent repression and alters the cell-specific transcriptional pattern characteristic of the B lymphocyte. Remarkably, exogenous expression of BCL-6 in a plasma cell line leads, in an MTA3-dependent manner, to repression of plasma cell-specific transcripts, reactivation of the B cell transcriptional program, expression of B lymphocyte cell surface markers, and reprogramming of cell fate.

Acetylation↗
PubMed2004

Hormonal regulation of metastasis-associated protein 3 transcription in breast cancer cells.

Metastasis-associated protein 3 (MTA3) is a cell type-specific subunit of the Mi-2/NuRD transcriptional corepressor complex. In breast cancer cells, MTA3 and the Mi-2/NuRD complex mediate repression of Snail, a transcription factor that promotes epithelial to mesenchymal transitions. Thus, MTA3 functions to maintain a differentiated, epithelial status in breast cancer. Interestingly, in mammary epithelial cells, MTA3 biosynthesis requires both functional estrogen receptor (ER) and estradiol. Here we have investigated the molecular basis for estrogen and ER-dependent expression of MTA3 in breast cancer cells. Molecular dissection of the MTA3 promoter using transient transfection assays identified a composite element required for high-level transcription consisting of an SP1 site in close proximity to a consensus estrogen response element half-site. Depletion of either SP1 or ER-alpha by RNA interference led to loss of MTA3 transcript in multiple breast cancer cell lines, indicating a requirement for both transcription factors in expression of endogenous MTA3. The MTA3 gene thus joins a growing list of loci regulated by both SP1 and ER.

Base Sequence↗
PubMed2004

Mi-2/NuRD: multiple complexes for many purposes.

The vertebrate Mi-2/NuRD complex is a multi-subunit protein complex containing both histone deacetylase and nucleosome-dependent ATPase subunits. Current models predict that this complex functions primarily in transcriptional repression. Surprisingly, every subunit of this complex presents heterogeneity at the protein and gene level. This raises the intriguing possibility of functional specialization resulting from incorporation of unique gene products into the complex. The MTA (metastasis-associated) proteins represent one class of alternative subunits of the human Mi-2/NuRD complex. The members of this family in human cells are differentially expressed depending on cell type and on physiologic parameters. We summarize evidence supporting the view that the alternative subunits of the complex that have arisen during vertebrate evolution endow unique functional properties.

Adenosine Triphosphatases↗
PubMed2004

Dynamic regulation of DNA methylation coupled transcriptional repression: BDNF regulation by MeCP2.

A recurrent theme in eukaryotic genome regulation stipulates that the properties of DNA are strongly influenced by the nucleoprotein complex into which it is assembled. Methylation of cytosine residues in vertebrate genomes has been implicated in influencing the assembly of locally repressive chromatin architecture. Current models suggest that covalent modification of DNA results in heritable, long-term transcriptional silencing. In October of 2003, two manuscripts were published that challenge important aspects of this model, suggesting that modulation of both DNA methylation itself, as well as the machinery implicated in its interpretation, are involved in acute gene regulation.

Animals↗
PubMed2004

Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes.

Chromatin remodeling complexes consist of multiple subunits, some of which are in intimate contact with DNA while others are not. The ability to effectively cross-link proteins to DNA with formaldehyde is impacted by the average distance between the two species. Productive cross-linking of proteins not in direct contact with DNA is greatly facilitated by the inclusion of an initial cross-linking reaction using bifunctional imidoester cross-linking reagents.

Animals↗
PubMed2004

Aberrant expression of the transcription factors snail and slug alters the response to genotoxic stress.

Snail and Slug are closely related transcriptional repressors involved in embryonic patterning during metazoan development. In human cancer, aberrant expression of Snail and/or Slug has been correlated with invasive growth potential, a property primarily attributed to their ability to directly repress transcription of genes whose products are involved in cell-cell adhesion, such as E-cadherin, occludin, and claudins. To investigate the molecular mechanisms of alterations in epithelial cell fate mediated by aberrant expression of Snail or Slug, we analyzed the consequences of exogenous expression of these factors in human cancer cells. Aberrant expression of either Snail or Slug led to changes in cell morphology, the loss of normal cell-cell contacts, and the acquisition of invasive growth properties. Snail or Slug expression also promoted resistance to programmed cell death elicited by DNA damage. Detailed molecular analysis revealed direct transcriptional repression of multiple factors with well-documented roles in programmed cell death. Depletion of endogenous Snail by RNA interference led to increased sensitivity to DNA damage accompanied by increased expression of the proapoptotic factors identified as targets of Snail. Thus, aberrant expression of Snail or Slug may promote tumorigenesis through increased resistance to programmed cell death.

Animals↗
PubMed2003

Mi-2 beta associates with BRG1 and RET finger protein at the distinct regions with transcriptional activating and repressing abilities.

Mi-2 beta is the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Here we show that the amino-terminal and carboxyl-terminal regions of Mi-2 beta have distinct transcriptional activities and bind to BRG1, a component of the SWI/SNF complex, and the RET finger protein (RFP), respectively. Analysis by luciferase reporter assay revealed that the amino-terminal region of Mi-2 beta has a strong transactivating ability, whereas its carboxyl-terminal region has transcriptional repressive activity. Co-localization and association of Mi-2, RFP, and histone deacetylase 1 suggested that these proteins cooperate in transcriptional repression. Furthermore, the functional importance of the association of Mi-2 beta and RFP was confirmed by using Rfp-/- fibroblasts. On the other hand, we demonstrated that Mi-2 and BRG1 were associated with each other and that the bromodomain region of BRG1 strongly suppressed transactivation by the amino-terminal region of Mi-2 beta. The findings that Mi-2 beta interacts with both transactivating and repressing proteins and directly associates with another chromatin remodeling protein, BRG1, provide new insight into the formation of multiprotein supercomplex involved in transcriptional regulation.

Adenosine Triphosphatases↗
PubMed2003

Chromatin compaction by human MeCP2. Assembly of novel secondary chromatin structures in the absence of DNA methylation.

MeCP2 is a transcriptional repressor that contains an N-terminal methylated DNA-binding domain, a central transcription regulation domain, and a C-terminal domain of unknown function. Whereas current models of MeCP2 function evoke localized recruitment of histone deacetylases to specific methylated regions of the genome, it is unclear whether MeCP2 requires DNA methylation to bind to chromatin or whether MeCP2 binding influences chromatin structure in the absence of other proteins. To address these issues, we have characterized the complexes formed between MeCP2 and biochemically defined nucleosomal arrays. At molar ratios near 1 MeCP2/nucleosome, unmethylated nucleosomal arrays formed both extensively condensed ellipsoidal particles and oligomeric suprastructures. Furthermore, MeCP2-mediated chromatin compaction occurred in the absence of monovalent or divalent cations, in distinct contrast to all other known chromatin-condensing proteins. Analysis of specific missense and nonsense MeCP2 mutants indicated that the ability to condense chromatin resides in region(s) of the protein other than the methylated DNA-binding domain. These data demonstrate that MeCP2 assembles novel secondary chromatin structures independent of DNA modification and suggest that the ability of MeCP2 to silence chromatin may be related in part to its effects on large-scale chromatin organization.

Chromatin↗
PubMed2003

Nucleosome sliding induced by the xMi-2 complex does not occur exclusively via a simple twist-diffusion mechanism.

ATP-dependent chromatin remodeling complexes can induce the translocation (sliding) of nucleosomes in cis along DNA, but the mechanism by which sliding occurs is not well defined. We previously presented evidence that sliding induced by the human SWI/SNF complex does not occur solely via a proposed "twist-diffusion" mechanism whereby the DNA rotates about its helical axis without displacement from the surface of the nucleosome (Aoyagi, S., and Hayes, J. J. (2002) Mol. Cell. Biol. 22, 7484-7490). Here we examined whether the Xenopus Mi-2 nucleosome remodeling complex induces nucleosome sliding via a twist-diffusion mechanism with nucleosomes assembled onto DNA templates containing branched DNA structures expected to sterically hinder rotation of the DNA helix on the nucleosome surface. We find that the branched DNA-containing nucleosomes undergo xMi-2-catalyzed sliding at a rate and extent identical to that of nucleosomes assembled on native DNA fragments. These results indicate that both the hSWI/SNF and xMi-2 complexes induce nucleosome sliding via a mechanism(s) other than simple twist diffusion and are consistent with models in which the DNA largely maintains its rotational orientation with respect to the histone surface.

Animals↗
PubMed2003

MTA3, a Mi-2/NuRD complex subunit, regulates an invasive growth pathway in breast cancer.

Estrogen receptor is a key regulator of proliferation and differentiation in mammary epithelia and represents a crucial prognostic indicator and therapeutic target in breast cancer. Mechanistically, estrogen receptor induces changes in gene expression through direct gene activation and also through the biological functions of target loci. Here, we identify the product of human MTA3 as an estrogen-dependent component of the Mi-2/NuRD transcriptional corepressor in breast epithelial cells and demonstrate that MTA3 constitutes a key component of an estrogen-dependent pathway regulating growth and differentiation. The absence of estrogen receptor or of MTA3 leads to aberrant expression of the transcriptional repressor Snail, a master regulator of epithelial to mesenchymal transitions. Aberrant Snail expression results in loss of expression of the cell adhesion molecule E-cadherin, an event associated with changes in epithelial architecture and invasive growth. These results establish a mechanistic link between estrogen receptor status and invasive growth of breast cancers.

Amino Acid Sequence↗
PubMed2003

The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties.

The methyl-CpG binding domain (MBD) family of proteins was defined based on sequence similarity in their DNA binding domains. In light of their high degree of conservation, it is of inherent interest to determine the genomic distribution of these proteins, and their associated co-repressor complexes. One potential determinant of specificity resides in differences in the intrinsic DNA binding properties of the various MBD proteins. In this report, we use a capillary electrophoretic mobility shift assay (CEMSA) with laser-induced fluorescence (LIF) and neutral capillaries to calculate MBD-DNA binding affinities. MBD proteins were assayed on pairs of methylated and unmethylated duplex oligos corresponding to the promoter regions of the BRCA1, MLH1, GSTP1 and p16(INK4a) genes, and binding affinities for each case were calculated by Scatchard analyses. With the exception of mammalian MBD3 and Xenopus MBD3 LF, all the MBD proteins showed higher affinity for methylated DNA (in the nanomolar range) than for unmethylated DNA (in the micromolar range). Significant differences between MBD proteins in the affinity for methylated DNA were observed, ranging within two orders of magnitude. By mutational analysis of MBD3 and using CEMSA, we demonstrate the critical role of specific residues within the MBD in conferring selectivity for methylated DNA. Interestingly, the binding affinity of specific MBD proteins for methylated DNA fragments from naturally occurring sequences are affected by local methyl-CpG spacing.

Amino Acid Sequence↗