Publications by authors named "Jikui Song"

69Publications

YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression.

Nat Chem Biol 2020 Nov 16. Epub 2020 Nov 16.

Department of Chemistry, University of California, Riverside, Riverside, CA, USA.

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November 2020

Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.

Nucleic Acids Res 2020 11;48(20):11495-11509

Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.

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November 2020

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation.

Nat Commun 2020 07 24;11(1):3723. Epub 2020 Jul 24.

Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.

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July 2020

Inhibiting Matrix Metalloproteinase-2 Activation by Perturbing Protein-Protein Interactions Using a Cyclic Peptide.

J Med Chem 2020 07 18;63(13):6979-6990. Epub 2020 Jun 18.

Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States.

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July 2020

Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.

Nat Commun 2020 05 8;11(1):2294. Epub 2020 May 8.

Department of Biochemistry, University of California, Riverside, CA, 92521, USA.

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May 2020

A DNA aptamer for binding and inhibition of DNA methyltransferase 1.

Nucleic Acids Res 2019 12;47(22):11527-11537

Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA.

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December 2019

Dissect the DNMT3A- and DNMT3B-mediated DNA Co-methylation through a Covalent Complex Approach.

J Mol Biol 2020 01 11;432(2):569-575. Epub 2019 Nov 11.

Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA; Department of Biochemistry, University of California, Riverside, CA, USA. Electronic address:

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January 2020

Structure and regulation of ZCCHC4 in mA-methylation of 28S rRNA.

Nat Commun 2019 11 6;10(1):5042. Epub 2019 Nov 6.

Department of Biochemistry, University of California, Riverside, CA, 92521, USA.

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November 2019

Protein Interactions at Oxidized 5-Methylcytosine Bases.

J Mol Biol 2019 Aug 8. Epub 2019 Aug 8.

Department of Biochemistry, University of California Riverside, Riverside, CA 92521, USA.

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August 2019

Structural basis for the ORC1-Cyclin A association.

Protein Sci 2019 09 31;28(9):1727-1733. Epub 2019 Jul 31.

Department of Biochemistry, University of California, Riverside, California.

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September 2019

Suppression of Type I Interferon Signaling by NS5.

Viruses 2018 12 14;10(12). Epub 2018 Dec 14.

Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.

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December 2018

Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation.

Genes (Basel) 2018 Dec 11;9(12). Epub 2018 Dec 11.

Department of Biochemistry, University of California, Riverside, CA 92521, USA.

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December 2018

CARM1 suppresses serine synthesis by promoting PKM2 activity.

J Biol Chem 2018 09 21;293(39):15290-15303. Epub 2018 Aug 21.

From the Departments of Cancer Genetics and Epigenetics and

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September 2018

Structure-Based Design of Novel EphA2 Agonistic Agents with Nanomolar Affinity in Vitro and in Cell.

ACS Chem Biol 2018 09 29;13(9):2633-2644. Epub 2018 Aug 29.

Division of Biomedical Sciences, School of Medicine , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.

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September 2018

Structure and function of Zika virus NS5 protein: perspectives for drug design.

Cell Mol Life Sci 2018 05 8;75(10):1723-1736. Epub 2018 Feb 8.

Department of Biochemistry, University of California, Riverside, CA, 92521, USA.

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May 2018

Structural basis for DNMT3A-mediated de novo DNA methylation.

Nature 2018 02 7;554(7692):387-391. Epub 2018 Feb 7.

Department of Biochemistry, University of California, Riverside, California 92521, USA.

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February 2018

An Intramolecular Interaction of UHRF1 Reveals Dual Control for Its Histone Association.

Structure 2018 02 25;26(2):304-311.e3. Epub 2018 Jan 25.

Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA; Department of Biochemistry, University of California, Riverside, CA 92521, USA. Electronic address:

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February 2018

Mechanism of host substrate acetylation by a YopJ family effector.

Nat Plants 2017 Jul 24;3:17115. Epub 2017 Jul 24.

Department of Biochemistry, University of California, Riverside, California 92521, USA.

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July 2017

The structure of Zika virus NS5 reveals a conserved domain conformation.

Nat Commun 2017 03 27;8:14763. Epub 2017 Mar 27.

Department of Biochemistry, University of California, Riverside, Riverside, California 92521, USA.

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March 2017

Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family.

Nat Struct Mol Biol 2016 09 15;23(9):847-52. Epub 2016 Aug 15.

Department of Biochemistry, University of California, Riverside, Riverside, California, USA.

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September 2016

Are there specific readers of oxidized 5-methylcytosine bases?

Bioessays 2016 10 2;38(10):1038-47. Epub 2016 Aug 2.

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.

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October 2016

BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2.

PLoS Pathog 2016 Feb 4;12(2):e1005414. Epub 2016 Feb 4.

Department of Biochemistry, University of California, Riverside, Riverside, California, United States of America.

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February 2016

Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration.

Cell Rep 2016 Jan 7;14(3):493-505. Epub 2016 Jan 7.

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA; Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA. Electronic address:

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January 2016

Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis.

Proc Natl Acad Sci U S A 2016 Jan 25;113(1):E41-50. Epub 2015 Nov 25.

Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521; Department of Botany and Plant Sciences, University of California, Riverside, CA 92521;

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January 2016

An Allosteric Interaction Links USP7 to Deubiquitination and Chromatin Targeting of UHRF1.

Cell Rep 2015 Sep 20;12(9):1400-6. Epub 2015 Aug 20.

Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA. Electronic address:

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September 2015

Two serine residues in Pseudomonas syringae effector HopZ1a are required for acetyltransferase activity and association with the host co-factor.

New Phytol 2015 Dec 23;208(4):1157-68. Epub 2015 Jun 23.

Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.

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December 2015

Crystal Structure of Human DNA Methyltransferase 1.

J Mol Biol 2015 Jul 10;427(15):2520-2531. Epub 2015 Jun 10.

Department of Biochemistry, University of California, Riverside, CA 92521, USA. Electronic address:

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July 2015

A Meier-Gorlin syndrome mutation impairs the ORC1-nucleosome association.

ACS Chem Biol 2015 May 24;10(5):1176-80. Epub 2015 Feb 24.

†Department of Biochemistry, University of California, Riverside, California 92521, United States.

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May 2015

Arsenite binds to the RING finger domains of RNF20-RNF40 histone E3 ubiquitin ligase and inhibits DNA double-strand break repair.

J Am Chem Soc 2014 Sep 9;136(37):12884-7. Epub 2014 Sep 9.

Department of Chemistry, §Environmental Toxicology Graduate Program, and ∥Department of Biochemistry, University of California , Riverside, California 92521, United States.

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September 2014

Effects of Tet-induced oxidation products of 5-methylcytosine on Dnmt1- and DNMT3a-mediated cytosine methylation.

Mol Biosyst 2014 Jul 30;10(7):1749-52. Epub 2014 Apr 30.

Department of Chemistry, University of California, Riverside, CA 92521, USA.

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July 2014

Bacterial effector activates jasmonate signaling by directly targeting JAZ transcriptional repressors.

PLoS Pathog 2013 Oct 31;9(10):e1003715. Epub 2013 Oct 31.

Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America ; Center for Plant Cell Biology, University of California, Riverside, California, United States of America.

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October 2013

An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting.

Mol Cell 2013 Feb 27;49(3):571-82. Epub 2012 Dec 27.

UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.

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February 2013

The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome.

Nature 2012 Mar 7;484(7392):115-9. Epub 2012 Mar 7.

Department of Biology, Stanford University, Stanford, California 94305, USA.

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March 2012

Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.

Science 2012 Feb;335(6069):709-12

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

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February 2012

Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.

Science 2011 Feb 16;331(6020):1036-40. Epub 2010 Dec 16.

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

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February 2011

Structural insights into RNA recognition by the alternate-splicing regulator CUG-binding protein 1.

Structure 2010 Oct;18(10):1364-77

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

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October 2010

Cleavage of peptide bonds bearing ionizable amino acids at P(1) by serine proteases with hydrophobic S(1) pocket.

Biochem Biophys Res Commun 2010 Oct 26;400(4):507-10. Epub 2010 Aug 26.

Department of Chemistry, Indiana University Purdue University Fort Wayne, 2101 E. Coliseum Blvd., Fort Wayne, IN 46805, USA.

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October 2010

In vitro interaction of tubulin with the photoreceptor cGMP phosphodiesterase gamma-subunit.

Neurosci Lett 2010 Oct 22;482(3):225-9. Epub 2010 Jul 22.

Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.

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October 2010

Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression.

Cell 2010 Jun 10;141(7):1183-94. Epub 2010 Jun 10.

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

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June 2010

Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.

Nature 2009 Jun;459(7248):847-51

Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York 10065, USA.

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June 2009

Structural basis for RNA recognition by a type II poly(A)-binding protein.

Proc Natl Acad Sci U S A 2008 Oct 29;105(40):15317-22. Epub 2008 Sep 29.

Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA.

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October 2008

Structural basis for the catalytic mechanism of mammalian 25-kDa thiamine triphosphatase.

J Biol Chem 2008 Apr 14;283(16):10939-48. Epub 2008 Feb 14.

Center for Eukaryotic Structural Genomics and National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.

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April 2008

Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure.

Proc Natl Acad Sci U S A 2008 Feb 29;105(5):1505-10. Epub 2008 Jan 29.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA.

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February 2008

Small-scale, semi-automated purification of eukaryotic proteins for structure determination.

J Struct Funct Genomics 2007 Dec 6;8(4):153-66. Epub 2007 Nov 6.

The University of Wisconsin Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin, Room 141B, 433 Babcock Drive, Madison, WI 53706, USA.

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December 2007

Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics.

J Struct Funct Genomics 2007 Sep 6;8(2-3):73-84. Epub 2007 Sep 6.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

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September 2007

Solution structure of human sorting nexin 22.

Protein Sci 2007 May 30;16(5):807-14. Epub 2007 Mar 30.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.

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May 2007

Cautionary tail: the presence of an N-terminal tag on dynein light-chain Roadblock/LC7 affects its interaction with a functional partner.

Protein Pept Lett 2007 ;14(3):265-8

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA.

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June 2007

Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications.

Biochemistry 2006 Dec 8;45(51):15633-43. Epub 2006 Dec 8.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706-1544, USA.

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December 2006

Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold.

J Mol Biol 2007 Feb 11;366(1):155-64. Epub 2006 Nov 11.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.

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February 2007

Rieske protein from Thermus thermophilus: 15N NMR titration study demonstrates the role of iron-ligated histidines in the pH dependence of the reduction potential.

J Am Chem Soc 2006 Aug;128(33):10672-3

Graduate Program in Biophysics, Center for Eukaryotic Structural Genomics, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, University of Wisconsin, Madison, Wisconsin 53706, USA.

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August 2006

Solution structure of isoform 1 of Roadblock/LC7, a light chain in the dynein complex.

J Mol Biol 2005 Dec 2;354(5):1043-51. Epub 2005 Nov 2.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544, USA.

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December 2005

Probing the sweet determinants of brazzein: wild-type brazzein and a tasteless variant, brazzein-ins(R18a-I18b), exhibit different pH-dependent NMR chemical shifts.

Biochem Biophys Res Commun 2005 Sep;335(1):256-63

Department of Biochemistry, University of Wisconsin Madison, College of Agricultural and Life Sciences, USA.

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September 2005

Solution structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein.

Protein Sci 2005 Apr 1;14(4):1059-63. Epub 2005 Mar 1.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, 433 Babcock Drive, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.

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April 2005

Two conformational states of Turkey ovomucoid third domain at low pH: three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamics.

Biochemistry 2003 Jun;42(21):6380-91

National Magnetic Resonance Facility, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

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June 2003

Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant.

Biochemistry 2003 May;42(18):5186-94

National Magnetic Resonance Facility, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

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May 2003

NMR determination of pKa values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain.

Biochemistry 2003 Mar;42(10):2847-56

National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

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March 2003