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Items: 1 to 50 of 51

1.

Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.

Gutiérrez MP, MacAlpine HK, MacAlpine DM.

Genome Res. 2019 Jul;29(7):1123-1133. doi: 10.1101/gr.243386.118. Epub 2019 Jun 19.

2.

Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats.

Foss EJ, Gatbonton-Schwager T, Thiesen AH, Taylor E, Soriano R, Lao U, MacAlpine DM, Bedalov A.

PLoS Genet. 2019 May 13;15(5):e1008138. doi: 10.1371/journal.pgen.1008138. eCollection 2019 May.

3.

Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila.

Armstrong RL, Penke TJR, Strahl BD, Matera AG, McKay DJ, MacAlpine DM, Duronio RJ.

Genome Res. 2018 Nov;28(11):1688-1700. doi: 10.1101/gr.239913.118. Epub 2018 Oct 2.

4.

Nucleosomes influence multiple steps during replication initiation.

Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP.

Elife. 2017 Mar 21;6. pii: e22512. doi: 10.7554/eLife.22512.

5.

Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization.

Wang Y, Khan A, Marks AB, Smith OK, Giri S, Lin YC, Creager R, MacAlpine DM, Prasanth KV, Aladjem MI, Prasanth SG.

Nucleic Acids Res. 2017 Mar 17;45(5):2490-2502. doi: 10.1093/nar/gkw1211.

6.

DNA replication origins-where do we begin?

Prioleau MN, MacAlpine DM.

Genes Dev. 2016 Aug 1;30(15):1683-97. doi: 10.1101/gad.285114.116. Review.

7.

ORChestrating the human DNA replication program.

MacAlpine DM.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9136-8. doi: 10.1073/pnas.1610336113. Epub 2016 Aug 5. No abstract available.

8.

Noncoding Transcription Is a Driving Force for Nucleosome Instability in spt16 Mutant Cells.

Feng J, Gan H, Eaton ML, Zhou H, Li S, Belsky JA, MacAlpine DM, Zhang Z, Li Q.

Mol Cell Biol. 2016 Jun 15;36(13):1856-67. doi: 10.1128/MCB.00152-16. Print 2016 Jul 1.

9.

Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila.

Li Y, Armstrong RL, Duronio RJ, MacAlpine DM.

Nucleic Acids Res. 2016 Sep 6;44(15):7204-18. doi: 10.1093/nar/gkw333. Epub 2016 Apr 29.

10.

Mcm2-7 Is an Active Player in the DNA Replication Checkpoint Signaling Cascade via Proposed Modulation of Its DNA Gate.

Tsai FL, Vijayraghavan S, Prinz J, MacAlpine HK, MacAlpine DM, Schwacha A.

Mol Cell Biol. 2015 Jun;35(12):2131-43. doi: 10.1128/MCB.01357-14. Epub 2015 Apr 13.

11.

SnapShot: Origins of DNA replication.

Creager RL, Li Y, MacAlpine DM.

Cell. 2015 Apr 9;161(2):418-418.e1. doi: 10.1016/j.cell.2015.03.043.

12.

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.

Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM.

Genes Dev. 2015 Jan 15;29(2):212-24. doi: 10.1101/gad.247924.114.

13.

Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle.

Powell SK, MacAlpine HK, Prinz JA, Li Y, Belsky JA, MacAlpine DM.

EMBO J. 2015 Feb 12;34(4):531-43. doi: 10.15252/embj.201488307. Epub 2015 Jan 2.

14.

Rare codons capacitate Kras-driven de novo tumorigenesis.

Pershing NL, Lampson BL, Belsky JA, Kaltenbrun E, MacAlpine DM, Counter CM.

J Clin Invest. 2015 Jan;125(1):222-33. doi: 10.1172/JCI77627. Epub 2014 Dec 1.

15.

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA.

Genome Res. 2014 Nov;24(11):1751-64. doi: 10.1101/gr.178335.114. Epub 2014 Sep 12.

16.

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.

17.

DNA replication and transcription programs respond to the same chromatin cues.

Lubelsky Y, Prinz JA, DeNapoli L, Li Y, Belsky JA, MacAlpine DM.

Genome Res. 2014 Jul;24(7):1102-14. doi: 10.1101/gr.160010.113.

18.

Chromatin and DNA replication.

MacAlpine DM, Almouzni G.

Cold Spring Harb Perspect Biol. 2013 Aug 1;5(8):a010207. doi: 10.1101/cshperspect.a010207. Review.

19.

Rare codons regulate KRas oncogenesis.

Lampson BL, Pershing NL, Prinz JA, Lacsina JR, Marzluff WF, Nicchitta CV, MacAlpine DM, Counter CM.

Curr Biol. 2013 Jan 7;23(1):70-5. doi: 10.1016/j.cub.2012.11.031. Epub 2012 Dec 13.

20.

Identification of E2F target genes that are rate limiting for dE2F1-dependent cell proliferation.

Herr A, Longworth M, Ji JY, Korenjak M, Macalpine DM, Dyson NJ.

Dev Dyn. 2012 Nov;241(11):1695-707. doi: 10.1002/dvdy.23857. Epub 2012 Sep 17.

21.

Genome-wide localization of replication factors.

Lubelsky Y, MacAlpine HK, MacAlpine DM.

Methods. 2012 Jun;57(2):187-95. doi: 10.1016/j.ymeth.2012.03.022. Epub 2012 Mar 24.

PMID:
22465279
22.

Developmental control of gene copy number by repression of replication initiation and fork progression.

Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL.

Genome Res. 2012 Jan;22(1):64-75. doi: 10.1101/gr.126003.111. Epub 2011 Nov 16.

23.

Epigenome characterization at single base-pair resolution.

Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318-23. doi: 10.1073/pnas.1110731108. Epub 2011 Oct 24.

24.

Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression.

Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, MacAlpine DM, Orr-Weaver TL.

Genes Dev. 2011 Jul 1;25(13):1384-98. doi: 10.1101/gad.2043111.

25.

A cis-regulatory map of the Drosophila genome.

Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP.

Nature. 2011 Mar 24;471(7339):527-31. doi: 10.1038/nature09990.

26.

Defining the replication program through the chromatin landscape.

Ding Q, MacAlpine DM.

Crit Rev Biochem Mol Biol. 2011 Apr;46(2):165-79. doi: 10.3109/10409238.2011.560139. Review.

27.

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.

28.

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.

29.

Chromatin signatures of the Drosophila replication program.

Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM.

Genome Res. 2011 Feb;21(2):164-74. doi: 10.1101/gr.116038.110. Epub 2010 Dec 22.

30.

Preferential re-replication of Drosophila heterochromatin in the absence of geminin.

Ding Q, MacAlpine DM.

PLoS Genet. 2010 Sep 9;6(9):e1001112. doi: 10.1371/journal.pgen.1001112.

31.

The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin.

Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA.

Genes Dev. 2010 Jul 1;24(13):1418-33. doi: 10.1101/gad.1906410.

32.

Palmoplantar keratoderma as the initial sign in a peripheral T-cell lymphoma.

Wohltmann WE, MacAlpine DM, Hodson DS.

Dermatol Online J. 2010 May 15;16(5):3.

PMID:
20492820
33.

Conserved nucleosome positioning defines replication origins.

Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM.

Genes Dev. 2010 Apr 15;24(8):748-53. doi: 10.1101/gad.1913210. Epub 2010 Mar 29.

34.

Expression in aneuploid Drosophila S2 cells.

Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, Macalpine DM, Oliver B.

PLoS Biol. 2010 Feb 23;8(2):e1000320. doi: 10.1371/journal.pbio.1000320.

35.

Co-orientation of replication and transcription preserves genome integrity.

Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD.

PLoS Genet. 2010 Jan 15;6(1):e1000810. doi: 10.1371/journal.pgen.1000810.

36.

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.

MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM.

Genome Res. 2010 Feb;20(2):201-11. doi: 10.1101/gr.097873.109. Epub 2009 Dec 7.

37.

Unlocking the secrets of the genome.

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium.

Nature. 2009 Jun 18;459(7249):927-30. doi: 10.1038/459927a. No abstract available.

38.

Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila.

Bell O, Wirbelauer C, Hild M, Scharf AN, Schwaiger M, MacAlpine DM, Zilbermann F, van Leeuwen F, Bell SP, Imhof A, Garza D, Peters AH, Schübeler D.

EMBO J. 2007 Dec 12;26(24):4974-84. Epub 2007 Nov 15.

39.

Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells.

Georlette D, Ahn S, MacAlpine DM, Cheung E, Lewis PW, Beall EL, Bell SP, Speed T, Manak JR, Botchan MR.

Genes Dev. 2007 Nov 15;21(22):2880-96. Epub 2007 Oct 31.

40.

Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation.

Park EA, Macalpine DM, Orr-Weaver TL.

Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16739-46. Epub 2007 Oct 11.

41.

Genome-wide analysis of re-replication reveals inhibitory controls that target multiple stages of replication initiation.

Tanny RE, MacAlpine DM, Blitzblau HG, Bell SP.

Mol Biol Cell. 2006 May;17(5):2415-23. Epub 2006 Mar 8.

42.

A genomic view of eukaryotic DNA replication.

MacAlpine DM, Bell SP.

Chromosome Res. 2005;13(3):309-26. Review.

PMID:
15868424
43.

Coordination of replication and transcription along a Drosophila chromosome.

MacAlpine DM, Rodríguez HK, Bell SP.

Genes Dev. 2004 Dec 15;18(24):3094-105.

44.

The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.

Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'Neill LP, Turner BM, Delrow J, Bell SP, Groudine M.

Genes Dev. 2004 Jun 1;18(11):1263-71.

45.

Visualization of replication initiation and elongation in Drosophila.

Claycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL.

J Cell Biol. 2002 Oct 28;159(2):225-36. Epub 2002 Oct 28.

46.

Replication and preferential inheritance of hypersuppressive petite mitochondrial DNA.

MacAlpine DM, Kolesar J, Okamoto K, Butow RA, Perlman PS.

EMBO J. 2001 Apr 2;20(7):1807-17.

48.

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