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Items: 1 to 50 of 100

1.

Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP.

Zucconi BE, Makofske JL, Meyers DJ, Hwang Y, Wu M, Kuroda MI, Cole PA.

Biochemistry. 2019 Apr 23;58(16):2133-2143. doi: 10.1021/acs.biochem.9b00160. Epub 2019 Apr 11.

PMID:
30924641
2.

Sex-specific phenotypes of histone H4 point mutants establish dosage compensation as the critical function of H4K16 acetylation in Drosophila.

Copur Ö, Gorchakov A, Finkl K, Kuroda MI, Müller J.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):13336-13341. doi: 10.1073/pnas.1817274115. Epub 2018 Dec 10.

3.

"Z4" Complex Member Fusions in NUT Carcinoma: Implications for a Novel Oncogenic Mechanism.

Shiota H, Elya JE, Alekseyenko AA, Chou PM, Gorman SA, Barbash O, Becht K, Danga K, Kuroda MI, Nardi V, French CA.

Mol Cancer Res. 2018 Dec;16(12):1826-1833. doi: 10.1158/1541-7786.MCR-18-0474. Epub 2018 Aug 23.

PMID:
30139738
4.

Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila.

Kang H, Jung YL, McElroy KA, Zee BM, Wallace HA, Woolnough JL, Park PJ, Kuroda MI.

Genes Dev. 2017 Oct 1;31(19):1988-2002. doi: 10.1101/gad.305987.117. Epub 2017 Oct 25.

5.

Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma.

Alekseyenko AA, Walsh EM, Zee BM, Pakozdi T, Hsi P, Lemieux ME, Dal Cin P, Ince TA, Kharchenko PV, Kuroda MI, French CA.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4184-E4192. doi: 10.1073/pnas.1702086114. Epub 2017 May 8.

6.

upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks.

McElroy KA, Jung YL, Zee BM, Wang CI, Park PJ, Kuroda MI.

G3 (Bethesda). 2017 Feb 9;7(2):625-635. doi: 10.1534/g3.116.037788.

7.

Dosage Compensation in Drosophila-a Model for the Coordinate Regulation of Transcription.

Kuroda MI, Hilfiker A, Lucchesi JC.

Genetics. 2016 Oct;204(2):435-450. Review.

8.

The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns.

Zee BM, Dibona AB, Alekseyenko AA, French CA, Kuroda MI.

PLoS One. 2016 Oct 3;11(10):e0163820. doi: 10.1371/journal.pone.0163820. eCollection 2016.

9.

Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains.

Jung YL, Kang H, Park PJ, Kuroda MI.

Fly (Austin). 2015;9(4):178-82. doi: 10.1080/19336934.2016.1151988. No abstract available.

10.

Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry.

Zee BM, Alekseyenko AA, McElroy KA, Kuroda MI.

Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1784-9. doi: 10.1073/pnas.1522750113. Epub 2016 Feb 1.

11.

The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains.

Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA.

Genes Dev. 2015 Jul 15;29(14):1507-23. doi: 10.1101/gad.267583.115.

12.

Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila.

Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI.

Genes Dev. 2015 Jun 1;29(11):1136-50. doi: 10.1101/gad.260562.115.

13.

Dosage compensation in Drosophila.

Lucchesi JC, Kuroda MI.

Cold Spring Harb Perspect Biol. 2015 May 1;7(5). pii: a019398. doi: 10.1101/cshperspect.a019398. Review.

14.

BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes.

Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko PV, Kuroda MI.

Curr Protoc Mol Biol. 2015 Jan 5;109:21.30.1-32. doi: 10.1002/0471142727.mb2130s109.

15.

Comparative analysis of metazoan chromatin organization.

Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ.

Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415.

16.

Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs.

Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI.

Genes Dev. 2014 Jul 1;28(13):1445-60. doi: 10.1101/gad.241950.114.

17.

Are we there yet? Initial targeting of the Male-Specific Lethal and Polycomb group chromatin complexes in Drosophila.

McElroy KA, Kang H, Kuroda MI.

Open Biol. 2014 Mar 26;4:140006. doi: 10.1098/rsob.140006. Review.

18.

Impact of sequencing depth in ChIP-seq experiments.

Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.

Nucleic Acids Res. 2014 May;42(9):e74. doi: 10.1093/nar/gku178. Epub 2014 Mar 5.

19.

Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification.

Alekseyenko AA, Gorchakov AA, Kharchenko PV, Kuroda MI.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2488-93. doi: 10.1073/pnas.1400648111. Epub 2014 Feb 3.

20.

Transcriptional control of a whole chromosome: emerging models for dosage compensation.

Ferrari F, Alekseyenko AA, Park PJ, Kuroda MI.

Nat Struct Mol Biol. 2014 Feb;21(2):118-25. doi: 10.1038/nsmb.2763. Epub 2014 Feb 5. Review.

21.

"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.

Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI.

Cell Rep. 2013 Nov 14;5(3):629-36. doi: 10.1016/j.celrep.2013.09.037. Epub 2013 Oct 31. Erratum in: Cell Rep. 2013 Nov 27;5(4):1157.

22.

Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila.

Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MI.

Genes Dev. 2013 Apr 15;27(8):853-8. doi: 10.1101/gad.215426.113.

23.

Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters".

Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ.

Science. 2013 Apr 19;340(6130):273. doi: 10.1126/science.1231815.

24.

Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila.

Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI.

Nat Struct Mol Biol. 2013 Feb;20(2):202-9. doi: 10.1038/nsmb.2477. Epub 2013 Jan 6.

25.

Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.

Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC.

PLoS Genet. 2012 Sep;8(9):e1002954. doi: 10.1371/journal.pgen.1002954. Epub 2012 Sep 20.

26.

A genome-wide screen identifies genes that affect somatic homolog pairing in Drosophila.

Bateman JR, Larschan E, D'Souza R, Marshall LS, Dempsey KE, Johnson JE, Mellone BG, Kuroda MI.

G3 (Bethesda). 2012 Jul;2(7):731-40. doi: 10.1534/g3.112.002840. Epub 2012 Jul 1.

27.

Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation.

Larschan E, Soruco MM, Lee OK, Peng S, Bishop E, Chery J, Goebel K, Feng J, Park PJ, Kuroda MI.

PLoS Genet. 2012;8(7):e1002830. doi: 10.1371/journal.pgen.1002830. Epub 2012 Jul 26.

28.

Nature and function of insulator protein binding sites in the Drosophila genome.

Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V.

Genome Res. 2012 Nov;22(11):2188-98. doi: 10.1101/gr.138156.112. Epub 2012 Jul 5. Erratum in: Genome Res. 2013 Feb;23(2):409.

29.

Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.

Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen GH, Pirrotta V, Kuroda MI, Park PJ.

PLoS Genet. 2012;8(4):e1002646. doi: 10.1371/journal.pgen.1002646. Epub 2012 Apr 26. Erratum in: PLoS Genet. 2014 Jan;10(1). doi: 10.1371/annotation/39c76721-c8e1-4d42-ae6b-33063ce207d2.

30.

The genomic binding sites of a noncoding RNA.

Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20497-502. doi: 10.1073/pnas.1113536108. Epub 2011 Dec 5.

31.

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.

Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI.

Nature. 2011 Mar 3;471(7336):115-8. doi: 10.1038/nature09757.

32.

Evidence of activity-specific, radial organization of mitotic chromosomes in Drosophila.

Strukov YG, Sural TH, Kuroda MI, Sedat JW.

PLoS Biol. 2011 Jan 11;9(1):e1000574. doi: 10.1371/journal.pbio.1000574.

33.

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ.

Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22.

34.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

35.

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.

Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH.

Genome Res. 2011 Feb;21(2):147-63. doi: 10.1101/gr.110098.110. Epub 2010 Dec 22.

36.

An assessment of histone-modification antibody quality.

Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD.

Nat Struct Mol Biol. 2011 Jan;18(1):91-3. doi: 10.1038/nsmb.1972. Epub 2010 Dec 5.

37.

Quantized correlation coefficient for measuring reproducibility of ChIP-chip data.

Peng S, Kuroda MI, Park PJ.

BMC Bioinformatics. 2010 Jul 27;11:399. doi: 10.1186/1471-2105-11-399.

38.

Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X.

Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI.

Genes Dev. 2009 Oct 1;23(19):2266-71. doi: 10.1101/gad.1840409.

39.

Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation.

Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI.

Nat Struct Mol Biol. 2009 Aug;16(8):825-32. doi: 10.1038/nsmb.1644. Epub 2009 Aug 2.

40.

Drosophila dosage compensation: a complex voyage to the X chromosome.

Gelbart ME, Kuroda MI.

Development. 2009 May;136(9):1399-410. doi: 10.1242/dev.029645. Review.

41.

The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome.

Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI.

Nat Struct Mol Biol. 2008 Dec;15(12):1318-25. doi: 10.1038/nsmb.1520. Epub 2008 Nov 23.

42.

A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome.

Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI.

Cell. 2008 Aug 22;134(4):599-609. doi: 10.1016/j.cell.2008.06.033.

43.

Regulation of histone H4 Lys16 acetylation by predicted alternative secondary structures in roX noncoding RNAs.

Park SW, Kuroda MI, Park Y.

Mol Cell Biol. 2008 Aug;28(16):4952-62. doi: 10.1128/MCB.00219-08. Epub 2008 Jun 9.

44.

MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism.

Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI.

Mol Cell. 2007 Oct 12;28(1):121-33.

45.

Normalization and experimental design for ChIP-chip data.

Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ.

BMC Bioinformatics. 2007 Jun 25;8:219.

46.

Regional control of chromatin organization by noncoding roX RNAs and the NURF remodeling complex in Drosophila melanogaster.

Bai X, Larschan E, Kwon SY, Badenhorst P, Kuroda MI.

Genetics. 2007 Jul;176(3):1491-9. Epub 2007 May 16.

47.

MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome.

Larschan E, Alekseyenko AA, Lai WR, Park PJ, Kuroda MI.

Cold Spring Harb Symp Quant Biol. 2006;71:385-94.

PMID:
17381321
48.

Noncoding RNAs and intranuclear positioning in monoallelic gene expression.

Yang PK, Kuroda MI.

Cell. 2007 Feb 23;128(4):777-86. Review.

49.

Variable splicing of non-coding roX2 RNAs influences targeting of MSL dosage compensation complexes in Drosophila.

Park Y, Oh H, Meller VH, Kuroda MI.

RNA Biol. 2005 Oct-Dec;2(4):157-64. Epub 2005 Dec 27.

PMID:
17114930
50.

High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome.

Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI.

Genes Dev. 2006 Apr 1;20(7):848-57. Epub 2006 Mar 17.

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