Yang Shi

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Endoplasmic reticulum stress induction of the Grp78/BiP promoter: activating mechanisms mediated by YY1 and its interactive chromatin modifiers
    Peter Baumeister
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Ave, Room 5308, MC 9176, Los Angeles, CA 90089 9176, USA
    Mol Cell Biol 25:4529-40. 2005
  2. ncbi request reprint Targeted ablation of Par-4 reveals a cell type-specific susceptibility to apoptosis-inducing agents
    El Bachir Affar
    Department of Pathology, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA 02115, USA
    Cancer Res 66:3456-62. 2006
  3. ncbi request reprint Dynamic regulation of histone lysine methylation by demethylases
    Yang Shi
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Mol Cell 25:1-14. 2007
  4. ncbi request reprint Mammalian RNAi for the masses
    Yang Shi
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Trends Genet 19:9-12. 2003
  5. ncbi request reprint Coordinated histone modifications mediated by a CtBP co-repressor complex
    Yujiang Shi
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 422:735-8. 2003
  6. ncbi request reprint CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation
    Peter Mulligan
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Mol Cell 32:718-26. 2008
  7. ncbi request reprint An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription
    Amy K Walker
    Section of Developmental and Stem Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 279:15339-47. 2004
  8. pmc Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development
    Hank H Qi
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 466:503-7. 2010
  9. ncbi request reprint The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases
    Shigeki Iwase
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Cell 128:1077-88. 2007
  10. pmc SPR-5 is a histone H3K4 demethylase with a role in meiotic double-strand break repair
    Amanda C Nottke
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:12805-10. 2011

Detail Information

Publications89

  1. pmc Endoplasmic reticulum stress induction of the Grp78/BiP promoter: activating mechanisms mediated by YY1 and its interactive chromatin modifiers
    Peter Baumeister
    Department of Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, 1441 Eastlake Ave, Room 5308, MC 9176, Los Angeles, CA 90089 9176, USA
    Mol Cell Biol 25:4529-40. 2005
    ..A model for the ER stress-mediated transcription factor binding and chromatin modifications at the Grp78 promoter leading to its activation is proposed...
  2. ncbi request reprint Targeted ablation of Par-4 reveals a cell type-specific susceptibility to apoptosis-inducing agents
    El Bachir Affar
    Department of Pathology, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA 02115, USA
    Cancer Res 66:3456-62. 2006
    ..Taken together, our findings provide strong genetic evidence that the proapoptotic function of Par-4 is dependent on the cellular context and raise the possibility that alterations of Par-4 function may occur during carcinogenesis...
  3. ncbi request reprint Dynamic regulation of histone lysine methylation by demethylases
    Yang Shi
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Mol Cell 25:1-14. 2007
    ....
  4. ncbi request reprint Mammalian RNAi for the masses
    Yang Shi
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Trends Genet 19:9-12. 2003
    ....
  5. ncbi request reprint Coordinated histone modifications mediated by a CtBP co-repressor complex
    Yujiang Shi
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 422:735-8. 2003
    ..These findings identify a molecular mechanism by which CtBP mediates transcriptional repression and provide insight into CtBP participation in oncogenesis...
  6. ncbi request reprint CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation
    Peter Mulligan
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Mol Cell 32:718-26. 2008
    ....
  7. ncbi request reprint An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription
    Amy K Walker
    Section of Developmental and Stem Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 279:15339-47. 2004
    ..Our findings imply that in metazoans TFIID may be of widespread importance for transcription and for expression of tissue-specific genes...
  8. pmc Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development
    Hank H Qi
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 466:503-7. 2010
    ..Our findings indicate that an imbalance of histone methylation dynamics has a critical role in XLMR...
  9. ncbi request reprint The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases
    Shigeki Iwase
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Cell 128:1077-88. 2007
    ..Our findings thus identify a family of H3K4me3 demethylases and uncover a critical link between histone modifications and XLMR...
  10. pmc SPR-5 is a histone H3K4 demethylase with a role in meiotic double-strand break repair
    Amanda C Nottke
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:12805-10. 2011
    ..spr-5 mutants show no transcriptional misregulation of known DSBR involved genes. Instead, SPR-5 shows a rapid subcellular relocalization upon DSB-inducing treatment, which suggests that SPR-5 may function directly in DSBR...
  11. pmc Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression
    Fei Lan
    Department of Pathology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 448:718-22. 2007
    ....
  12. ncbi request reprint Regulation of LSD1 histone demethylase activity by its associated factors
    Yu Jiang Shi
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Mol Cell 19:857-64. 2005
    ..Taken together, these findings suggest that LSD1-mediated histone demethylation is regulated dynamically in vivo. This is expected to have profound effects on gene expression under both physiological and pathological conditions...
  13. ncbi request reprint The fission yeast Jmj2 reverses histone H3 Lysine 4 trimethylation
    Maite Huarte
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    J Biol Chem 282:21662-70. 2007
    ..Our findings identified a novel S. pombe histone demethylase with specificity toward di- and trimethylated histone H3-Lys-4 and a possible role in heterochromatin regulation...
  14. ncbi request reprint Histone demethylation mediated by the nuclear amine oxidase homolog LSD1
    Yujiang Shi
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Cell 119:941-53. 2004
    ..The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases...
  15. ncbi request reprint Yin Yang 1 physically interacts with Hoxa11 and represses Hoxa11-dependent transcription
    Margaret Po shan Luke
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 281:33226-32. 2006
    ..These findings not only provide a novel insight into YY1 function but also identify a new regulation of homeotic protein-mediated transcriptional regulation in general...
  16. pmc Yin Yang 1 deficiency in skeletal muscle protects against rapamycin-induced diabetic-like symptoms through activation of insulin/IGF signaling
    Sharon M Blättler
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cell Metab 15:505-17. 2012
    ..This was associated with H3K27 trimethylation leading to decreased gene expression and insulin signaling. These results have implications for rapamycin action in human diseases and biological processes such as longevity...
  17. ncbi request reprint Gene silencing by a DNA vector-based RNAi technology
    Guangchao Sui
    Department of Pathology, Harvard Medical School, Boston, MA, USA
    Methods Mol Biol 309:205-18. 2005
  18. pmc SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation
    Thomas F Westbrook
    Howard Hughes Medical Institute, Department of Genetics, Harvard Partners Center for Genetics and Genomics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 452:370-4. 2008
    ..Thus, REST is a key target in beta-TRCP-driven transformation and the beta-TRCP-REST axis is a new regulatory pathway controlling neurogenesis...
  19. ncbi request reprint Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases
    Johnathan R Whetstine
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Cell 125:467-81. 2006
    ..Our finding that this family of demethylases generates different methylated states at the same lysine residue provides a mechanism for fine-tuning histone methylation...
  20. pmc The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation
    Shuzhen Chen
    Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Children s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 26:1364-75. 2012
    ..Taken together, these findings provide new insight into the mechanisms by which JMJD3 regulates gene expression...
  21. pmc A YY1-INO80 complex regulates genomic stability through homologous recombination-based repair
    Su Wu
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 14:1165-72. 2007
    ..Collectively, these observations reveal a link between YY1 and INO80 and roles for both in HRR, providing new insight into mechanisms that control the cellular response to genotoxic stress...
  22. ncbi request reprint A histone H3 lysine 27 demethylase regulates animal posterior development
    Fei Lan
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 449:689-94. 2007
    ..Taken together, these findings identify a small family of H3K27 demethylases with important, evolutionarily conserved roles in H3K27 methylation regulation and in animal anterior-posterior development...
  23. pmc DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation
    Sebastian Dango
    Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 44:373-84. 2011
    ..X and 53BP1 foci formation. Our data provide a molecular mechanism by which ALKBH3 collaborates with ASCC to maintain genomic integrity in a cell-type specific manner...
  24. ncbi request reprint Yin Yang 1 is a negative regulator of p53
    Guangchao Sui
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Cell 117:859-72. 2004
    ..Taken together, these findings identify YY1 as a potential cofactor for Hdm2 in the regulation of p53 homeostasis and suggest a possible role for YY1 in tumorigenesis...
  25. pmc The G2/M regulator histone demethylase PHF8 is targeted for degradation by the anaphase-promoting complex containing CDC20
    Hui Jun Lim
    Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Boston Children s Hospital, Boston, Massachusetts, USA
    Mol Cell Biol 33:4166-80. 2013
    ..Taken together, these findings suggest that PHF8 is regulated by APC(cdc20) and plays an important role in the G2/M transition...
  26. pmc Parallel SCF adaptor capture proteomics reveals a role for SCFFBXL17 in NRF2 activation via BACH1 repressor turnover
    Meng Kwang Marcus Tan
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 52:9-24. 2013
    ..This work identifies a role for SCF(FBXL17) in controlling the threshold for NRF2-dependent gene activation and provides a framework for elucidating the functions of CRL adaptor proteins...
  27. pmc Acetylation regulates subcellular localization of the Wnt signaling nuclear effector POP-1
    Frederique Gay
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Genes Dev 17:717-22. 2003
    ..elegans embryogenesis. The conservation of these lysines among other LEF/TCF family members suggests that acetylation may be an important, evolutionarily conserved mechanism regulating subcellular distribution of LEF/TCF factors...
  28. pmc Defective mitochondrial morphology and bioenergetic function in mice lacking the transcription factor Yin Yang 1 in skeletal muscle
    Sharon M Blättler
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Mol Cell Biol 32:3333-46. 2012
    ..These results underscore the important role of YY1 in the maintenance of mitochondrial function and explain how its inactivation might contribute to exercise intolerance and mitochondrial myopathies...
  29. pmc Hypoxia potentiates microRNA-mediated gene silencing through posttranslational modification of Argonaute2
    Connie Wu
    Graduate Program in Biochemistry, Sackler School of Graduate Biomedical Sciences, Boston, Massachusetts 02111, USA
    Mol Cell Biol 31:4760-74. 2011
    ....
  30. pmc Yin Yang 1 is a critical regulator of B-cell development
    Huifei Liu
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 21:1179-89. 2007
    ..We provide evidence that YY1 binds the intronic Ei mu enhancer within the IgH locus, consistent with a direct role for YY1 in V(H)D(H)J(H) recombination. These findings identified YY1 as a critical regulator of early B-cell development...
  31. pmc Essential dosage-dependent functions of the transcription factor yin yang 1 in late embryonic development and cell cycle progression
    El Bachir Affar
    Harvard Medical School, Department of Pathology, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Mol Cell Biol 26:3565-81. 2006
    ..These data not only shed new light on the molecular basis for YY1 developmental roles and cellular functions, but also provide insight into the general mechanisms controlling eukaryotic cell proliferation, apoptosis, and differentiation...
  32. pmc RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination
    Adam G W Matthews
    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 450:1106-10. 2007
    ..Furthermore, our results provide the first evidence indicating that disrupting the read-out of histone modifications can cause an inherited human disease...
  33. ncbi request reprint S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription
    Fei Lan
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 26:89-101. 2007
    ....
  34. pmc Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation
    Rui Fang
    Division of Endocrinology, Diabetes, and Hypertension, Department of Medicine, Brigham and Women s Hospital, 221 Longwood Avenue, Boston, MA 02115, USA
    Mol Cell 39:222-33. 2010
    ..These data provide a possible molecular mechanism linking LSD2 to transcriptional regulation after initiation...
  35. pmc A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response
    Roman Alpatov
    Division of Newborn Medicine, Boston Children s Hospital, Boston, MA 02115, USA Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 157:869-81. 2014
    ..These findings suggest that nuclear FMRP regulates genomic stability at the chromatin interface and may impact gametogenesis and some developmental aspects of fragile X syndrome...
  36. pmc The conserved NAD(H)-dependent corepressor CTBP-1 regulates Caenorhabditis elegans life span
    Shuzhen Chen
    Department of Pathology, Harvard Medical School, 77 Ave Louis Pasteur, Boston MA 02115, USA
    Proc Natl Acad Sci U S A 106:1496-501. 2009
    ..Taken together, our data suggest that CTBP-1 controls life span probably through the regulation of lipid metabolism...
  37. pmc The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3
    Shaila Rahman
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell Biol 31:2641-52. 2011
    ..Our study thus identifies the ET domain as a second important transcriptional regulatory domain for Brd4 in addition to the carboxyl-terminal domain (CTD) that interacts with pTEFb...
  38. pmc Mechanisms involved in the regulation of histone lysine demethylases
    Fei Lan
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States
    Curr Opin Cell Biol 20:316-25. 2008
    ..The chemical mechanisms and substrate specificities have already been extensively discussed elsewhere. This review focuses primarily on regulatory mechanisms that modulate demethylase recruitment and activity...
  39. ncbi request reprint Differential contributions of Caenorhabditis elegans histone deacetylases to huntingtin polyglutamine toxicity
    Emily A Bates
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Neurosci 26:2830-8. 2006
    ..Our results suggest that polyglutamine expansions perturb transcription of CREB/CBP targets and that specific targeting of HDACs will be useful in reducing associated neurodegeneration...
  40. pmc ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome
    Shigeki Iwase
    Division of Newborn Medicine, Department of Medicine, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
    Nat Struct Mol Biol 18:769-76. 2011
    ....
  41. ncbi request reprint Regulation of tissue-specific and extracellular matrix-related genes by a class I histone deacetylase
    Johnathan R Whetstine
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 18:483-90. 2005
    ..Because human HDACs are targets for cancer therapy, these findings have significant implications in cancer treatment...
  42. pmc Developmental roles of the histone lysine demethylases
    Amanda Nottke
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Development 136:879-89. 2009
    ....
  43. pmc Loss of YY1 impacts the heterochromatic state and meiotic double-strand breaks during mouse spermatogenesis
    Su Wu
    Department of Pathology, Harvard Medical School, New Research Building 854b, Boston, MA 02115, USA
    Mol Cell Biol 29:6245-56. 2009
    ..Taken together, this study identifies an important role for YY1 in mouse meiosis and provides new insight into mechanisms that regulate mammalian spermatogenesis...
  44. pmc NXP-2 association with SUMO-2 depends on lysines required for transcriptional repression
    Adam Rosendorff
    Department of Medicine, Channing Laboratory, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 103:5308-13. 2006
    ..SUMO-2-associated proteins identified in this study may contribute to SUMO-dependent regulation of transcription or other processes...
  45. pmc A mechanism for transcriptional repression dependent on the BRCA1 E3 ubiquitin ligase
    Andrew A Horwitz
    Department of Pathology, Harvard Medical School and Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:6614-9. 2007
    ..These results define a biochemical mechanism by which the BRCA1 enzymatic activity regulates a key cellular process...
  46. pmc Prolyl 4-hydroxylation regulates Argonaute 2 stability
    Hank H Qi
    Department of Pathology, Harvard Medical School, New Research Building 854, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 455:421-4. 2008
    ..These findings identify hydroxylation as a post-translational modification important for Ago2 stability and effective RNA interference...
  47. pmc A new horizon for epigenetic medicine?
    Shuzhen Chen
    Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Boston Children s Hospital and Department of Cell Biology, Harvard Medical School, Boston MA, 02115, USA
    Cell Res 23:326-8. 2013
    ..The KDM6 inhibitor shows remarkable substrate selectivity and can inhibit transcription of a plethora of pro-inflammatory genes in cell culture by altering H3K27me3 level at some of the KDM6 target genes...
  48. ncbi request reprint Emerging roles for chromatin as a signal integration and storage platform
    Aimee I Badeaux
    Harvard Medical School, Boston Children s Hospital, Division of Newborn Medicine, 61 Binney Street, Enders 908, Boston, Massachusetts 02115, USA
    Nat Rev Mol Cell Biol 14:211-24. 2013
    ..The preponderance of covalent modifications on histone tails coupled with a relatively small number of functional outputs raises the possibility that chromatin acts as a site of signal integration and storage...
  49. pmc Microcephaly gene links trithorax and REST/NRSF to control neural stem cell proliferation and differentiation
    Yawei J Yang
    Division of Genetics and Manton Center for Orphan Disease Research, Boston Children s Hospital, Boston, MA 02115, USA
    Cell 151:1097-112. 2012
    ..Our results reveal ZNF335 as an essential link between H3K4 complexes and REST/NRSF and provide the first direct genetic evidence that this pathway regulates human neurogenesis and neuronal differentiation...
  50. pmc Translocations disrupting PHF21A in the Potocki-Shaffer-syndrome region are associated with intellectual disability and craniofacial anomalies
    Hyung Goo Kim
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, 02114, USA
    Am J Hum Genet 91:56-72. 2012
    ....
  51. ncbi request reprint Distinct passenger strand and mRNA cleavage activities of human Argonaute proteins
    Bingbing Wang
    Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Struct Mol Biol 16:1259-66. 2009
    ..We show that passenger strand cleavage and RNA chaperone activities that are intrinsic to both AGO1 and AGO2 are sufficient for RNA-induced silencing complex (RISC) loading...
  52. pmc Ligand binding to LRP1 transactivates Trk receptors by a Src family kinase-dependent pathway
    Yang Shi
    Department of Pathology, University of California San Diego, La Jolla, CA 92093 0612, USA
    Sci Signal 2:ra18. 2009
    ..Trk receptor transactivation provides a mechanism by which diverse LRP1 ligands may show neurotrophic activity...
  53. pmc Regulation of cytokine expression by Schwann cells in response to α2-macroglobulin binding to LRP1
    Yang Shi
    Department of Pathology, UCSD School of Medicine, La Jolla, California 92093, USA
    J Neurosci Res 89:544-51. 2011
    ..Inhibiting ERK/MAP kinase activation blocked expression of MCP-1. These studies support a model in which LRP1 regulates multiple aspects of Schwann cell physiology in the response to PNS injury...
  54. pmc Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome
    Hyung Goo Kim
    Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
    Am J Hum Genet 83:511-9. 2008
    ..Our findings indicate that both normosmic IHH and KS are mild allelic variants of CHARGE syndrome and are caused by CHD7 mutations...
  55. ncbi request reprint A two-tiered transcription regulation mechanism that protects germ cell identity
    Yang Shi
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Mol Cell 12:1062-4. 2003
  56. ncbi request reprint Histone lysine demethylases: emerging roles in development, physiology and disease
    Yang Shi
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Rev Genet 8:829-33. 2007
    ..These advances have also catalysed a resurgence of interest in epigenetic regulators as potential therapeutic targets...
  57. pmc Histone methylation: a dynamic mark in health, disease and inheritance
    Eric L Greer
    Cell Biology Department, Harvard Medical School and Division of Newborn Medicine, Children s Hospital Boston, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nat Rev Genet 13:343-57. 2012
    ..The importance of appropriately maintaining or reprogramming histone methylation is illustrated by its links to disease and ageing and possibly to transmission of traits across generations...
  58. ncbi request reprint Metabolic enzymes and coenzymes in transcription--a direct link between metabolism and transcription?
    Yujiang Shi
    Department of Pathology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA 02115, USA
    Trends Genet 20:445-52. 2004
    ....
  59. ncbi request reprint Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases
    Nima Mosammaparast
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Annu Rev Biochem 79:155-79. 2010
    ..Here, we examine these and related facets of histone demethylases discovered to date, focusing on their biochemistry, structure, and enzymology...
  60. pmc A DNA vector-based RNAi technology to suppress gene expression in mammalian cells
    Guangchao Sui
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:5515-20. 2002
    ..These findings highlight the general utility of this DNA vector-based RNAi technology in suppressing gene expression in mammalian cells...
  61. pmc CDK-9/cyclin T (P-TEFb) is required in two postinitiation pathways for transcription in the C. elegans embryo
    Eun Yong Shim
    Center for Blood Research, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 16:2135-46. 2002
    ....
  62. pmc Emerging roles for chromatin as a signal integration and storage platform
    Aimee I Badeaux
    Harvard Medical School, Boston Children s Hospital, Division of Newborn Medicine, 61 Binney Street, Enders 908, Boston, Massachusetts 02115, USA
    Nat Rev Mol Cell Biol 14:211-24. 2013
    ..The preponderance of covalent modifications on histone tails coupled with a relatively small number of functional outputs raises the possibility that chromatin acts as a site of signal integration and storage...
  63. ncbi request reprint RNA interference reveals a requirement for myocyte enhancer factor 2A in activity-dependent neuronal survival
    Brice Gaudilliere
    Department of Pathology, Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115
    J Biol Chem 277:46442-6. 2002
    ..In addition, our findings indicate that RNAi does operate in postmitotic mammalian neurons and thus offers a rapid genetic method of studying gene function in the development and function of the mammalian nervous system...
  64. ncbi request reprint Histone and DNA modifications in mental retardation
    Shigeki Iwase
    Department of Pathology, Harvard Medical School, 77 Ave Louis Pasteur, Boston, MA 02115, USA
    Prog Drug Res 67:147-73. 2011
    ..In this review, we discuss recent studies on epigenetic regulation in MR and explore the concept of epigenetic therapy for MR...
  65. pmc Stable expression of small interfering RNA sensitizes TEL-PDGFbetaR to inhibition with imatinib or rapamycin
    Jing Chen
    Howard Hughes Medical Institute, Division of Hematology, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    J Clin Invest 113:1784-91. 2004
    ..Although siRNA delivery in vivo is a challenging problem, stable expression of siRNA, which targets oncogenic fusion genes, may potentiate the effects of conventional therapy for hematologic malignancies...
  66. ncbi request reprint Par-4 links dopamine signaling and depression
    Sang Ki Park
    Department of Pathology, Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Cell 122:275-87. 2005
    ..Remarkably, Par-4DeltaLZ mice display significantly increased depression-like behaviors. Collectively, these results provide evidence that Par-4 constitutes a molecular link between impaired dopamine signaling and depression...
  67. ncbi request reprint Small RNA: can RNA interference be exploited for therapy?
    Nathan R Wall
    Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
    Lancet 362:1401-3. 2003
    ....
  68. pmc Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells
    Yufei Xu
    Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 42:451-64. 2011
    ..This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 targets, ultimately contributing to mESC differentiation and the onset of embryonic development...
  69. pmc Functional requirement for histone deacetylase 1 in Caenorhabditis elegans gonadogenesis
    Pascale Dufourcq
    Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell Biol 22:3024-34. 2002
    ..Our findings reveal a novel and specific function for the ubiquitously expressed HDA-1 in C. elegans gonadogenesis and place hda-1 in the Notch signaling pathway...
  70. pmc HAT activity is essential for CBP-1-dependent transcription and differentiation in Caenorhabditis elegans
    Martin Victor
    Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    EMBO Rep 3:50-5. 2002
    ..Our findings demonstrate that HAT activity is of primary importance for CBP-1 to regulate transcription and to promote differentiation during C. elegans embryogenesis...
  71. ncbi request reprint Homeotic transformations of the axial skeleton of YY1 mutant mice and genetic interaction with the Polycomb group gene Ring1/Ring1A
    Mar Lorente
    Developmental and Cell Biology, Centro de Investigaciones Biologicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
    Mech Dev 123:312-20. 2006
    ..In addition, YY1 forms complexes with Ring1 and other class II PcG proteins such as Rnf2 and Bmi1 in GST pull down experiments in transfected cells. These findings provide evidence for a PcG function for YY1 in vertebrates...
  72. ncbi request reprint Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis
    Hongliu Ding
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605 2324, USA
    Aging Cell 2:209-17. 2003
    ..Thus, RNAi is a promising therapy for ALS and other disorders caused by dominant, gain-of-function gene mutations...
  73. pmc Nuclear speckle-associated protein Pnn/DRS binds to the transcriptional corepressor CtBP and relieves CtBP-mediated repression of the E-cadherin gene
    Roman Alpatov
    Department of Anatomy and Cell Biology, 1600 SW Archer Rd, University of Florida College of Medicine, Gainesville, FL 32610 0235, USA
    Mol Cell Biol 24:10223-35. 2004
    ..This interaction may reflect the existence of coupling factors involved in CtBP-mediated transcriptional regulation and mRNA processing events...
  74. ncbi request reprint Phosphorylation by the beta-catenin/MAPK complex promotes 14-3-3-mediated nuclear export of TCF/POP-1 in signal-responsive cells in C. elegans
    Miao Chia Lo
    Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
    Cell 117:95-106. 2004
    ..Our results suggest a model whereby Wnt/MAPK signaling downregulates POP-1 levels in responsive cells, in part by increasing nuclear LIT-1 levels, thereby increasing POP-1 phosphorylation and PAR-5-mediated nuclear export...
  75. pmc Smad6 recruits transcription corepressor CtBP to repress bone morphogenetic protein-induced transcription
    Xia Lin
    Michael E DeBakey Department of Surgery, Baylor College of Medicine, One Baylor Plaza, Room 131D, Houston, TX 77030, USA
    Mol Cell Biol 23:9081-93. 2003
    ..We conclude that the nuclear functions and physical interaction of Smad6 and CtBP provide a novel mechanism for the transcriptional regulation by inhibitory Smads...
  76. ncbi request reprint Ineffectiveness of histone deacetylase inhibitors to induce apoptosis involves the transcriptional activation of NF-kappa B through the Akt pathway
    Marty W Mayo
    Department of Surgery, The University of Virginia, Charlottesville, Virginia 22908, USA
    J Biol Chem 278:18980-9. 2003
    ..Our study indicates that the ineffectiveness of HDAC inhibitors to induce apoptosis in NSCLC cancer cells is associated with the ability of these molecules to stimulate NF-kappa B-dependent transcription and cell survival...
  77. pmc ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression
    Xiaobing Shi
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Nature 442:96-9. 2006
    ..Together, our findings establish a pivotal role for trimethylation of H3K4 in gene repression and, potentially, tumour suppressor mechanisms...
  78. ncbi request reprint Structural insights into histone demethylation by JMJD2 family members
    Zhongzhou Chen
    Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206, USA
    Cell 125:691-702. 2006
    ..Sited-directed mutagenesis in conjunction with demethylase activity assays allowed us to propose a molecular model for substrate selection by the JMJD2 histone demethylase family...
  79. pmc Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin
    Fei Li
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 135:272-83. 2008
    ..We suggest that Lid2 enzymatic activity in euchromatin is regulated through a dynamic interplay with other histone-modification enzymes. Our findings provide mechanistic insight into the coordination of H3K4 and H3K9 methylation...
  80. pmc Structural basis of the recognition of a methylated histone tail by JMJD2A
    Zhongzhou Chen
    Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206, USA
    Proc Natl Acad Sci U S A 104:10818-23. 2007
    ..These results provide insights into the mechanisms and specificity of histone demethylation...
  81. ncbi request reprint New nomenclature for chromatin-modifying enzymes
    C David Allis
    Cell 131:633-6. 2007
  82. pmc p53-targeted LSD1 functions in repression of chromatin structure and transcription in vivo
    Wen Wei Tsai
    Dept of Biochemistry and Molecular Biology, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 1000, Houston, TX 77030, USA
    Mol Cell Biol 28:5139-46. 2008
    ..These findings reveal that LSD1 is targeted to chromatin by p53, likely in a gene-specific manner, and define a molecular mechanism by which p53 mediates transcription repression in vivo during differentiation...
  83. ncbi request reprint Activation of protein kinases in chronically hypoxic infant human and rabbit hearts: role in cardioprotection
    Parvaneh Rafiee
    Division of Pediatric Surgery, Medical College of Wisconsin, Milwaukee 53226, USA
    Circulation 106:239-45. 2002
    ..However, the signaling pathways by which infant hearts adapt to chronic hypoxia and resist subsequent surgical ischemia is unknown...
  84. pmc An enhanced U6 promoter for synthesis of short hairpin RNA
    Xu Gang Xia
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Nucleic Acids Res 31:e100. 2003
    ..Thus, this enhanced U6 promoter is useful where limited choices of shRNA sequences preclude the selection of a highly efficient RNAi target region...
  85. pmc The transcription factor Yin Yang 1 is essential for oligodendrocyte progenitor differentiation
    Ye He
    Department of Neuroscience and Cell Biology, R Wood Johnson Medical School, Piscataway, NJ 08854, USA
    Neuron 55:217-30. 2007
    ..Thus, we identify YY1 as an essential component of the transcriptional network regulating the transition of oligodendrocyte progenitors from cell cycle exit to differentiation...
  86. ncbi request reprint Ndel1 controls the dynein-mediated transport of vimentin during neurite outgrowth
    Su Yeon Shim
    Department of Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Calgary T2N 4N1, Canada
    J Biol Chem 283:12232-40. 2008
    ..Our findings reveal a novel regulatory mechanism of vimentin transport during neurite extension that may have implications in diseases featuring transport/trafficking defects and impaired regeneration...
  87. pmc In vivo tumor secretion probing via ultrafiltration and tissue chamber: implication for anti-cancer drugs targeting secretome
    Chun Ming Huang
    Division of Dermatology, Department of Medicine, University of California, San Diego, CA 92161, USA
    Recent Pat Anticancer Drug Discov 3:48-54. 2008
    ..Many detection methods have been patented regarding probes and peptide used for identification of tumors...
  88. ncbi request reprint A heat shock protein 90 binding domain in endothelial nitric-oxide synthase influences enzyme function
    Hao Xu
    Department of Surgery, Division of Pediatric Surgery, Medical College of Wisconsin, Children s Research Institute, Cardiovascular Research Center, Milwaukee, WI 53226, USA
    J Biol Chem 282:37567-74. 2007
    ..Such chaperone-dependent signaling may play an important role in modulating the balance of *NO and O(2)(*) generation from eNOS and, therefore, vascular function...
  89. ncbi request reprint Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch
    Mary E Donohoe
    Howard Hughes Medical Institute, USA
    Mol Cell 25:43-56. 2007
    ..Yy1 and Ctcf associate through specific protein-protein interactions and together transactivate Tsix. We propose that the Ctcf-Yy1-Tsix complex functions as a key component of the X chromosome binary switch...

Research Grants34

  1. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2009
    ..Findings will also shed new light on molecular mechanisms that control germ cell functions and will impact on our understanding of analogous processes in higher eukaryotes. ..
  2. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2005
    ..elegans, and will shed significant new light on how their homologous proteins function in mammals. ..
  3. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2006
    ..abstract_text> ..
  4. Investigation of an unconventional co-repressor complex
    Yang Shi; Fiscal Year: 2006
    ..Based on our strong initial results, new paradigms are likely to emerge from the proposed studies that will significantly impact our views of eukaryotic gene regulation. ..
  5. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2006
    ..elegans, and will shed significant new light on how their homologous proteins function in mammals. [unreadable] [unreadable]..
  6. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2005
    ..abstract_text> ..
  7. Histone Demethylases and Regulation of Chromatin and Transcription in Eukaryotes
    Yang Shi; Fiscal Year: 2006
    ..Based on our exciting initial results, the proposed studies are likely to result in new paradigms that will significantly impact our views of eukaryotic chromatin and transcriptional regulation. ..
  8. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2007
    ..abstract_text> ..
  9. Investigation of an unconventional co-repressor complex
    Yang Shi; Fiscal Year: 2007
    ..Based on our strong initial results, new paradigms are likely to emerge from the proposed studies that will significantly impact our views of eukaryotic gene regulation. ..
  10. Histone Demethylases and Regulation of Chromatin and Transcription in Eukaryotes
    Yang Shi; Fiscal Year: 2007
    ..Based on our exciting initial results, the proposed studies are likely to result in new paradigms that will significantly impact our views of eukaryotic chromatin and transcriptional regulation. ..
  11. Histone Demethylases and Regulation of Chromatin and Transcription in Eukaryotes
    Yang Shi; Fiscal Year: 2008
    ..Based on our exciting initial results, the proposed studies are likely to result in new paradigms that will significantly impact our views of eukaryotic chromatin and transcriptional regulation. ..
  12. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2008
    ..Findings will also shed new light on molecular mechanisms that control germ cell functions and will impact on our understanding of analogous processes in higher eukaryotes. ..
  13. Investigation of an unconventional co-repressor complex
    Yang Shi; Fiscal Year: 2009
    ..Findings will provide new insights into mechanisms that control these processes and may help future development of small molecules that modulate metabolism, aging and oncogenesis. ..
  14. Histone Demethylases and Regulation of Chromatin and Transcription in Eukaryotes
    Yang Shi; Fiscal Year: 2009
    ..Based on our exciting initial results, the proposed studies are likely to result in new paradigms that will significantly impact our views of eukaryotic chromatin and transcriptional regulation. ..
  15. Investigation of an unconventional co-repressor complex
    Yang Shi; Fiscal Year: 2005
    ..Based on our strong initial results, new paradigms are likely to emerge from the proposed studies that will significantly impact our views of eukaryotic gene regulation. ..
  16. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2005
    ..abstract_text> ..
  17. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 1999
    ..elegans, and will shed light on how the homologous proteins p300 and CBP function in mammalian cells. ..
  18. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 1999
    ..Finally, as an important step towards understanding the molecular mechanisms of transcriptional repression mediated by YY1, we will identify and clone target proteins for the repressor domain of YY1. ..
  19. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2000
    ..abstract_text> ..
  20. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2000
    ..elegans, and will shed light on how the homologous proteins p300 and CBP function in mammalian cells. ..
  21. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2001
    ..abstract_text> ..
  22. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2001
    ..elegans, and will shed light on how the homologous proteins p300 and CBP function in mammalian cells. ..
  23. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2002
    ..abstract_text> ..
  24. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2002
    ..elegans, and will shed light on how the homologous proteins p300 and CBP function in mammalian cells. ..
  25. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2002
    ..elegans, and will shed light on how the homologous proteins p300 and CBP function in mammalian cells. ..
  26. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2003
    ..abstract_text> ..
  27. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2003
    ..elegans, and will shed significant new light on how their homologous proteins function in mammals. ..
  28. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2004
    ..abstract_text> ..
  29. TRANSCRIPTION COFACTORS IN DIFFERENTIATION
    Yang Shi; Fiscal Year: 2004
    ..elegans, and will shed significant new light on how their homologous proteins function in mammals. ..
  30. Investigation of an unconventional co-repressor complex
    Yang Shi; Fiscal Year: 2004
    ..Based on our strong initial results, new paradigms are likely to emerge from the proposed studies that will significantly impact our views of eukaryotic gene regulation. ..
  31. TRANSCRIPTIONAL REPRESSION AND ACTIVATION BY YY1
    Yang Shi; Fiscal Year: 2009
    ..abstract_text> ..