Sriharsa Pradhan

Summary

Affiliation: New England Biolabs
Country: USA

Publications

  1. pmc The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity
    Sriharsa Pradhan
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    EMBO J 21:779-88. 2002
  2. ncbi request reprint UHRF1 plays a role in maintaining DNA methylation in mammalian cells
    Magnolia Bostick
    Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Science 317:1760-4. 2007
  3. doi request reprint CXXC domain of human DNMT1 is essential for enzymatic activity
    Mihika Pradhan
    New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938 2723, USA
    Biochemistry 47:10000-9. 2008
  4. pmc Automethylation of G9a and its implication in wider substrate specificity and HP1 binding
    Hang Gyeong Chin
    New England Biolabs, 240 County Road, Ipswich, MA 01938 2723, USA
    Nucleic Acids Res 35:7313-23. 2007
  5. pmc Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase
    Pierre Olivier Esteve
    New England Biolabs 240 Country Road, Ipswich, MA 01938 2723, USA
    Nucleic Acids Res 33:3211-23. 2005
  6. pmc UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells
    Jong Kyong Kim
    New England Biolabs, Ipswich, MA 01938 2723, USA
    Nucleic Acids Res 37:493-505. 2009
  7. pmc Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes
    Jolyon Terragni
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, United States
    Biochemistry 51:1009-19. 2012
  8. pmc Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes
    Shannon Morey Kinney
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, USA
    J Biol Chem 286:24685-93. 2011
  9. ncbi request reprint Methyllysine reader plant homeodomain (PHD) finger protein 20-like 1 (PHF20L1) antagonizes DNA (cytosine-5) methyltransferase 1 (DNMT1) proteasomal degradation
    Pierre Olivier Esteve
    From New England Biolabs Inc, Ipswich, Massachusetts 01938 and
    J Biol Chem 289:8277-87. 2014
  10. pmc A method for selectively enriching microbial DNA from contaminating vertebrate host DNA
    George R Feehery
    New England Biolabs Inc, Ipswich, Massachusetts, United States of America
    PLoS ONE 8:e76096. 2013

Collaborators

Detail Information

Publications40

  1. pmc The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity
    Sriharsa Pradhan
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    EMBO J 21:779-88. 2002
    ..Weak interaction of Rb pockets A and B with Dnmt1 was also observed. Overexpression of Rb leads to hypomethylation of the cellular DNA, suggesting that Rb may modulate Dnmt1 activity during DNA replication in the cell cycle...
  2. ncbi request reprint UHRF1 plays a role in maintaining DNA methylation in mammalian cells
    Magnolia Bostick
    Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Science 317:1760-4. 2007
    ..These data suggest that UHRF1 may help recruit DNMT1 to hemimethylated DNA to facilitate faithful maintenance of DNA methylation...
  3. doi request reprint CXXC domain of human DNMT1 is essential for enzymatic activity
    Mihika Pradhan
    New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938 2723, USA
    Biochemistry 47:10000-9. 2008
    ..Thus, the CXXC domain encompassing the amino terminus region of DNMT1 cooperates with the catalytic domain for DNA methyltransferase activity...
  4. pmc Automethylation of G9a and its implication in wider substrate specificity and HP1 binding
    Hang Gyeong Chin
    New England Biolabs, 240 County Road, Ipswich, MA 01938 2723, USA
    Nucleic Acids Res 35:7313-23. 2007
    ..Thus, apart from transcriptional repression and regulatory roles of lysine methylation, the non-histone protein methylation may create binding sites for cellular protein-protein interactions...
  5. pmc Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase
    Pierre Olivier Esteve
    New England Biolabs 240 Country Road, Ipswich, MA 01938 2723, USA
    Nucleic Acids Res 33:3211-23. 2005
    ..Thus, distinct domains modulate nuclear targeting and catalytic functions of G9a...
  6. pmc UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells
    Jong Kyong Kim
    New England Biolabs, Ipswich, MA 01938 2723, USA
    Nucleic Acids Res 37:493-505. 2009
    ..Thus, our results suggest that UHRF1 may serve as a focal point of transcriptional regulation mediated by G9a and other chromatin modification enzymes...
  7. pmc Biochemical characterization of recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine in unique genomes
    Jolyon Terragni
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, United States
    Biochemistry 51:1009-19. 2012
    ..A comparison between cancer and healthy tissue genomes suggested a lower percentage of 5-hmC in cancer, which may reflect the global hypomethylation of 5-mC observed during oncogenesis...
  8. pmc Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes
    Shannon Morey Kinney
    New England Biolabs, Inc, Ipswich, Massachusetts 01938, USA
    J Biol Chem 286:24685-93. 2011
    ..Finally, using a quantitative PCR approach, we established that a portion of VANGL1 and EGFR gene body methylation in human tissue DNA samples is indeed hydroxymethylation...
  9. ncbi request reprint Methyllysine reader plant homeodomain (PHD) finger protein 20-like 1 (PHF20L1) antagonizes DNA (cytosine-5) methyltransferase 1 (DNMT1) proteasomal degradation
    Pierre Olivier Esteve
    From New England Biolabs Inc, Ipswich, Massachusetts 01938 and
    J Biol Chem 289:8277-87. 2014
    ..These results demonstrate that the MBT domain of PHF20L1 reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation. ..
  10. pmc A method for selectively enriching microbial DNA from contaminating vertebrate host DNA
    George R Feehery
    New England Biolabs Inc, Ipswich, Massachusetts, United States of America
    PLoS ONE 8:e76096. 2013
    ..Enrichment using the MBD-Fc method holds promise for targeted microbiome sequence analysis across a broad range of sample types. ..
  11. pmc 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
    Hume Stroud
    Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, CA 90095, USA
    Genome Biol 12:R54. 2011
    ..There is growing evidence that TET proteins, which convert 5-methylcytosine (5mC) to 5hmC, play important biological roles. To further understand the function of 5hmC, an analysis of the genome-wide localization of this mark is required...
  12. pmc Epigenetic mechanisms in mammals
    J K Kim
    New England Biolabs, Ipswich, MA 01938, USA
    Cell Mol Life Sci 66:596-612. 2009
    ..Thus, complex mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a well-choreographed set of events that take place during mammalian development...
  13. pmc PKC isoforms interact with and phosphorylate DNMT1
    Geneviève Lavoie
    Institut National de la Recherche Scientifique, INRS Institut Armand Frappier, Laval, QC, Canada
    BMC Biol 9:31. 2011
    ..The PKC family consists of at least 12 isoforms that possess distinct differences in structure, substrate requirement, expression and localization...
  14. pmc SET7/9 mediated methylation of non-histone proteins in mammalian cells
    Sriharsa Pradhan
    New England Biolabs Inc, Ipswich, MA, USA
    Epigenetics 4:383-7. 2009
    ..Thus a fine-tuning and balance between cellular SET7/9 and LSD interaction with DNMT1 may be means for epigenetic gene regulation...
  15. ncbi request reprint Mammalian DNA (cytosine-5) methyltransferases and their expression
    Sriharsa Pradhan
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Clin Immunol 109:6-16. 2003
    ..In mammals, DNA methylation participates in gene expression, protection of the genome against selfish DNA, parental imprinting, mammalian X chromosome inactivation, developmental regulation, T cell development, and various diseases...
  16. ncbi request reprint Allosteric activator domain of maintenance human DNA (cytosine-5) methyltransferase and its role in methylation spreading
    Sriharsa Pradhan
    New England Biolabs, 32 Tozer Road, Beverly, Massachusetts 01915, USA
    Biochemistry 42:5321-32. 2003
    ..Retinoblastoma gene product (Rb), a negative regulator of DNA methylation, bound to the allosteric site of hDNMT1 and inhibited methylation, suggesting Rb may regulate methylation spreading...
  17. pmc Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication
    Pierre Olivier Esteve
    New England Biolabs, Ipswich, Massachusetts 01938, USA
    Genes Dev 20:3089-103. 2006
    ..Thus, direct cooperation between DNMT1 and G9a provides a mechanism of coordinated DNA and H3K9 methylation during cell division...
  18. ncbi request reprint Catalytic properties and kinetic mechanism of human recombinant Lys-9 histone H3 methyltransferase SUV39H1: participation of the chromodomain in enzymatic catalysis
    Hang Gyeong Chin
    New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA
    Biochemistry 45:3272-84. 2006
    ..Thus, SUV39H1 utilizes both the chromodomain and the SET domain for catalysis...
  19. ncbi request reprint Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase
    Debasis Patnaik
    New England Biolabs, Beverly, MA 01915, USA
    J Biol Chem 279:53248-58. 2004
    ....
  20. ncbi request reprint Sequence specificity and role of proximal amino acids of the histone H3 tail on catalysis of murine G9A lysine 9 histone H3 methyltransferase
    Hang Gyeong Chin
    New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938 2723, USA
    Biochemistry 44:12998-3006. 2005
    ..Thus, Ser-10/Thr-11 phosphorylation impairs Lys-9 methylation. These data suggest that the sequence context of the modified residue affects G9a activity and the modification in the proximal amino acids influences methylation...
  21. pmc Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells
    Pierre Olivier Esteve
    New England Biolabs Incorporated, 240 County Road, Ipswich, MA 01938, USA
    Proc Natl Acad Sci U S A 106:5076-81. 2009
    ..Overexpression of SET7 leads to decreased DNMT1 levels, and siRNA-mediated knockdown of SET7 stabilizes DNMT1. These results demonstrate that signaling through SET7 represents a means of DNMT1 enzyme turnover...
  22. ncbi request reprint Molecular mechanisms of transactivation and doxorubicin-mediated repression of survivin gene in cancer cells
    Pierre Olivier Esteve
    New England Biolabs, Ipswich, Massachusetts 01938 2723, USA
    J Biol Chem 282:2615-25. 2007
    ..These data suggest that the Sp1 transcription factor acts as a platform for recruitment of transcriptional repressors...
  23. pmc The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA
    Sophie Laget
    New England Biolabs, Ipswich, Massachusetts, United States of America
    PLoS ONE 5:e11982. 2010
    ..It is unknown whether MBD5 or MBD6 also bind methylated DNA; this question has interest for basic research, but also practical consequences for human health, as MBD5 deletions are the likely cause of certain cases of mental retardation...
  24. pmc High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells
    Zhiyi Sun
    New England Biolabs Inc, 240 County Road, Ipswich, MA 01938, USA
    Cell Rep 3:567-76. 2013
    ..We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus...
  25. pmc Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases
    Gun Do Kim
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    EMBO J 21:4183-95. 2002
    ..In vivo co-expression of hDNMT1 and hDNMT3a or hDNMT3b leads to methylation spreading in the genome, suggesting co-operation between de novo and maintenance enzymes during DNA methylation...
  26. pmc A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability
    Pierre Olivier Esteve
    New England Biolabs, Ipswich, Massachusetts, USA
    Nat Struct Mol Biol 18:42-8. 2011
    ..In mammalian cells, phosphorylated DNMT1 is more stable than methylated DNMT1. These results reveal cross-talk on DNMT1, through modifications mediated by AKT1 and SET7, that affects cellular DNMT1 levels...
  27. pmc A unique family of Mrr-like modification-dependent restriction endonucleases
    Yu Zheng
    New England Biolabs, Inc, 240 County Road, Ipswich, MA, 01938, USA
    Nucleic Acids Res 38:5527-34. 2010
    ..The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms...
  28. pmc Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine
    Hua Wang
    New England Biolabs, Inc, 240 County Road, Ipswich, MA 01938, USA
    Nucleic Acids Res 39:9294-305. 2011
    ..Our study offers unique tools for determining more accurate hydroxymethylomes in mammalian cells...
  29. pmc Human maintenance DNA (cytosine-5)-methyltransferase and p53 modulate expression of p53-repressed promoters
    Pierre Olivier Esteve
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA
    Proc Natl Acad Sci U S A 102:1000-5. 2005
    ..Normal human fibroblasts also exhibited similar DNMT1- and p53-mediated methylation of the survivin promoter, suggesting cooperation between p53 and DNMT1 in gene silencing...
  30. pmc Protein trans-splicing in transgenic plant chloroplast: reconstruction of herbicide resistance from split genes
    Hang Gyeong Chin
    New England Biolabs, 32 Tozer Road, Beverly, MA 01915 5054, USA
    Proc Natl Acad Sci U S A 100:4510-5. 2003
    ..Furthermore, these transgenic plants displayed improved resistance to the herbicide N-(phosphonomethyl)glycine (glyphosate) when compared with wild-type N. tabacum...
  31. doi request reprint Ten eleven translocation enzymes and 5-hydroxymethylation in mammalian development and cancer
    Shannon R Morey Kinney
    New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
    Adv Exp Med Biol 754:57-79. 2013
    ..Much has been revealed about this interesting DNA modification in recent years, but more research is needed for understanding the role of TET proteins and 5hmC in gene regulation and disease...
  32. ncbi request reprint Protein splicing elements and plants: from transgene containment to protein purification
    Thomas C Evans
    New England Biolabs, Inc, Beverly, Massachusetts 01915, USA
    Annu Rev Plant Biol 56:375-92. 2005
    ..Finally, relevant techniques that may be used in plants in the future are discussed...
  33. ncbi request reprint DNA damage-induced down-regulation of human Cdc25C and Cdc2 is mediated by cooperation between p53 and maintenance DNA (cytosine-5) methyltransferase 1
    Gerald Le Gac
    New England Biolabs, Ipswich, Massachusetts 01938, USA
    J Biol Chem 281:24161-70. 2006
    ..Thus, the general mechanism of p53-mediated gene repression may involve recruitment of other repressive factors...
  34. doi request reprint Evaluation of UDP-GlcN derivatives for selective labeling of 5-(hydroxymethyl)cytosine
    Nan Dai
    New England Biolabs, Inc 240 County Road, Ipswich, MA 01938 USA
    Chembiochem 14:2144-52. 2013
    ..Alternative substrates for β-GT and correlated glycosyltransferases might prove useful for the study of the function and dynamics of 5-hmC and other modified nucleotides, as well as for multiplex analysis. ..
  35. doi request reprint Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells
    Shannon R Morey Kinney
    New England Biolabs, Ipswich, Massachusetts, USA
    Prog Mol Biol Transl Sci 101:311-33. 2011
    ..These regulatory processes can be disrupted in disease or by environmental factors, resulting in altered DNMT expression and aberrant DNA methylation patterns...
  36. pmc Functional cooperation between HP1 and DNMT1 mediates gene silencing
    Andrea Smallwood
    Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
    Genes Dev 21:1169-78. 2007
    ..Additionally, silencing of the Survivin gene coincides with recruitment of G9a and HP1 in DNMT1 wild-type but not null cells. We conclude that direct interactions between HP1 and DNMT1 mediate silencing of euchromatic genes...
  37. pmc Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3
    Anders M Lindroth
    Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095 1606, USA
    EMBO J 23:4286-96. 2004
    ..Our results suggest a model in which H3K9 methylation by KYP, and H3K27 methylation by an unknown enzyme provide a combinatorial histone code for the recruitment of CMT3 to silent loci...
  38. ncbi request reprint Inhibition of poly(ADP-ribosyl)ation induces DNA hypermethylation: a possible molecular mechanism
    Giuseppe Zardo
    Department of Cellular Biotechnologies and Haematology, University of Rome La Sapienza, Rome, Italy
    FASEB J 16:1319-21. 2002
    ..Increase of DNMT1 results in a premature PCNA-DNMT1 complex formation, which facilitates robust maintenance, as well as de novo DNA methylation processes during the G1/S border, which leads to abnormal hypermethylation...
  39. pmc Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    Shawn J Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
    Nature 452:215-9. 2008
    ....
  40. pmc Mediator links epigenetic silencing of neuronal gene expression with x-linked mental retardation
    Ning Ding
    Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245, USA
    Mol Cell 31:347-59. 2008
    ..These findings implicate Mediator in epigenetic restriction of neuronal gene expression to the nervous system and suggest a pathologic basis for MED12-associated XLMR involving impaired REST-dependent neuronal gene regulation...