Ali Shilatifard

Summary

Affiliation: Stowers Institute for Medical Research
Country: USA

Publications

  1. ncbi request reprint Regulation of heat shock gene expression by RNA polymerase II elongation factor, Elongin A
    Mark Gerber
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Health Sciences Center, Saint Louis, Missouri 63104, USA
    J Biol Chem 280:4017-20. 2005
  2. ncbi request reprint Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS
    Jung Shin Lee
    Stowers Institute for Medical Research, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Cell 131:1084-96. 2007
  3. pmc Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation
    Ali Shilatifard
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Curr Opin Cell Biol 20:341-8. 2008
  4. pmc Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1
    Yoh hei Takahashi
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 29:3478-86. 2009
  5. pmc The COMPASS family of H3K4 methylases in Drosophila
    Man Mohan
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 31:4310-8. 2011
  6. pmc Structural analysis of the core COMPASS family of histone H3K4 methylases from yeast to human
    Yoh hei Takahashi
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Proc Natl Acad Sci U S A 108:20526-31. 2011
  7. pmc Regulation of the transcriptional activity of poised RNA polymerase II by the elongation factor ELL
    Edwin R Smith
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Proc Natl Acad Sci U S A 105:8575-9. 2008
  8. pmc AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia
    Chengqi Lin
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell 37:429-37. 2010
  9. pmc The super elongation complex family of RNA polymerase II elongation factors: gene target specificity and transcriptional output
    Zhuojuan Luo
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Mol Cell Biol 32:2608-17. 2012
  10. pmc Cse4 is part of an octameric nucleosome in budding yeast
    Raymond Camahort
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Mol Cell 35:794-805. 2009

Research Grants

Collaborators

Detail Information

Publications87

  1. ncbi request reprint Regulation of heat shock gene expression by RNA polymerase II elongation factor, Elongin A
    Mark Gerber
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Health Sciences Center, Saint Louis, Missouri 63104, USA
    J Biol Chem 280:4017-20. 2005
    ..Our data represent the first demonstration of an essential role for an RNA polymerase II elongation factor in the regulation of heat shock gene expression in an animal model...
  2. ncbi request reprint Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS
    Jung Shin Lee
    Stowers Institute for Medical Research, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Cell 131:1084-96. 2007
    ..Cps35 is also required for proper H3K79 trimethylation. These findings offer insight into the molecular role of Cps35 in translating the H2B monoubiquitination signal into H3 methylation...
  3. pmc Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation
    Ali Shilatifard
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Curr Opin Cell Biol 20:341-8. 2008
    ....
  4. pmc Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1
    Yoh hei Takahashi
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 29:3478-86. 2009
    ..Our studies provide a molecular basis for the way in which H3K4 trimethylation is regulated by Tyr1052 and the Cps40 subunit of COMPASS...
  5. pmc The COMPASS family of H3K4 methylases in Drosophila
    Man Mohan
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 31:4310-8. 2011
    ..Taken together, this study provides a springboard for the functional dissection of the COMPASS family members and their role in the regulation of histone H3K4 methylation throughout development in Drosophila...
  6. pmc Structural analysis of the core COMPASS family of histone H3K4 methylases from yeast to human
    Yoh hei Takahashi
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Proc Natl Acad Sci U S A 108:20526-31. 2011
    ..This structural arrangement suggested that COMPASS family members function as exo-methylases, which we have confirmed by in vitro and in vivo studies...
  7. pmc Regulation of the transcriptional activity of poised RNA polymerase II by the elongation factor ELL
    Edwin R Smith
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Proc Natl Acad Sci U S A 105:8575-9. 2008
    ..Consistent with a role in elongation, dELL knockdown reduces the levels of phosphorylated Pol II at heat-shock loci. This study implicates dELL in the expression of loci regulated by Pol II elongation...
  8. pmc AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia
    Chengqi Lin
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell 37:429-37. 2010
    ..Knockdown of AFF4 in leukemic cells shows reduction in MLL chimera target gene expression, suggesting that AFF4/SEC could be a key regulator in the pathogenesis of leukemia through many of the MLL partners...
  9. pmc The super elongation complex family of RNA polymerase II elongation factors: gene target specificity and transcriptional output
    Zhuojuan Luo
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Mol Cell Biol 32:2608-17. 2012
    ..These findings suggest that AFF4/SEC could be a potential therapeutic target for the treatment of leukemia or other cancers associated with MYC overexpression...
  10. pmc Cse4 is part of an octameric nucleosome in budding yeast
    Raymond Camahort
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Mol Cell 35:794-805. 2009
    ..Taken together, our experimental evidence supports the model that the Cse4 nucleosome is an octamer, containing two copies each of Cse4, H2A, H2B, and H4...
  11. pmc Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation
    Janet L Thornton
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 28:115-20. 2014
    ..Our study demonstrates that the monoubiquitination machinery and Cps35/Swd2 function to focus COMPASS's H3K4me3 activity at promoter-proximal regions in a context-dependent manner. ..
  12. pmc The little elongation complex functions at initiation and elongation phases of snRNA gene transcription
    Deqing Hu
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell 51:493-505. 2013
    ....
  13. pmc Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II
    Pengfei Wang
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 29:6074-85. 2009
    ..Together these data provide insight into the redundancy and specialization of COMPASS-like complexes in mammals and provide evidence for a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation...
  14. pmc Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1
    Jung Shin Lee
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 26:914-9. 2012
    ....
  15. pmc Polycomb repressive complex 2-dependent and -independent functions of Jarid2 in transcriptional regulation in Drosophila
    Hans Martin Herz
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Mol Cell Biol 32:1683-93. 2012
    ..Identification of Jarid2 as a conserved PRC2 interactor in flies provides an opportunity to begin to probe some of its novel functions in Drosophila development...
  16. pmc ELL-associated factors 1 and 2 are positive regulators of RNA polymerase II elongation factor ELL
    Stephanie E Kong
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Proc Natl Acad Sci U S A 102:10094-8. 2005
    ..Our findings provide insights into the structure and function of ELL family transcription factors, and they bring to light direct roles for the EAF proteins in regulation of RNA polymerase II transcription...
  17. pmc Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS
    Min Wu
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 28:7337-44. 2008
    ..Given our in vivo and in vitro observations, it appears that the human Set1 complex plays a more widespread role in H3K4 trimethylation than do the MLL complexes in mammalian cells...
  18. pmc Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom)
    Man Mohan
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 24:574-89. 2010
    ..Overall, our study describes for the first time the components of DotCom and links the specific regulation of H3K79 trimethylation by Dot1 and its associated factors to the Wnt/Wingless signaling pathway...
  19. pmc Dot1 and histone H3K79 methylation in natural telomeric and HM silencing
    Yoh hei Takahashi
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell 42:118-26. 2011
    ..Therefore, commonly used URA3 reporter assays may not report on natural PEV, and therefore, studies concerning the epigenetic mechanism of silencing in yeast should also employ assays reporting on natural gene expression patterns...
  20. pmc The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers
    Deqing Hu
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Mol Cell Biol 33:4745-54. 2013
    ....
  21. pmc The little elongation complex regulates small nuclear RNA transcription
    Edwin R Smith
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Mol Cell 44:954-65. 2011
    ..The specialization of the SEC and LEC complexes for mRNA and snRNA-containing genes, respectively, suggests the presence of specific classes of elongation factors for each class of genes transcribed by RNA polymerase II...
  22. pmc Human mediator subunit MED26 functions as a docking site for transcription elongation factors
    Hidehisa Takahashi
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Cell 146:92-104. 2011
    ....
  23. ncbi request reprint The super elongation complex (SEC) family in transcriptional control
    Zhuojuan Luo
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
    Nat Rev Mol Cell Biol 13:543-7. 2012
    ..Recent studies have shown that the SEC belongs to a larger family of SEC-like complexes, which includes SEC-L2 and SEC-L3, each with distinct gene target specificities...
  24. pmc Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1
    Shima Nakanishi
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    J Cell Biol 186:371-7. 2009
    ..Therefore, we generated the entire histone H2A and H2B alanine-scanning mutant strains in another background, which does not express wild-type histones...
  25. doi request reprint Enhancer biology and enhanceropathies
    Edwin Smith
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Nat Struct Mol Biol 21:210-9. 2014
    ..New mutations of enhancer sequences and of the protein factors regulating enhancer function in human disease continue to be identified, contributing to a growing class of 'enhanceropathies'. ..
  26. pmc Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4
    Hans Martin Herz
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Genes Dev 26:2604-20. 2012
    ....
  27. doi request reprint The curious case of bivalent marks
    Hans Martin Herz
    Stowers Institute for Medical Research, 1000 East 50 th Street, Kansas City, MO 64110, USA
    Dev Cell 17:301-3. 2009
    ..In this issue of Developmental Cell, Akkers et al. report that Xenopus tropicalis embryos transition through early development without the requirement for bivalently marked promoters...
  28. pmc The super elongation complex (SEC) and MLL in development and disease
    Edwin Smith
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 25:661-72. 2011
    ..Here, we review the normal developmental roles of MLL and the SEC, and how MLL fusion proteins can mediate leukemogenesis...
  29. pmc The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells
    Deqing Hu
    Stowers Institute for Medical Research, Kansas City, Missouri, USA
    Nat Struct Mol Biol 20:1093-7. 2013
    ....
  30. pmc Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription
    Bing Li
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    J Biol Chem 284:7970-6. 2009
    ..Transcription analysis and genome-wide histone modification studies on these mutants suggested that K36me2 is sufficient to target Rpd3S in vivo, thereby maintaining a functional Set2-Rpd3S pathway...
  31. pmc A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation
    Shima Nakanishi
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
    Nat Struct Mol Biol 15:881-8. 2008
    ..This library will be a valuable tool for defining the role of histone residues in processes requiring chromatin...
  32. pmc Enhancer malfunction in cancer
    Hans Martin Herz
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Mol Cell 53:859-66. 2014
    ..We propose that cancer-associated mutations in MLL3 and MLL4 exert their properties through the malfunction of Trr/MLL3/MLL4-dependent enhancers. ..
  33. pmc The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation
    Chengqi Lin
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Cell 152:144-56. 2013
    ..These findings raise the possibility that transcription factors could prime gene expression by marking enhancers in ES cells or even as early as in the germ cell state...
  34. doi request reprint Global proteomic analysis of Saccharomyces cerevisiae identifies molecular pathways of histone modifications
    Jessica Jackson
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Methods Mol Biol 548:175-86. 2009
    ....
  35. pmc Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)
    Chengqi Lin
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 25:1486-98. 2011
    ..Our findings suggest that SEC is a major class of active P-TEFb-containing complexes required for transcriptional activation in response to environmental cues such as differentiation signals...
  36. pmc The language of histone crosstalk
    Jung Shin Lee
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Cell 142:682-5. 2010
    ..However, recent studies indicate that histone modifications have context-dependent effects, making their interplay more like a language within the chromatin signaling pathway than a code...
  37. pmc Transcriptional elongation checkpoint control in development and disease
    Edwin Smith
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 27:1079-88. 2013
    ....
  38. doi request reprint Licensed to elongate: a molecular mechanism for MLL-based leukaemogenesis
    Man Mohan
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
    Nat Rev Cancer 10:721-8. 2010
    ..These studies provide evidence for the importance of the regulation of Pol II elongation in disease pathogenesis and suggest that MLL chimaeras function by licensing Pol II transcription elongation without the appropriate checkpoints...
  39. pmc The JARID2-PRC2 duality
    Hans Martin Herz
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 24:857-61. 2010
    ..Here, we discuss the implications of these studies for an improved understanding of PcG function in development...
  40. pmc Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II
    Edwin R Smith
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell Biol 28:1041-6. 2008
    ..Our data indicate that dUTX is intimately associated with actively transcribed genes and may provide a paradigm for how H3K27 demethylation is required for the activation of preinitiated Pol II on transcriptionally poised genes...
  41. pmc The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes
    Edwin Smith
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Mol Cell 40:689-701. 2010
    ..Here, we have reviewed recent findings on the molecular basis for the recruitment of the chromatin-modifying machineries and their diverse and varied biological outcomes...
  42. ncbi request reprint The A, B, Gs of silencing
    Edwin Smith
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Genes Dev 21:1141-4. 2007
  43. doi request reprint A histone modifier's ill-gotten copy gains
    Ryan Rickels
    Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
    Cell 154:477-9. 2013
    ..Black et al. (2013) now demonstrate that the overexpression of a histone demethylase induces transient copy gain of specific genomic loci known to harbor proto-oncogenes. ..
  44. pmc The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis
    Ali Shilatifard
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Annu Rev Biochem 81:65-95. 2012
    ..The misregulation of histone H2B monoubiquitination and H3K4 methylation result in the pathogenesis of human diseases, including cancer. Recent findings in this regard are also examined...
  45. ncbi request reprint Preparation and assay of RNA polymerase II elongation factors elongin and ELL
    Stephanie E Kong
    Stowers Institute Medical Research, 1000 E 50th Street, Kansas City, Missouri 64110, USA
    Methods Enzymol 371:276-83. 2003
  46. ncbi request reprint Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes
    Melissa M Steward
    Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Blvd, St Louis, Missouri 63104, USA
    Nat Struct Mol Biol 13:852-4. 2006
    ..These findings offer insight into the molecular role of ASH2L, and by extension that of WDR5, in proper H3K4 trimethylation...
  47. ncbi request reprint The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p
    Adam Wood
    Department of Biochemistry, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
    J Biol Chem 278:34739-42. 2003
    ..Thus, in addition to its role during the elongation phase of transcription, the Paf1 complex appears to activate the function but not the placement of the Rad6-Bre1 ubiquitin-protein ligase at the promoters of active genes...
  48. ncbi request reprint Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6
    Jim Dover
    Department of Biochemistry, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
    J Biol Chem 277:28368-71. 2002
    ..Ubiquitination of histone H2B on lysine 123 is the signal for the methylation of histone H3, which leads to silencing of genes located near telomeres...
  49. ncbi request reprint Leaving a mark: the many footprints of the elongating RNA polymerase II
    Joel C Eissenberg
    Edward A Doisy Department of Biochemistry and Molecular Biology and the Cancer Center, St Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA
    Curr Opin Genet Dev 16:184-90. 2006
    ..These findings expand the role for RNA polymerase II elongation in targeting chromatin modifications to include a histone methyl mark more commonly associated with gene silencing...
  50. ncbi request reprint The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS
    Adam Wood
    Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, Missouri 63104, USA
    Mol Cell 20:589-99. 2005
    ..Our results identify in vivo substrates for Bur1/Bur2, thus linking its role to transcriptional elongation and demonstrating a potential activation mechanism for histone H2B monoubiquitination by the Rad6/Bre1 complex...
  51. ncbi request reprint Recruitment of MLL by HMG-domain protein iBRAF promotes neural differentiation
    Christopher Wynder
    The Wistar Institute, 3601 Spruce St, Philadelphia, PA 19104, USA
    Nat Cell Biol 7:1113-7. 2005
    ..Moreover, depletion of iBRAF abrogates recruitment of MLL and enhancement of histone H3K4 trimethylation. Together, these results indicate that the HMG-domain protein iBRAF has a key role in the initiation of neuronal differentiation...
  52. ncbi request reprint The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation
    Nevan J Krogan
    Banting and Best Department of Medical Research, Department of Molecular and Medical Genetics, University of Toronto, Toronto, M5G 1L6, Ontario, Canada
    Mol Cell 11:721-9. 2003
    ..Collectively, our results suggest that the Paf1 complex is required for histone H3 methylation, therefore linking transcriptional elongation to chromatin methylation...
  53. ncbi request reprint Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression
    Jessica Schneider
    Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, Missouri 63104, USA
    Mol Cell 19:849-56. 2005
    ....
  54. pmc Mutational analysis of an RNA polymerase II elongation factor in Drosophila melanogaster
    Mark A Gerber
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, MO 63104, USA
    Mol Cell Biol 25:7803-11. 2005
    ....
  55. ncbi request reprint A COMPASS in the voyage of defining the role of trithorax/MLL-containing complexes: linking leukemogensis to covalent modifications of chromatin
    Kristen Tenney
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Health Sciences Center, Saint Louis, MO 63104, USA
    J Cell Biochem 95:429-36. 2005
    ..In this review, we will discuss the recent findings regarding the molecular mechanism and consequences of histone modification by the MLL related protein containing complex COMPASS...
  56. ncbi request reprint Global proteomic analysis of S. cerevisiae (GPS) to identify proteins required for histone modifications
    Jessica Schneider
    Saint Louis University School of Medicine, Department of Biochemistry, St Louis, Missouri 63104
    Methods Enzymol 377:227-34. 2004
  57. ncbi request reprint Cross-talking histones: implications for the regulation of gene expression and DNA repair
    Adam Wood
    Department of Biochemistry, Saint Louis School of Medicine, MO 63104, USA
    Biochem Cell Biol 83:460-7. 2005
    ..This review details efforts made towards understanding the regulatory mechanisms and biological significance of COMPASS and Dot1p-mediated histone methylation...
  58. pmc Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II
    Nevan J Krogan
    Banting and Best Department of Medical Research, Toronto Yeast Proteomics Organization, University of Toronto, Toronto, Ontario, Canada M5G 1L6
    Mol Cell Biol 23:4207-18. 2003
    ..SET2 also interacts genetically with components of the Set1 and Set3 complexes, suggesting that Set1, Set2, and Set3 similarly affect transcription by RNAPII...
  59. ncbi request reprint Transcriptional elongation by RNA polymerase II and histone methylation
    Mark Gerber
    Department of Biochemistry and the St Louis University Cancer Center, St Louis University School of Medicine, St Louis, Missouri 63104, USA
    J Biol Chem 278:26303-6. 2003
    ..In this article, we will review the recent literature linking the key biochemical process of transcriptional elongation by RNA polymerase II to histone methylation by COMPASS, Dot1p, and Set2 methyltransferases...
  60. ncbi request reprint Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter
    Adam Wood
    Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA
    Mol Cell 11:267-74. 2003
    ..These results suggest that Bre1 is the likely E3 enzyme that directs Rad6 to modify chromatin and ultimately to affect gene expression...
  61. ncbi request reprint Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing
    N C Tolga Emre
    Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19024, USA
    Mol Cell 17:585-94. 2005
    ..Our results suggest that these H2B-deubiquitylating enzymes have distinct genomic functions...
  62. ncbi request reprint Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II
    Rushad Pavri
    Howard Hughes Medical Institute, Department of Biochemistry, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 683 Hoes Lane, Piscataway, NJ 08854, USA
    Cell 125:703-17. 2006
    ....
  63. ncbi request reprint Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein
    Min Gyu Lee
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    Cell 128:877-87. 2007
    ....
  64. ncbi request reprint The trithorax-group gene in Drosophila little imaginal discs encodes a trimethylated histone H3 Lys4 demethylase
    Joel C Eissenberg
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Blvd, St Louis, Missouri 63104, USA
    Nat Struct Mol Biol 14:344-6. 2007
    ....
  65. pmc Histone H3 K4 demethylation during activation and attenuation of GAL1 transcription in Saccharomyces cerevisiae
    Kristin Ingvarsdottir
    Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    Mol Cell Biol 27:7856-64. 2007
    ..Thus, analysis of lysine demethylation in yeast provides new insight into the physiological roles of jumonji demethylase enzymes...
  66. ncbi request reprint Covalent modifications of histones during development and disease pathogenesis
    Sukesh R Bhaumik
    Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA
    Nat Struct Mol Biol 14:1008-16. 2007
    ..We also discuss how perturbation of the activity of this enzymatic machinery can cause developmental defects and disease...
  67. pmc Ctk complex-mediated regulation of histone methylation by COMPASS
    Adam Wood
    Saint Louis University School of Medicine, Department of Biochemistry, 1402 South Grand Blvd, St Louis, MO 63104, USA
    Mol Cell Biol 27:709-20. 2007
    ..Our study suggests a role for the Ctk complex in the regulation of the pattern of H3K4 mono-, di-, and trimethylation via COMPASS...
  68. ncbi request reprint Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II
    Jessica Schneider
    Department of Biochemistry, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
    J Biol Chem 281:37270-4. 2006
    ..This histone modification is also associated with some of the transcriptionally active puff sites in Drosophila. Our results indicate a new role for the Rtt109 protein in the proper regulation of H3K56 acetylation...
  69. ncbi request reprint Cdk9 is an essential kinase in Drosophila that is required for heat shock gene expression, histone methylation and elongation factor recruitment
    Joel C Eissenberg
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Blvd, St Louis, MO 63104, USA
    Mol Genet Genomics 277:101-14. 2007
    ..Binding of the RNA Polymerase II elongation factor ELL was reduced in knockdown chromosomes, suggesting that ELL is recruited to active polymerase via CTD phosphorylation...
  70. ncbi request reprint Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression
    Ali Shilatifard
    Saint Louis University School of Medicine and the Saint Louis University Cancer Center, St Louis, Missouri 63104, USA
    Annu Rev Biochem 75:243-69. 2006
    ....
  71. ncbi request reprint Packing for the germy: the role of histone H4 Ser1 phosphorylation in chromatin compaction and germ cell development
    Kristy D Wendt
    Department of Biochemistry, Saint Louis University School of Medicine, Missouri 63104, USA
    Genes Dev 20:2487-91. 2006
  72. ncbi request reprint A site to remember: H3K36 methylation a mark for histone deacetylation
    Jung Shin Lee
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO 63104, USA
    Mutat Res 618:130-4. 2007
    ..These modifications provide restoration of normal chromatin structure in the wake of elongating Pol II and prevent inappropriate initiation within protein-coding regions masked by chromatin...
  73. pmc RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach
    Nevan J Krogan
    Banting and Best Department of Medical Research Department of Molecular and Medical Genetics, University of Toronto TYPO, Toronto Yeast Proteomics Organization, Toronto, Ontario, Canada
    Mol Cell Biol 22:6979-92. 2002
    ..Spt5, Spt6, and Iws1 are phosphorylated on consensus CKII sites in vivo, conceivably by the Chd1/CKII associated with Spt16/Pob3. All the elongation factors but Elongator copurified with RNAPII...
  74. pmc dELL is an essential RNA polymerase II elongation factor with a general role in development
    Joel C Eissenberg
    Edward A Doisy Department of Biochemistry and Molecular Biology, St Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA
    Proc Natl Acad Sci U S A 99:9894-9. 2002
    ..These data show that an ELL family elongation factor is essential, acts broadly in development, and is not functionally redundant to other elongation factors in vivo...
  75. ncbi request reprint Guided by COMPASS on a journey through chromosome segregation
    Adam Wood
    Nat Struct Mol Biol 12:839-40. 2005
  76. ncbi request reprint The RNA polymerase II elongation complex
    Ali Shilatifard
    Edward A Doisey Department of Biochemistry, St Louis University School of Medicine, St Louis, Missouri 63104, USA
    Annu Rev Biochem 72:693-715. 2003
    ..Below we describe these recent advances, which highlight the important role of the RNA polymerase II elongation complex in regulation of eukaryotic gene expression...
  77. pmc Molecular basis of p53 functional inactivation by the leukemic protein MLL-ELL
    Dmitri Wiederschain
    Department of Cancer Cell Biology, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Mol Cell Biol 23:4230-46. 2003
    ....
  78. ncbi request reprint Posttranslational modifications of histones by methylation
    Adam Wood
    Department of Biochemistry, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
    Adv Protein Chem 67:201-22. 2004
  79. ncbi request reprint Transcriptional blackjack with p21
    Adam Wood
    Department of Biochemistry, Saint Louis University School of Medicine, St Louis, MI 63104, USA
    Genes Dev 20:643-7. 2006
  80. pmc Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling
    Kristen Tenney
    Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO 63104, USA
    Proc Natl Acad Sci U S A 103:11970-4. 2006
    ..Here we demonstrate that the dRtf1 component of the Paf1 complex functions in Notch signaling...
  81. ncbi request reprint New nomenclature for chromatin-modifying enzymes
    C David Allis
    Cell 131:633-6. 2007
  82. ncbi request reprint COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression
    Nevan J Krogan
    Department of Biochemistry, St Louis University School of Medicine, St Louis, Missouri 63104, USA
    J Biol Chem 277:10753-5. 2002
    ..Set1 and several other components of COMPASS are also required for histone H3 methylation in vivo and for transcriptional silencing of a gene located near a chromosome telomere...
  83. ncbi request reprint Histone demethylation by hydroxylation: chemistry in action
    Jessica Schneider
    Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Blvd, St Louis, Missouri 63104, USA
    ACS Chem Biol 1:75-81. 2006
    ..This study broadens our understanding of different types of reaction mechanisms and cofactor requirements for a different category of histone demethylating machinery...
  84. ncbi request reprint Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    Nevan J Krogan
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada
    Nature 440:637-43. 2006
    ..The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology...
  85. pmc In vivo requirement of the RNA polymerase II elongation factor elongin A for proper gene expression and development
    Mark Gerber
    Edward A Doisy Department of Biochemistry and Molecular Biology, St Louis University Health Sciences Center, 1402 South Grand Blvd, St Louis, MO 63104, USA
    Mol Cell Biol 24:9911-9. 2004
    ..The discovery of the role of elongin A in an in vivo model system defines the novel contribution played by RNA polymerase II elongation machinery in regulation of gene expression that is required for proper development...
  86. ncbi request reprint Bur1/Bur2 and the Ctk complex in yeast: the split personality of mammalian P-TEFb
    Adam Wood
    Department of Biochemistry, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA
    Cell Cycle 5:1066-8. 2006
    ..Recent findings regarding the role of these kinases in histone tail modifications and transcriptional regulation is briefly reviewed below...
  87. pmc Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8
    Karl W Henry
    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
    Genes Dev 17:2648-63. 2003
    ..These results suggest that the histone H2B ubiquitylation state is dynamic during transcription, and that the sequence of histone modifications helps to control transcription...

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