6 results on '"D A Underhill"'
Search Results
2. Mechanisms governing the accessibility of DNA damage proteins to constitutive heterochromatin
- Author
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Anastasia Roemer, Lanah Mohammed, Hilmar Strickfaden, D. Alan Underhill, and Michael J. Hendzel
- Subjects
constitutive heterochromatin ,accessibility ,phase separation ,diffusion ,cell nucleus ,live cell imaging microscopy ,Genetics ,QH426-470 - Abstract
Chromatin is thought to regulate the accessibility of the underlying DNA sequence to machinery that transcribes and repairs the DNA. Heterochromatin is chromatin that maintains a sufficiently high density of DNA packing to be visible by light microscopy throughout the cell cycle and is thought to be most restrictive to transcription. Several studies have suggested that larger proteins and protein complexes are attenuated in their access to heterochromatin. In addition, heterochromatin domains may be associated with phase separated liquid condensates adding further complexity to the regulation of protein concentration within chromocenters. This provides a solvent environment distinct from the nucleoplasm, and proteins that are not size restricted in accessing this liquid environment may partition between the nucleoplasm and heterochromatin based on relative solubility. In this study, we assessed the accessibility of constitutive heterochromatin in mouse cells, which is organized into large and easily identifiable chromocenters, to fluorescently tagged DNA damage response proteins. We find that proteins larger than the expected 10 nm size limit can access the interior of heterochromatin. We find that the sensor proteins Ku70 and PARP1 enrich in mouse chromocenters. At the same time, MRE11 shows variability within an asynchronous population that ranges from depleted to enriched but is primarily homogeneously distribution between chromocenters and the nucleoplasm. While larger downstream proteins such as ATM, BRCA1, and 53BP1 are commonly depleted in chromocenters, they show a wide range of concentrations, with none being depleted beyond approximately 75%. Contradicting exclusively size-dependent accessibility, many smaller proteins, including EGFP, are also depleted in chromocenters. Our results are consistent with minimal size-dependent selectivity but a distinct solvent environment explaining reduced concentrations of diffusing nucleoplasmic proteins within the volume of the chromocenter.
- Published
- 2022
- Full Text
- View/download PDF
3. Comparative analyses of SUV420H1 isoforms and SUV420H2 reveal differences in their cellular localization and effects on myogenic differentiation.
- Author
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Leanna W K Tsang, Ninghe Hu, and D Alan Underhill
- Subjects
Medicine ,Science - Abstract
BACKGROUND:Methylation of histone H4 on lysine 20 plays critical roles in chromatin structure and function via mono- (H4K20me1), di- (H4K20me2), and trimethyl (H4K20me3) derivatives. In previous analyses of histone methylation dynamics in mid-gestation mouse embryos, we documented marked changes in H4K20 methylation during cell differentiation. These changes were particularly robust during myogenesis, both in vivo and in cell culture, where we observed a transition from H4K20me1 to H4K20me3. To assess the significance of this change, we used a gain-of-function strategy involving the lysine methyltransferases SUV420H1 and SUV420H2, which catalyze H4K20me2 and H4K20me3. At the same time, we characterized a second isoform of SUV420H1 (designated SUV420H1_i2) and compared the activity of all three SUV420H proteins with regard to localization and H4K20 methylation. PRINCIPAL FINDINGS:Immunofluorescence revealed that exogenous SUV420H1_i2 was distributed throughout the cell, while a substantial portion of SUV420H1_i1 and SUV420H2 displayed the expected association with constitutive heterochromatin. Moreover, SUV420H1_i2 distribution was unaffected by co-expression of heterochromatin protein-1α, which increased the targeting of SUV420H1_i1 and SUV420H2 to regions of pericentromeric heterochromatin. Consistent with their distributions, SUV420H1_i2 caused an increase in H4K20me3 levels throughout the nucleus, whereas SUV420H1_i1 and SUV420H2 facilitated an increase in pericentric H4K20me3. Striking differences continued when the SUV420H proteins were tested in the C2C12 myogenic model system. Specifically, although SUV420H1_i2 induced precocious appearance of the differentiation marker Myogenin in the presence of mitogens, only SUV420H2 maintained a Myogenin-enriched population over the course of differentiation. Paradoxically, SUV420H1_i1 could not be expressed in C2C12 cells, which suggests it is under post-transcriptional or post-translational control. CONCLUSIONS:These data indicate that SUV420H proteins differ substantially in their localization and activity. Importantly, SUV420H2 can induce a transition from H4K20me1 to H4K20me3 in regions of constitutive heterochromatin that is sufficient to enhance myogenic differentiation, suggesting it can act an as epigenetic 'switch' in this process.
- Published
- 2010
- Full Text
- View/download PDF
4. Helix 2 of the paired domain plays a key role in the regulation of DNA-binding by the Pax-3 homeodomain
- Author
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D A Underhill, Philippe Gros, and A Fortin
- Subjects
Recombinant Fusion Proteins ,Molecular Sequence Data ,Context (language use) ,Biology ,Transfection ,DNA-binding protein ,Protein Structure, Secondary ,Genetics ,Animals ,Paired Box Transcription Factors ,Amino Acid Sequence ,Binding site ,Transcription factor ,Peptide sequence ,PAX3 Transcription Factor ,Sequence Deletion ,Homeodomain Proteins ,COS cells ,Binding Sites ,Antibodies, Monoclonal ,DNA ,Molecular biology ,Fusion protein ,Protein Structure, Tertiary ,DNA-Binding Proteins ,COS Cells ,Mutagenesis, Site-Directed ,Homeobox ,Electrophoresis, Polyacrylamide Gel ,DNA Probes ,Research Article ,Transcription Factors - Abstract
Pax3 contains two structurally independent DNA-binding domains, a paired domain (PD) and a homeodomain (HD). Biochemical and mutagenesis studies have shown that both domains are functionally interdependent. In particular, it has been shown that the PD can regulate the DNA-binding specificity and dimerization potential of the HD. To delineate Pax3 protein segments that are involved in the regulation of HD DNA-binding, a series of chimeric proteins were created in which the HD and linker region were gradually replaced with corresponding sequences from a heterologous HD protein, Phox. Characterization of chimeric proteins by electrophoretic mobility shift analysis (EMSA) suggests that a portion of the linker region contributes to the functional interaction between the PD and HD. In addition, stepwise removal of sequences from the Pax3 PD was used to define regions within this domain that are involved in the regulation of HD DNA-binding. EMSA of these proteins in the context of the chimeric Pax3/Phox backbone provided two key findings: (i) the C-terminal subdomain of the PD does not play a major role in the regulation of HD DNA-binding and (ii) the N-terminal subdomain and, in particular, the second alpha-helix are essential for modulation of HD DNA-binding. Significantly, deletion of helix 2 was found to be sufficient to uncouple regulation of HD DNA-binding by the PD.
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- 1998
5. Analysis of the mouse Splotch-delayed mutation indicates that the Pax-3 paired domain can influence homeodomain DNA-binding activity
- Author
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Kyle Vogan, Philippe Gros, and D A Underhill
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Reading Frames ,Mutant ,Blotting, Western ,Molecular Sequence Data ,Glycine ,Biology ,medicine.disease_cause ,Arginine ,Kidney ,Transfection ,DNA-binding protein ,Polymerase Chain Reaction ,Mice ,Chlorocebus aethiops ,medicine ,Animals ,Paired Box Transcription Factors ,Point Mutation ,Amino Acid Sequence ,Neural Tube Defects ,Gene ,Peptide sequence ,Transcription factor ,PAX3 Transcription Factor ,DNA Primers ,Homeodomain Proteins ,Mutation ,Multidisciplinary ,Base Sequence ,Point mutation ,Immune Sera ,DNA ,Molecular biology ,Mice, Mutant Strains ,Recombinant Proteins ,body regions ,DNA-Binding Proteins ,Kinetics ,embryonic structures ,Homeobox ,Research Article ,Transcription Factors - Abstract
The murine Pax-3 protein contains two DNA-binding domains, a paired domain and a homeodomain, and alterations in the Pax-3 gene are responsible for the neural tube defects observed in the Splotch (Sp) mouse mutant. Of five Sp alleles, Splotch-delayed (Spd) is the only one that encodes a full-length Pax-3 protein, containing a single glycine-to-arginine substitution within the paired domain. To better understand the consequence of this mutation on Pax-3 function, we have analyzed the DNA-binding properties of wild-type and Spd Pax-3, using oligonucleotides that bind primarily to the paired domain (e5) or exclusively to the homeodomain (P2). Wild-type Pax-3 was found to bind e5 in a specific manner. In contrast, the Spd mutation reduced binding of Pax-3 to e5 17-fold, revealing a defect in DNA binding by the paired domain. Surprisingly, the Spd mutation also drastically reduced the homeodomain-specific binding to P2 by 21-fold when compared with the wild-type protein. Interestingly, a deletion which removes the Spd mutation was found to restore P2-binding activity, suggesting that within the full-length Pax-3 protein, the paired domain and homeodomain may interact. We conclude, therefore, that the Spd mutation is phenotyically expressed in vitro by a defect in the DNA-binding properties of Pax-3. Furthermore, it is apparent that the paired domain and homeodomain of Pax-3 do not function as independent domains, since a mutation in the former impairs the DNA-binding activity of the latter.
- Published
- 1995
6. CERN Computer Newsletter
- Author
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D. J. Underhill and E. McIntosh
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- 1988
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