Experts and Doctors on chromatin in Davis, California, United States


Locale: Davis, California, United States
Topic: chromatin

Top Publications

  1. LaSalle J, Powell W, Yasui D. Epigenetic layers and players underlying neurodevelopment. Trends Neurosci. 2013;36:460-70 pubmed publisher
  2. LaSalle J, Hogart A, Thatcher K. Rett syndrome: a Rosetta stone for understanding the molecular pathogenesis of autism. Int Rev Neurobiol. 2005;71:131-65 pubmed
  3. Jimenez Ruiz A, Zhang Q, Shen C. In vivo binding of trimethylpsoralen detects DNA structural alterations associated with transcribing regions in the human beta-globin cluster. J Biol Chem. 1995;270:28978-81 pubmed
    ..Alternatively, it could result from localized DNA supercoiling, but not from widespread torsional stress across the entire beta-like globin locus as hypothesized previously. ..
  4. Samaco R, Hogart A, LaSalle J. Epigenetic overlap in autism-spectrum neurodevelopmental disorders: MECP2 deficiency causes reduced expression of UBE3A and GABRB3. Hum Mol Genet. 2005;14:483-92 pubmed
    ..These results suggest an overlapping pathway of gene dysregulation within 15q11-q13 in Rett, Angelman and autism and implicate MeCP2 in the regulation of UBE3A and GABRB3 expressions in the postnatal mammalian brain. ..
  5. Lui D, Peoples Holst T, Mell J, Wu H, Dean E, Burgess S. Analysis of close stable homolog juxtaposition during meiosis in mutants of Saccharomyces cerevisiae. Genetics. 2006;173:1207-22 pubmed
    ..Taken together, these results support the notion that meiotic recombination plays a major role in the high levels of homolog interaction observed during budding yeast meiosis. ..
  6. Gompers A, Su Feher L, Ellegood J, Copping N, Riyadh M, Stradleigh T, et al. Germline Chd8 haploinsufficiency alters brain development in mouse. Nat Neurosci. 2017;20:1062-1073 pubmed publisher
    ..This integrative analysis offers an initial picture of the consequences of Chd8 haploinsufficiency for brain development. ..
  7. Langley C, Stevens K, Cardeno C, Lee Y, Schrider D, Pool J, et al. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 2012;192:533-98 pubmed publisher
    ..Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species. ..
  8. Johnson L, Du J, Hale C, Bischof S, Feng S, Chodavarapu R, et al. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014;507:124-128 pubmed publisher
  9. Campbell M, Chang P, Huerta S, Izumiya C, Davis R, Tepper C, et al. Protein arginine methyltransferase 1-directed methylation of Kaposi sarcoma-associated herpesvirus latency-associated nuclear antigen. J Biol Chem. 2012;287:5806-18 pubmed publisher
    ..These results suggest that residue 20 is important for modulation of a subset of LANA functions and properties of this residue, including the hydrophobic character induced by arginine methylation, may contribute to the observed effects. ..

More Information


  1. Sinitsyna N, Reznikova T, Qin Q, Song H, Phillips M, Rice R. Arsenite suppression of involucrin transcription through AP1 promoter sites in cultured human keratinocytes. Toxicol Appl Pharmacol. 2010;243:275-82 pubmed publisher
    ..These findings help trace a mechanism by which transcriptional effects of arsenite become manifest and help rationalize the unique action of arsenite, compared to the other agents, to preserve proliferative ability. ..
  2. Leung K, Vallero R, DuBose A, Resnick J, LaSalle J. Imprinting regulates mammalian snoRNA-encoding chromatin decondensation and neuronal nucleolar size. Hum Mol Genet. 2009;18:4227-38 pubmed publisher
    ..These results are relevant to understanding the molecular pathogenesis of multiple human neurodevelopmental disorders, including PWS and some causes of autism. ..
  3. Galvez A, Huang L, Magbanua M, Dawson K, Rodriguez R. Differential expression of thrombospondin (THBS1) in tumorigenic and nontumorigenic prostate epithelial cells in response to a chromatin-binding soy peptide. Nutr Cancer. 2011;63:623-36 pubmed publisher
    ..Histone hypoacetylation and DNA hypermethylation in the 5' region of THBS1 may explain the inability of lunasin to upregulate this gene in RWPE-2 cells. ..
  4. Gordon C, Hartono S, Chedin F. Inactive DNMT3B splice variants modulate de novo DNA methylation. PLoS ONE. 2013;8:e69486 pubmed publisher
    ..This may account for some of the changes in DNA methylation patterns observed during development and disease. ..
  5. Powell W, Coulson R, Gonzales M, Crary F, Wong S, Adams S, et al. R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Proc Natl Acad Sci U S A. 2013;110:13938-43 pubmed publisher
    ..Our study holds promise for targeted therapies to the Snord116 locus for both AS and PWS. ..
  6. Yasui D, Scoles H, Horike S, Meguro Horike M, Dunaway K, Schroeder D, et al. 15q11.2-13.3 chromatin analysis reveals epigenetic regulation of CHRNA7 with deficiencies in Rett and autism brain. Hum Mol Genet. 2011;20:4311-23 pubmed publisher
    ..Thus, loss of long-range chromatin interactions within 15q11.2-13.3 may contribute to multiple human neurodevelopmental disorders. ..
  7. Checchi P, Engebrecht J. Caenorhabditis elegans histone methyltransferase MET-2 shields the male X chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation. PLoS Genet. 2011;7:e1002267 pubmed publisher
  8. Schwartz E, Wright W, Ehmsen K, Evans J, Stahlberg H, Heyer W. Mus81-Mms4 functions as a single heterodimer to cleave nicked intermediates in recombinational DNA repair. Mol Cell Biol. 2012;32:3065-80 pubmed publisher
    ..We infer that Mus81-dependent crossing over occurs in a noncanonical manner that does not involve the coordinated cleavage of classic Holliday junctions. ..
  9. Schroeder D, Blair J, Lott P, Yu H, Hong D, Crary F, et al. The human placenta methylome. Proc Natl Acad Sci U S A. 2013;110:6037-42 pubmed publisher
    ..These results suggest that PMDs are a developmentally dynamic feature of the methylome that are relevant for understanding both normal development and cancer and may be of use as epigenetic biomarkers...
  10. Blahnik K, Dou L, Echipare L, Iyengar S, O Geen H, Sanchez E, et al. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS ONE. 2011;6:e17121 pubmed publisher
    ..We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription. ..
  11. Walley J, Rowe H, Xiao Y, Chehab E, Kliebenstein D, Wagner D, et al. The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathog. 2008;4:e1000237 pubmed publisher
    ..These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks. ..
  12. Xu Y, Zhang J, Chen X. The activity of p53 is differentially regulated by Brm- and Brg1-containing SWI/SNF chromatin remodeling complexes. J Biol Chem. 2007;282:37429-35 pubmed
    ..Thus, we hypothesize that the potential tumor suppressor function for Brg1 is mediated in part through the p53 pathway. ..
  13. Nazarov I, Smirnova A, Krutilina R, Svetlova M, Solovjeva L, Nikiforov A, et al. Dephosphorylation of histone gamma-H2AX during repair of DNA double-strand breaks in mammalian cells and its inhibition by calyculin A. Radiat Res. 2003;160:309-17 pubmed
    ..Our results confirm the tight association between DSBs and gamma-H2AX and the coupling of its in situ dephosphorylation to DSB repair. ..
  14. Alexeev A, Mazin A, Kowalczykowski S. Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat Struct Biol. 2003;10:182-6 pubmed
    ..On the basis of these data, we propose that Rad54 facilitates chromatin remodeling and, perhaps more generally, protein clearing at the homology search step of genetic recombination. ..
  15. Siino J, Nazarov I, Svetlova M, Solovjeva L, Adamson R, Zalenskaya I, et al. Photobleaching of GFP-labeled H2AX in chromatin: H2AX has low diffusional mobility in the nucleus. Biochem Biophys Res Commun. 2002;297:1318-23 pubmed
    ..This suggests that gamma-H2AX formation in chromatin is unlikely to occur by diffusion of free histone and gamma-H2AX dephosphorylation may involve the mammalian protein phosphatase 1alpha. ..
  16. Matthies H, Messina L, Namba R, Greer K, Walker M, Hawley R. Mutations in the alpha-tubulin 67C gene specifically impair achiasmate segregation in Drosophila melanogaster. J Cell Biol. 1999;147:1137-44 pubmed
    ..These results suggest that the accurate segregation of achiasmate chromosomes requires the proper balancing of forces acting on the chromosomes during prometaphase. ..
  17. Leonhardt E, Henderson D, Rinehart J, Boyd J. Characterization of the mus308 gene in Drosophila melanogaster. Genetics. 1993;133:87-96 pubmed
    ..In addition, observations of elevated embryo mortality are potentially explained by an aberrant distribution of nuclear material in early embryos which is similar to that seen in the mutant giant nuclei. ..
  18. Yang Y, McBride K, Hensley S, Lu Y, Chedin F, Bedford M. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell. 2014;53:484-97 pubmed publisher
    ..By reducing negative supercoiling and resolving R loops, TOP3B promotes transcription, protects against DNA damage, and reduces the frequency of chromosomal translocations...
  19. O Geen H, Ren C, Nicolet C, Perez A, Halmai J, Le V, et al. dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Res. 2017;45:9901-9916 pubmed publisher
    ..The easily programmable dCas9 toolkit allowed precise control of epigenetic information and dissection of the relationship between the epigenome and gene regulation...
  20. Iyengar S, Farnham P. KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem. 2011;286:26267-76 pubmed publisher
  21. Wienholz B, Kareta M, Moarefi A, Gordon C, Ginno P, Chedin F. DNMT3L modulates significant and distinct flanking sequence preference for DNA methylation by DNMT3A and DNMT3B in vivo. PLoS Genet. 2010;6:e1001106 pubmed publisher
    ..This study offers insights into the manner by which DNA methylation patterns are deposited and reveals a new level of interplay between members of the de novo DNMT family. ..
  22. Levine M, Eckert M, Begun D. Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia. Mol Biol Evol. 2011;28:249-56 pubmed publisher
    ..melanogaster populations. ..
  23. Cotterman R, Jin V, Krig S, Lemen J, Wey A, Farnham P, et al. N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res. 2008;68:9654-62 pubmed publisher
    ..These findings support a new dual model for Myc chromatin function with important implications for the role of Myc in cancer and stem cell biology, including that of induced pluripotent stem cells. ..
  24. Waddell D, Baehr L, van den Brandt J, Johnsen S, Reichardt H, Furlow J, et al. The glucocorticoid receptor and FOXO1 synergistically activate the skeletal muscle atrophy-associated MuRF1 gene. Am J Physiol Endocrinol Metab. 2008;295:E785-97 pubmed publisher
    ..These findings present new insights into the role of the GR and FOXO family of transcription factors in the transcriptional regulation of the MuRF1 gene, a direct target of the GR in skeletal muscle. ..