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Items: 1 to 50 of 207

1.

Missense Mutations in NKAP Cause a Disorder of Transcriptional Regulation Characterized by Marfanoid Habitus and Cognitive Impairment.

Fiordaliso SK, Iwata-Otsubo A, Ritter AL, Quesnel-Vallières M, Fujiki K, Nishi E, Hancarova M, Miyake N, Morton JEV, Lee S, Hackmann K, Bando M, Masuda K, Nakato R, Arakawa M, Bhoj E, Li D, Hakonarson H, Takeda R, Harr M, Keena B, Zackai EH, Okamoto N, Mizuno S, Ko JM, Valachova A, Prchalova D, Vlckova M, Pippucci T, Seiler C, Choi M, Matsumoto N, Di Donato N, Barash Y, Sedlacek Z, Shirahige K, Izumi K.

Am J Hum Genet. 2019 Sep 30. pii: S0002-9297(19)30348-9. doi: 10.1016/j.ajhg.2019.09.009. [Epub ahead of print]

PMID:
31587868
2.

Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken.

Yamashita S, Kataoka K, Yamamoto H, Kato T, Hara S, Yamaguchi K, Renard-Guillet C, Katou Y, Shirahige K, Ochi H, Ogino H, Uchida T, Inui M, Takada S, Shigenobu S, Asahara H.

Sci Rep. 2019 Aug 29;9(1):12560. doi: 10.1038/s41598-019-48979-4.

3.

Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation.

Kanatsu-Shinohara M, Yamamoto T, Toh H, Kazuki Y, Kazuki K, Imoto J, Ikeo K, Oshima M, Shirahige K, Iwama A, Nabeshima Y, Sasaki H, Shinohara T.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16404-16409. doi: 10.1073/pnas.1904980116. Epub 2019 Jul 29.

PMID:
31358627
4.

The novel lncRNA CALIC upregulates AXL to promote colon cancer metastasis.

Kawasaki Y, Miyamoto M, Oda T, Matsumura K, Negishi L, Nakato R, Suda S, Yokota N, Shirahige K, Akiyama T.

EMBO Rep. 2019 Aug;20(8):e47052. doi: 10.15252/embr.201847052. Epub 2019 Jul 29.

PMID:
31353791
5.

Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks.

Hiraga SI, Monerawela C, Katou Y, Shaw S, Clark KR, Shirahige K, Donaldson AD.

EMBO Rep. 2019 Jul;20(7):e48152. doi: 10.15252/embr.201948152. Epub 2019 Jun 26. No abstract available.

6.

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

Makino Y, Jensen NH, Yokota N, Rossner MJ, Akiyama H, Shirahige K, Okada Y.

Sci Rep. 2019 Apr 15;9(1):6063. doi: 10.1038/s41598-019-42578-z.

7.

Cornelia de Lange syndrome, related disorders, and the Cohesin complex: Abstracts from the 8th biennial scientific and educational symposium 2018.

Kline AD, Krantz ID, Bando M, Shirahige K, Chea S, Sakata T, Rao S, Dorsett D, Singh VP, Gerton JL, Horsfield JA, Calof AL, Katz O, Grados M, Raible S, Barañano K, Lyon G, Musio A, Carrico CS, Clemens DK, Caudill P, Massa V, McGill BE, Dommestrup A, O'Connor J, Haaland RE.

Am J Med Genet A. 2019 Jun;179(6):1080-1090. doi: 10.1002/ajmg.a.61108. Epub 2019 Mar 15.

PMID:
30874362
8.

Cux2 refines the forelimb field by controlling expression of Raldh2 and Hox genes.

Ueda S, Cordeiro IR, Moriyama Y, Nishimori C, Kai KI, Yu R, Nakato R, Shirahige K, Tanaka M.

Biol Open. 2019 Feb 1;8(2). pii: bio040584. doi: 10.1242/bio.040584.

9.

Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion.

Matsuda T, Irie T, Katsurabayashi S, Hayashi Y, Nagai T, Hamazaki N, Adefuin AMD, Miura F, Ito T, Kimura H, Shirahige K, Takeda T, Iwasaki K, Imamura T, Nakashima K.

Neuron. 2019 Feb 6;101(3):472-485.e7. doi: 10.1016/j.neuron.2018.12.010. Epub 2019 Jan 9.

PMID:
30638745
10.

A chromatin integration labelling method enables epigenomic profiling with lower input.

Harada A, Maehara K, Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, Kimura H, Ohkawa Y.

Nat Cell Biol. 2019 Feb;21(2):287-296. doi: 10.1038/s41556-018-0248-3. Epub 2018 Dec 10.

PMID:
30532068
11.

Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation.

Gali VK, Dickerson D, Katou Y, Fujiki K, Shirahige K, Owen-Hughes T, Kubota T, Donaldson AD.

PLoS Genet. 2018 Nov 12;14(11):e1007783. doi: 10.1371/journal.pgen.1007783. eCollection 2018 Nov.

12.

Maternal Protein Restriction Alters the Renal Ptger1 DNA Methylation State in SHRSP Offspring.

Miyoshi M, Sato M, Saito K, Otani L, Shirahige K, Miura F, Ito T, Jia H, Kato H.

Nutrients. 2018 Oct 5;10(10). pii: E1436. doi: 10.3390/nu10101436.

13.

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

Yoshida K, Muratani M, Araki H, Miura F, Suzuki T, Dohmae N, Katou Y, Shirahige K, Ito T, Ishii S.

Nat Commun. 2018 Sep 24;9(1):3885. doi: 10.1038/s41467-018-06243-9.

14.

Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks.

Hiraga SI, Monerawela C, Katou Y, Shaw S, Clark KR, Shirahige K, Donaldson AD.

EMBO Rep. 2018 Sep;19(9). pii: e46222. doi: 10.15252/embr.201846222. Epub 2018 Aug 13. Erratum in: EMBO Rep. 2019 Jul;20(7):e48152.

15.

Temporal Regulation of ESCO2 Degradation by the MCM Complex, the CUL4-DDB1-VPRBP Complex, and the Anaphase-Promoting Complex.

Minamino M, Tei S, Negishi L, Kanemaki MT, Yoshimura A, Sutani T, Bando M, Shirahige K.

Curr Biol. 2018 Aug 20;28(16):2665-2672.e5. doi: 10.1016/j.cub.2018.06.037. Epub 2018 Aug 9.

16.

Re-evaluating the Localization of Sperm-Retained Histones Revealed the Modification-Dependent Accumulation in Specific Genome Regions.

Yamaguchi K, Hada M, Fukuda Y, Inoue E, Makino Y, Katou Y, Shirahige K, Okada Y.

Cell Rep. 2018 Jun 26;23(13):3920-3932. doi: 10.1016/j.celrep.2018.05.094.

17.

Somatic copy number alterations have prognostic impact in patients with ovarian clear cell carcinoma.

Morikawa A, Hayashi T, Kobayashi M, Kato Y, Shirahige K, Itoh T, Urashima M, Okamoto A, Akiyama T.

Oncol Rep. 2018 Jul;40(1):309-318. doi: 10.3892/or.2018.6419. Epub 2018 May 8.

PMID:
29749539
18.

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

Nakato R, Shirahige K.

Bioinformatics. 2018 Jul 15;34(14):2356-2363. doi: 10.1093/bioinformatics/bty137.

PMID:
29528371
19.

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

Kuroki S, Nakai Y, Maeda R, Okashita N, Akiyoshi M, Yamaguchi Y, Kitano S, Miyachi H, Nakato R, Ichiyanagi K, Shirahige K, Kimura H, Shinkai Y, Tachibana M.

Stem Cell Reports. 2018 Apr 10;10(4):1340-1354. doi: 10.1016/j.stemcr.2018.02.002. Epub 2018 Mar 8.

20.

Population structure of Escherichia coli O26 : H11 with recent and repeated stx2 acquisition in multiple lineages.

Ogura Y, Gotoh Y, Itoh T, Sato MP, Seto K, Yoshino S, Isobe J, Etoh Y, Kurogi M, Kimata K, Maeda E, Piérard D, Kusumoto M, Akiba M, Tominaga K, Kirino Y, Kato Y, Shirahige K, Ooka T, Ishijima N, Lee KI, Iyoda S, Mainil JG, Hayashi T.

Microb Genom. 2017 Nov;3(11). doi: 10.1099/mgen.0.000141.

21.

Errata: Functional annotation of chemical libraries across diverse biological processes.

Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.

Nat Chem Biol. 2017 Nov 21;13(12):1286. doi: 10.1038/nchembio1217-1286a.

PMID:
29161247
22.

Errata: Functional annotation of chemical libraries across diverse biological processes.

Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.

Nat Chem Biol. 2017 Nov 21;13(12):1286. doi: 10.1038/nchembio1217-1286b.

PMID:
29161244
23.

The HSF1-PARP13-PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis.

Fujimoto M, Takii R, Takaki E, Katiyar A, Nakato R, Shirahige K, Nakai A.

Nat Commun. 2017 Nov 21;8(1):1638. doi: 10.1038/s41467-017-01807-7.

24.

Cohesin Ubiquitylation and Mobilization Facilitate Stalled Replication Fork Dynamics.

Frattini C, Villa-Hernández S, Pellicanò G, Jossen R, Katou Y, Shirahige K, Bermejo R.

Mol Cell. 2017 Nov 16;68(4):758-772.e4. doi: 10.1016/j.molcel.2017.10.012. Epub 2017 Nov 9.

25.

DBTSS/DBKERO for integrated analysis of transcriptional regulation.

Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S, Nakai K, Suzuki Y.

Nucleic Acids Res. 2018 Jan 4;46(D1):D229-D238. doi: 10.1093/nar/gkx1001.

26.

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

Hirano T, Nishiyama T, Shirahige K.

Genes Cells. 2017 Nov;22(11):934-938. doi: 10.1111/gtc.12539. Epub 2017 Oct 25.

27.

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

Nakato R, Shirahige K.

Methods Mol Biol. 2018;1672:631-643. doi: 10.1007/978-1-4939-7306-4_41.

PMID:
29043652
28.

interleukin-11 induces and maintains progenitors of different cell lineages during Xenopus tadpole tail regeneration.

Tsujioka H, Kunieda T, Katou Y, Shirahige K, Fukazawa T, Kubo T.

Nat Commun. 2017 Sep 8;8(1):495. doi: 10.1038/s41467-017-00594-5.

29.

Functional annotation of chemical libraries across diverse biological processes.

Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H, Gebre AA, Kubo K, Torres NP, LeBlanc MA, Andrusiak K, Okamoto R, Yoshimura M, DeRango-Adem E, van Leeuwen J, Shirahige K, Baryshnikova A, Brown GW, Hirano H, Costanzo M, Andrews B, Ohya Y, Osada H, Yoshida M, Myers CL, Boone C.

Nat Chem Biol. 2017 Sep;13(9):982-993. doi: 10.1038/nchembio.2436. Epub 2017 Jul 24. Erratum in: Nat Chem Biol. 2017 Nov 21;13(12 ):1286. Nat Chem Biol. 2017 Nov 21;13(12 ):1286.

30.

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

Koui Y, Kido T, Ito T, Oyama H, Chen SW, Katou Y, Shirahige K, Miyajima A.

Stem Cell Reports. 2017 Aug 8;9(2):490-498. doi: 10.1016/j.stemcr.2017.06.010. Epub 2017 Jul 27.

31.

MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress.

Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7671-7676. doi: 10.1073/pnas.1620208114. Epub 2017 Jul 3.

32.

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

Kagami A, Sakuno T, Yamagishi Y, Ishiguro T, Tsukahara T, Shirahige K, Tanaka K, Watanabe Y.

EMBO Rep. 2017 Jul;18(7):1263. doi: 10.15252/embr.201744401. No abstract available.

33.

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex.

Sakai A, Nakato R, Ling Y, Hou X, Hara N, Iijima T, Yanagawa Y, Kuwano R, Okuda S, Shirahige K, Sugiyama S.

Front Neurosci. 2017 May 31;11:307. doi: 10.3389/fnins.2017.00307. eCollection 2017.

34.

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

Zhang J, Shi D, Li X, Ding L, Tang J, Liu C, Shirahige K, Cao Q, Lou H.

EMBO Rep. 2017 Aug;18(8):1294-1305. doi: 10.15252/embr.201643807. Epub 2017 Jun 14.

35.

Two Components of Aversive Memory in Drosophila, Anesthesia-Sensitive and Anesthesia-Resistant Memory, Require Distinct Domains Within the Rgk1 Small GTPase.

Murakami S, Minami-Ohtsubo M, Nakato R, Shirahige K, Tabata T.

J Neurosci. 2017 May 31;37(22):5496-5510. doi: 10.1523/JNEUROSCI.3648-16.2017. Epub 2017 Apr 17.

36.

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

Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T.

J Exp Med. 2017 May 1;214(5):1431-1452. doi: 10.1084/jem.20161517. Epub 2017 Apr 13.

37.

Identification of a variant-specific phosphorylation of TH2A during spermiogenesis.

Hada M, Masuda K, Yamaguchi K, Shirahige K, Okada Y.

Sci Rep. 2017 Apr 7;7:46228. doi: 10.1038/srep46228.

38.

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

Kline AD, Krantz ID, Deardorff MA, Shirahige K, Dorsett D, Gerton JL, Wu M, Mehta D, Mills JA, Carrico CS, Noon S, Herrera PS, Horsfield JA, Bettale C, Morgan J, Huisman SA, Moss J, McCleery J, Grados M, Hansen BD, Srivastava S, Taylor-Snell E, Kerr LM, Katz O, Calof AL, Musio A, Egense A, Haaland RE.

Am J Med Genet A. 2017 May;173(5):1172-1185. doi: 10.1002/ajmg.a.38161. Epub 2017 Feb 12.

39.

ChIP-seq Analysis of Condensin Complex in Cultured Mammalian Cells.

Sakata T, Shirahige K, Sutani T.

Methods Mol Biol. 2017;1515:257-271.

PMID:
27797085
40.

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

Taniue K, Kurimoto A, Takeda Y, Nagashima T, Okada-Hatakeyama M, Katou Y, Shirahige K, Akiyama T.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):12739-12744. doi: 10.1073/pnas.1605938113. Epub 2016 Oct 21.

41.

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

Abe T, Kawasumi R, Arakawa H, Hori T, Shirahige K, Losada A, Fukagawa T, Branzei D.

Oncotarget. 2016 Oct 18;7(42):67934-67947. doi: 10.18632/oncotarget.11982.

42.

MYU, a Target lncRNA for Wnt/c-Myc Signaling, Mediates Induction of CDK6 to Promote Cell Cycle Progression.

Kawasaki Y, Komiya M, Matsumura K, Negishi L, Suda S, Okuno M, Yokota N, Osada T, Nagashima T, Hiyoshi M, Okada-Hatakeyama M, Kitayama J, Shirahige K, Akiyama T.

Cell Rep. 2016 Sep 6;16(10):2554-2564. doi: 10.1016/j.celrep.2016.08.015. Epub 2016 Aug 25.

43.

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

Nishi E, Masuda K, Arakawa M, Kawame H, Kosho T, Kitahara M, Kubota N, Hidaka E, Katoh Y, Shirahige K, Izumi K.

Am J Med Genet A. 2016 Nov;170(11):2889-2894. doi: 10.1002/ajmg.a.37826. Epub 2016 Aug 26.

PMID:
27566442
44.

Attaching Accessory Devices to the Replisome.

Sutani T, Shirahige K.

Mol Cell. 2016 Aug 4;63(3):347-8. doi: 10.1016/j.molcel.2016.07.017.

45.

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

Izumi K, Brett M, Nishi E, Drunat S, Tan ES, Fujiki K, Lebon S, Cham B, Masuda K, Arakawa M, Jacquinet A, Yamazumi Y, Chen ST, Verloes A, Okada Y, Katou Y, Nakamura T, Akiyama T, Gressens P, Foo R, Passemard S, Tan EC, El Ghouzzi V, Shirahige K.

Am J Hum Genet. 2016 Aug 4;99(2):451-9. doi: 10.1016/j.ajhg.2016.06.011. Epub 2016 Jul 28.

46.

Physical Association of Saccharomyces cerevisiae Polo-like Kinase Cdc5 with Chromosomal Cohesin Facilitates DNA Damage Response.

Pakchuen S, Ishibashi M, Takakusagi E, Shirahige K, Sutani T.

J Biol Chem. 2016 Aug 12;291(33):17228-46. doi: 10.1074/jbc.M116.727438. Epub 2016 Jun 20.

47.

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

Fujiki K, Shirahige K, Kaur M, Deardorff MA, Conlin LK, Krantz ID, Izumi K.

Mol Genet Genomic Med. 2016 Jan 20;4(3):257-61. doi: 10.1002/mgg3.200. eCollection 2016 May.

48.

DNMT3A R882 mutants interact with polycomb proteins to block haematopoietic stem and leukaemic cell differentiation.

Koya J, Kataoka K, Sato T, Bando M, Kato Y, Tsuruta-Kishino T, Kobayashi H, Narukawa K, Miyoshi H, Shirahige K, Kurokawa M.

Nat Commun. 2016 Mar 24;7:10924. doi: 10.1038/ncomms10924.

49.

Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages.

Yoshida K, Renard-Guillet C, Inoue K, Shirahige K, Okada-Hatakeyama M, Ishii S.

Genom Data. 2015 Dec 1;7:90-1. doi: 10.1016/j.gdata.2015.11.028. eCollection 2016 Mar.

50.

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.

Nakato R, Shirahige K.

Brief Bioinform. 2017 Mar 1;18(2):279-290. doi: 10.1093/bib/bbw023. Review.

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