List of works - Katsuhiko Shirahige

5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex

scientific journal article

A checkpoint control linking meiotic S phase and recombination initiation in fission yeast

scientific article

A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands

scientific article

A mesodermal factor, T, specifies mouse germ cell fate by directly activating germline determinants

scientific article

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

scientific article

A wave of nascent transcription on activated human genes

scholarly article

ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects

scientific article published on 27 July 2016

ASBEL-TCF3 complex is required for the tumorigenicity of colorectal cancer cells

scientific article published on 21 October 2016

ATF1 modulates the heat shock response by regulating the stress-inducible heat shock factor 1 transcription complex

scientific article published on 13 October 2014

Abnormality in initiation program of DNA replication is monitored by the highly repetitive rRNA gene array on chromosome XII in budding yeast

scientific article published on 13 November 2006

Acetylation regulates monopolar attachment at multiple levels during meiosis I in fission yeast

scientific article

Amyloid precursor protein is a primary androgen target gene that promotes prostate cancer growth

scientific article published in January 2009

An In Vitro Human Liver Model by iPSC-Derived Parenchymal and Non-parenchymal Cells ⬇️

scientific article published on 11 July 2017

An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion

scientific article published on September 2010

An integrated map of p53-binding sites and histone modification in the human ENCODE regions

scientific article

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

scientific article

Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae

scientific article

BRCA2 coordinates the activities of cell-cycle kinases to promote genome stability

scientific article

Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast ⬇️

scientific article published on 22 September 2008

Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association

scientific article

Budding yeast Wpl1(Rad61)-Pds5 complex counteracts sister chromatid cohesion-establishing reaction

scientific article published on 5 March 2009

ChIP-on-chip analysis of DNA topoisomerases

scientific article

Chromatin determinants of the inner-centromere rely on replication factors with functions that impart cohesion

scientific article published on 12 September 2016

Chromatin immunoprecipitation protocol for mammalian cells

scientific article published in January 2014

Chromosomal association of the Smc5/6 complex reveals that it functions in differently regulated pathways

scientific article

Chromosome length influences replication-induced topological stress

scientific article published in Nature

Clinical, developmental and molecular update on Cornelia de Lange syndrome and the cohesin complex: abstracts from the 2014 Scientific and Educational Symposium

scientific article published on 21 April 2015

Cohesin Acetylation Promotes Sister Chromatid Cohesion Only in Association with the Replication Machinery ⬇️

scientific article published on August 15, 2012

Cohesin relocation from sites of chromosomal loading to places of convergent transcription

scientific article published on 30 June 2004

Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis

scientific article published on 27 February 2018

Condensin-dependent rDNA decatenation introduces a temporal pattern to chromosome segregation

scientific article published in July 2008

Cornelia de Lange syndrome and molecular implications of the cohesin complex: Abstracts from the 7th biennial scientific and educational symposium 2016.

scientific article published on 12 February 2017

Cornelia de Lange syndrome: further delineation of phenotype, cohesin biology and educational focus, 5th Biennial Scientific and Educational Symposium abstracts

scientific article published on 6 February 2014

Csm3, Tof1, and Mrc1 form a heterotrimeric mediator complex that associates with DNA replication forks

scientific article published on 8 October 2009

Ctf4 coordinates the progression of helicase and DNA polymerase alpha.

scientific article

DBTMEE: a database of transcriptome in mouse early embryos

scientific article published on 21 October 2014

DBTSS/DBKERO for integrated analysis of transcriptional regulation

scientific article published on 8 November 2017

DROMPA: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data ⬇️

scientific article published on May 15, 2013

Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior

scientific article

Different requirements for the association of ATR-ATRIP and 9-1-1 to the stalled replication forks

scientific article published on 20 May 2006

Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis

scientific article published in July 2014

Displacement and re-accumulation of centromeric cohesin during transient pre-anaphase centromere splitting

scientific article

Dissecting the first and the second meiotic divisions using a marker-less drug-hypersensitive fission yeast.

scientific article published on 3 March 2014

During replication stress, non-SMC element 5 (NSE5) is required for Smc5/6 protein complex functionality at stalled forks

scientific article published on 2 February 2012

Elevation of insulin-like growth factor binding protein-2 level in Pallister-Killian syndrome: implications for the postnatal growth retardation phenotype

scientific article published on 21 April 2015

Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype

scientific article published on 10 January 2012

Establishment of sister chromatid cohesion at the S. cerevisiae replication fork

scientific article

Eukaryotic replisome components cooperate to process histones during chromosome replication.

scientific article published on 14 March 2013

Evidence that Loading of Cohesin Onto Chromosomes Involves Opening of Its SMC Hinge

article

Exome Sequencing Identification of EP300 Mutation in a Proband with Coloboma and Imperforate Anus: Possible Expansion of the Phenotypic Spectrum of Rubinstein-Taybi Syndrome

scientific article published on 3 March 2015

Exome sequencing-based identification of mutations in non-syndromic genes among individuals with apparently syndromic features

scientific article published on 26 August 2016

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex

scientific article published on 31 May 2017

Genome-wide DNA methylation analysis in cohesin mutant human cell lines

scientific article

Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor

scientific article published on February 2014

Genome-wide expression analysis of genes affected by amino acid sensor Ssy1p in Saccharomyces cerevisiae

scientific article

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

scientific article published on 24 June 2011

Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters

scientific article

Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast

scientific article published on 15 February 2007

Genomic approach for the understanding of dynamic aspect of chromosome behavior

scientific article published in January 2006

Glucose-dependent cell size is regulated by a G protein-coupled receptor system in yeast Saccharomyces cerevisiae

scientific article published in March 2005

HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle

scientific article

Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis

scientific article published on February 2011

Hot debate in hot springs: Report on the second international meeting on SMC proteins

scientific article

Identification and characterization of rns4/vps32 mutation in the RNase T1 expression-sensitive strain of Saccharomyces cerevisiae: Evidence for altered ambient response resulting in transportation of the secretory protein to vacuoles

scientific article published in June 2005

Identification of a variant-specific phosphorylation of TH2A during spermiogenesis

scientific article published on 07 April 2017

Identification of cis-acting sites for condensin loading onto budding yeast chromosomes

scientific article

Importance of Polη for damage-induced cohesion reveals differential regulation of cohesion establishment at the break site and genome-wide ⬇️

scientific article

Inactivation of SMC2 shows a synergistic lethal response in MYCN-amplified neuroblastoma cells

scientific article

Involvement of RAD9-dependent damage checkpoint control in arrest of cell cycle, induction of cell death, and chromosome instability caused by defects in origin recognition complex in Saccharomyces cerevisiae

scientific article published on April 2002

Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment

scientific article

Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance

scientific article

Mapping of histone-binding sites in histone replacement-completed spermatozoa

scientific article published in Nature Communications

Meiotic cohesins modulate chromosome compaction during meiotic prophase in fission yeast

scientific article

Meiotic recombination-related DNA synthesis and its implications for cross-over and non-cross-over recombinant formation

scholarly article

Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1.

scientific article

Mosaic ratio quantification of isochromosome 12p in Pallister-Killian syndrome using droplet digital PCR.

scientific article published on 20 January 2016

Mrc1 and DNA polymerase epsilon function together in linking DNA replication and the S phase checkpoint

scientific article

Mre11 mediates gene regulation in yeast spore development

scientific article

Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast

scientific article

Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing

scientific article published on 8 December 2011

PPARγ-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine

scientific article published on January 2013

PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells

scientific article

Pds5 promotes and protects cohesin acetylation

scientific article published on 22 July 2013

Postreplicative Formation of Cohesion Is Required for Repair and Induced by a Single DNA Break

scientific article published on 13 July 2007

Protein phosphatase 2A protects centromeric sister chromatid cohesion during meiosis I.

scientific article

Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells

scientific article

RSC Nucleosome-remodeling complex plays prominent roles in transcriptional regulation throughout budding yeast gametogenesis

scientific article

Rad51 suppresses gross chromosomal rearrangement at centromere in Schizosaccharomyces pombe

scientific article published on 16 October 2008

Rapid Discovery of Highly Potent and Selective Inhibitors of Histone Deacetylase 8 Using Click Chemistry to Generate Candidate Libraries ⬇️

scientific article published on November 12, 2012

Rec8 guides canonical Spo11 distribution along yeast meiotic chromosomes

scientific article published on 13 May 2009

Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest

scientific article published on 12 November 2010

Reciprocal association of the budding yeast ATM-related proteins Tel1 and Mec1 with telomeres in vivo

scientific article published in May 2004

Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms

scientific article

Relationship between G+C content, ORF-length and mRNA concentration in Saccharomyces cerevisiae

scientific article

Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements

scientific article

Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases

scientific article

Rif1 is a global regulator of timing of replication origin firing in fission yeast

scientific article

Rtt101-Mms1-Mms22 coordinates replication-coupled sister chromatid cohesion and nucleosome assembly

scientific article published on 14 June 2017

Rtt107 is required for recruitment of the SMC5/6 complex to DNA double strand breaks

scientific article published on 3 June 2011

S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex

scientific article

SCF(Dia2) regulates DNA replication forks during S-phase in budding yeast

scientific article

Screening for candidate genes involved in tolerance to organic solvents in yeast

scientific article published on 22 February 2006

Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile

scientific article published on 8 March 2018

Sensory-neuron subtype-specific transcriptional programs controlling dendrite morphogenesis: genome-wide analysis of Abrupt and Knot/Collier

scientific article published on 27 November 2013

Single cell RNA-sequencing identified Dec2 as a suppressive factor for spermatogonial differentiation by inhibiting Sohlh1 expression

Sororin mediates sister chromatid cohesion by antagonizing Wapl

scientific article

Sphingolipids regulate telomere clustering by affecting the transcription of genes involved in telomere homeostasis

scientific article published on 4 June 2015

Spo13 facilitates monopolin recruitment to kinetochores and regulates maintenance of centromeric cohesion during yeast meiosis

scientific article

Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA.

scientific article published in January 2018

Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast

scientific article

Temporal and spatial regulation of eukaryotic DNA replication: from regulated initiation to genome-scale timing program

scientific article

The direct binding of Mrc1, a checkpoint mediator, to Mcm6, a replication helicase, is essential for the replication checkpoint against methyl methanesulfonate-induced stress

scientific article published on 20 July 2009

The inheritance of histone modifications depends upon the location in the chromosome in Saccharomyces cerevisiae

scientific article

The kinetochore proteins Pcs1 and Mde4 and heterochromatin are required to prevent merotelic orientation

scientific article published on July 2007

The prereplication complex recruits XEco2 to chromatin to promote cohesin acetylation in Xenopus egg extracts

scientific article published on 3 May 2012

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation

scientific article published on August 2007

Transcriptional dysregulation in NIPBL and cohesin mutant human cells

scientific article

Unique gene expression profile of the proliferating Xenopus tadpole tail blastema cells deciphered by RNA-sequencing analysis

scientific article published on 16 March 2015

Yeast Pho85 kinase is required for proper gene expression during the diauxic shift

scientific article published in August 2004

List of works by Katsuhiko Shirahige

5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex

A checkpoint control linking meiotic S phase and recombination initiation in fission yeast

A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands

A mesodermal factor, T, specifies mouse germ cell fate by directly activating germline determinants

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

A wave of nascent transcription on activated human genes

ARCN1 Mutations Cause a Recognizable Craniofacial Syndrome Due to COPI-Mediated Transport Defects

ASBEL-TCF3 complex is required for the tumorigenicity of colorectal cancer cells

ATF1 modulates the heat shock response by regulating the stress-inducible heat shock factor 1 transcription complex

Abnormality in initiation program of DNA replication is monitored by the highly repetitive rRNA gene array on chromosome XII in budding yeast

Acetylation regulates monopolar attachment at multiple levels during meiosis I in fission yeast

Amyloid precursor protein is a primary androgen target gene that promotes prostate cancer growth

An In Vitro Human Liver Model by iPSC-Derived Parenchymal and Non-parenchymal Cells ⬇️

An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion

An integrated map of p53-binding sites and histone modification in the human ENCODE regions

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae

BRCA2 coordinates the activities of cell-cycle kinases to promote genome stability

Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast ⬇️

Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association

Budding yeast Wpl1(Rad61)-Pds5 complex counteracts sister chromatid cohesion-establishing reaction

ChIP-on-chip analysis of DNA topoisomerases

Chromatin determinants of the inner-centromere rely on replication factors with functions that impart cohesion

Chromatin immunoprecipitation protocol for mammalian cells

Chromosomal association of the Smc5/6 complex reveals that it functions in differently regulated pathways

Chromosome length influences replication-induced topological stress

Clinical, developmental and molecular update on Cornelia de Lange syndrome and the cohesin complex: abstracts from the 2014 Scientific and Educational Symposium

Cohesin Acetylation Promotes Sister Chromatid Cohesion Only in Association with the Replication Machinery ⬇️

Cohesin relocation from sites of chromosomal loading to places of convergent transcription

Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis

Condensin-dependent rDNA decatenation introduces a temporal pattern to chromosome segregation

Cornelia de Lange syndrome and molecular implications of the cohesin complex: Abstracts from the 7th biennial scientific and educational symposium 2016.

Cornelia de Lange syndrome: further delineation of phenotype, cohesin biology and educational focus, 5th Biennial Scientific and Educational Symposium abstracts

Csm3, Tof1, and Mrc1 form a heterotrimeric mediator complex that associates with DNA replication forks

Ctf4 coordinates the progression of helicase and DNA polymerase alpha.

DBTMEE: a database of transcriptome in mouse early embryos

DBTSS/DBKERO for integrated analysis of transcriptional regulation

DROMPA: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data ⬇️

Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior

Different requirements for the association of ATR-ATRIP and 9-1-1 to the stalled replication forks

Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis

Displacement and re-accumulation of centromeric cohesin during transient pre-anaphase centromere splitting

Dissecting the first and the second meiotic divisions using a marker-less drug-hypersensitive fission yeast.

During replication stress, non-SMC element 5 (NSE5) is required for Smc5/6 protein complex functionality at stalled forks

Elevation of insulin-like growth factor binding protein-2 level in Pallister-Killian syndrome: implications for the postnatal growth retardation phenotype

Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype

Establishment of sister chromatid cohesion at the S. cerevisiae replication fork

Eukaryotic replisome components cooperate to process histones during chromosome replication.

Evidence that Loading of Cohesin Onto Chromosomes Involves Opening of Its SMC Hinge

Exome Sequencing Identification of EP300 Mutation in a Proband with Coloboma and Imperforate Anus: Possible Expansion of the Phenotypic Spectrum of Rubinstein-Taybi Syndrome

Exome sequencing-based identification of mutations in non-syndromic genes among individuals with apparently syndromic features

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex

Genome-wide DNA methylation analysis in cohesin mutant human cell lines

Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor

Genome-wide expression analysis of genes affected by amino acid sensor Ssy1p in Saccharomyces cerevisiae

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters

Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast

Genomic approach for the understanding of dynamic aspect of chromosome behavior

Glucose-dependent cell size is regulated by a G protein-coupled receptor system in yeast Saccharomyces cerevisiae

HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle

Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis

Hot debate in hot springs: Report on the second international meeting on SMC proteins

Identification and characterization of rns4/vps32 mutation in the RNase T1 expression-sensitive strain of Saccharomyces cerevisiae: Evidence for altered ambient response resulting in transportation of the secretory protein to vacuoles

Identification of a variant-specific phosphorylation of TH2A during spermiogenesis

Identification of cis-acting sites for condensin loading onto budding yeast chromosomes

Importance of Polη for damage-induced cohesion reveals differential regulation of cohesion establishment at the break site and genome-wide ⬇️

Inactivation of SMC2 shows a synergistic lethal response in MYCN-amplified neuroblastoma cells

Involvement of RAD9-dependent damage checkpoint control in arrest of cell cycle, induction of cell death, and chromosome instability caused by defects in origin recognition complex in Saccharomyces cerevisiae

Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment

Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance

Mapping of histone-binding sites in histone replacement-completed spermatozoa

Meiotic cohesins modulate chromosome compaction during meiotic prophase in fission yeast

Meiotic recombination-related DNA synthesis and its implications for cross-over and non-cross-over recombinant formation

Monopolar attachment of sister kinetochores at meiosis I requires casein kinase 1.

Mosaic ratio quantification of isochromosome 12p in Pallister-Killian syndrome using droplet digital PCR.

Mrc1 and DNA polymerase epsilon function together in linking DNA replication and the S phase checkpoint

Mre11 mediates gene regulation in yeast spore development

Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast