Ali Shilatifard

Summary

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Michael P Washburn
  • Xin Gao
  • Ying Zhang
  • Min Wu
  • Jerry L Workman
  • Joan W Conaway
  • Ronald C Conaway
  • Bing Li
  • Sue L Jaspersen
  • Ramin Shiekhattar
  • Mary Ann Osley
  • Jennifer L Gerton
  • Matthew D Simon
  • Dongxiao Zhu
  • Sukesh R Bhaumik
  • Henrietta Szutorisz
  • Michael S Kobor
  • Kai Ge
  • Masamitsu Yamaguchi
  • Chengqi Lin
  • Edwin R Smith
  • Hans Martin Herz
  • Yoh hei Takahashi
  • Laurence Florens
  • Deqing Hu
  • Edwin Smith
  • Jung Shin Lee
  • Jessica Jackson
  • Man Mohan
  • Shima Nakanishi
  • Zhuojuan Luo
  • Alexander S Garrett
  • Christopher Seidel
  • Joel C Eissenberg
  • Alexander S Garruss
  • Selene K Swanson
  • Marc A Morgan
  • Nima Mohaghegh
  • Anita Saraf
  • Hidehisa Takahashi
  • Janet L Thornton
  • Malcolm Cook
  • Ryan Rickels
  • Gerwin H Westfield
  • Georgios Skiniotis
  • Erin Guest
  • Skylar Martin-Brown
  • Madelaine Gogol
  • Ka Chun Lai
  • Raymond C Trievel
  • Robb Krumlauf
  • Pengfei Wang
  • Raymond Camahort
  • Brian W Sanderson
  • Benjamin Winter
  • Jean Francois Couture
  • Ashley R Woodfin
  • Joseph M Varberg
  • Fengli Guo
  • Selene Swanson
  • Kuangyu Yen
  • Kaiwei Liang
  • Kristen Mickey
  • Caitlynn Miller
  • Jeffrey S Haug
  • B Franklin Pugh
  • Olaf Voets
  • Stacy Marshall
  • C Peter Verrijzer
  • David Casto
  • Chris Seidel
  • Shigeo Sato
  • Chris W Seidel
  • Chieri Tomomori-Sato
  • Thomas Hentrich
  • Julia M Schulze
  • Janet Thornton
  • Charles A S Banks
  • Austin N Oleskie
  • Tari J Parmely
  • Bony De Kumar
  • Stephanie E Kong
  • Leanne M Wiedemann
  • Mark Mattingly
  • Manjunatha Shivaraju
  • Jennifer M Gardner
  • Tara Alexander
  • Brian D Strahl
  • Zu Wen Sun
  • Mahesh B Chandrasekharan

Detail Information

Publications41

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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
    ....
  11. 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...
  12. 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. ..
  13. 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...
  14. 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...
  15. 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
    ....
  16. 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...
  17. 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...
  18. 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
    ....
  19. 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...
  20. ncbi 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...
  21. 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
    ....
  22. 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
    ....
  23. 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...
  24. doi 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'. ..
  25. 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
    ....
  26. ncbi 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...
  27. doi 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 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
    ....
  29. 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...
  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 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...
  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. doi 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
    ....
  34. 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...
  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 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
    ....
  37. doi 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...
  38. 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...
  39. 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...
  40. 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...
  41. doi 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. ..

Research Grants19

  1. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2001
    ....
  2. Chromatin Modification by Histone Ubiquitination and Methylations
    Ali Shilatifard; Fiscal Year: 2010
    ....
  3. Mammalian H3K4 Methylases, Chromosomal Translocations and Human Leukemia
    Ali Shilatifard; Fiscal Year: 2010
    ..Therefore, detailed knowledge of the molecular functions of MLL and its family members will be critical for the detection, diagnosis and treatment of human leukemia. ..
  4. Chromatin Modification by Histone Ubiquitination and Methylations
    Ali Shilatifard; Fiscal Year: 2009
    ....
  5. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2009
    ..Results obtained from these proposed studies will be instrumental in designing targeted therapies for the treatment of such hematological malignancies. ..
  6. Chromatin Modification by Histone Ubiquitination
    Ali Shilatifard; Fiscal Year: 2006
    ..abstract_text> ..
  7. Chromatin Modification by Histone Ubiquitination
    Ali Shilatifard; Fiscal Year: 2007
    ..abstract_text> ..
  8. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2007
    ..Results obtained from these proposed studies will be instrumental in designing targeted therapies for the treatment of such hematological malignancies. ..
  9. Chromatin Modification by Histone Ubiquitination
    Ali Shilatifard; Fiscal Year: 2006
    ..abstract_text> ..
  10. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2006
    ..Results obtained from these proposed studies will be instrumental in designing targeted therapies for the treatment of such hematological malignancies. ..
  11. Chromatin Modification by Histone Ubiquitination
    Ali Shilatifard; Fiscal Year: 2005
    ..abstract_text> ..
  12. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2005
    ..Results obtained from these proposed studies will be instrumental in designing targeted therapies for the treatment of such hematological malignancies. ..
  13. Chromatin Modification by Histone Ubiquitination
    Ali Shilatifard; Fiscal Year: 2004
    ..abstract_text> ..
  14. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2004
    ....
  15. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2003
    ....
  16. Physiological Role of MLL and ELL Proteins in Leukemia
    Ali Shilatifard; Fiscal Year: 2002
    ....
  17. Dot 1 Complex, Transcriptional Elongation Control and Human Cancer
    Ali Shilatifard; Fiscal Year: 2011
    ....