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Items: 43

1.

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing.

Shao W, Alcantara SG, Zeitlinger J.

Elife. 2019 Apr 25;8. pii: e41461. doi: 10.7554/eLife.41461.

2.

Author Correction: Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.

Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L.

Cell Res. 2018 Oct;28(10):1042. doi: 10.1038/s41422-018-0083-x.

3.

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing.

Miller DE, Staber C, Zeitlinger J, Hawley RS.

G3 (Bethesda). 2018 Oct 3;8(10):3131-3141. doi: 10.1534/g3.118.200160.

4.

Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion.

Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L.

Cell Res. 2018 Sep;28(9):904-917. doi: 10.1038/s41422-018-0072-0. Epub 2018 Jul 31. Erratum in: Cell Res. 2018 Aug 27;:.

PMID:
30065315
5.

Capicua controls Toll/IL-1 signaling targets independently of RTK regulation.

Papagianni A, Forés M, Shao W, He S, Koenecke N, Andreu MJ, Samper N, Paroush Z, González-Crespo S, Zeitlinger J, Jiménez G.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1807-1812. doi: 10.1073/pnas.1713930115. Epub 2018 Feb 5.

6.

Hoxa1 targets signaling pathways during neural differentiation of ES cells and mouse embryogenesis.

De Kumar B, Parker HJ, Paulson A, Parrish ME, Zeitlinger J, Krumlauf R.

Dev Biol. 2017 Dec 1;432(1):151-164. doi: 10.1016/j.ydbio.2017.09.033. Epub 2017 Oct 2.

7.

Hippo Reprograms the Transcriptional Response to Ras Signaling.

Pascual J, Jacobs J, Sansores-Garcia L, Natarajan M, Zeitlinger J, Aerts S, Halder G, Hamaratoglu F.

Dev Cell. 2017 Sep 25;42(6):667-680.e4. doi: 10.1016/j.devcel.2017.08.013.

8.

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.

De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R.

Genome Res. 2017 Sep;27(9):1501-1512. doi: 10.1101/gr.219386.116. Epub 2017 Aug 7.

9.

Paused RNA polymerase II inhibits new transcriptional initiation.

Shao W, Zeitlinger J.

Nat Genet. 2017 Jul;49(7):1045-1051. doi: 10.1038/ng.3867. Epub 2017 May 15.

PMID:
28504701
10.

Drosophila poised enhancers are generated during tissue patterning with the help of repression.

Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J.

Genome Res. 2017 Jan;27(1):64-74. doi: 10.1101/gr.209486.116. Epub 2016 Nov 14.

11.

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis.

Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J.

Genome Biol. 2016 Sep 27;17(1):196.

12.

Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis: A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015.

Arnosti DN, Fay JC, Zeitlinger J.

Bioessays. 2015 Oct;37(10):1042-4. doi: 10.1002/bies.201500106. Epub 2015 Sep 10.

PMID:
26354485
13.

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.

Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C.

Genome Res. 2015 Nov;25(11):1703-14. doi: 10.1101/gr.192542.115. Epub 2015 Sep 2.

14.

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.

He Q, Johnston J, Zeitlinger J.

Nat Biotechnol. 2015 Apr;33(4):395-401. doi: 10.1038/nbt.3121. Epub 2015 Mar 9.

15.

TRF2, but not TBP, mediates the transcription of ribosomal protein genes.

Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT.

Genes Dev. 2014 Jul 15;28(14):1550-5. doi: 10.1101/gad.245662.114. Epub 2014 Jun 23.

16.

RNA polymerase II pausing during development.

Gaertner B, Zeitlinger J.

Development. 2014 Mar;141(6):1179-83. doi: 10.1242/dev.088492. Review.

17.

Molecular evolution of the Yap/Yorkie proto-oncogene and elucidation of its core transcriptional program.

Ikmi A, Gaertner B, Seidel C, Srivastava M, Zeitlinger J, Gibson MC.

Mol Biol Evol. 2014 Jun;31(6):1375-90. doi: 10.1093/molbev/msu071. Epub 2014 Feb 8.

18.

Identification of transcription factor binding sites from ChIP-seq data at high resolution.

Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A.

Bioinformatics. 2013 Nov 1;29(21):2705-13. doi: 10.1093/bioinformatics/btt470. Epub 2013 Aug 24.

19.

A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J.

Elife. 2013 Aug 13;2:e00861. doi: 10.7554/eLife.00861.

20.

Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.

Lagha M, Bothma JP, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine MS.

Cell. 2013 May 23;153(5):976-87. doi: 10.1016/j.cell.2013.04.045.

21.

Poised RNA polymerase II changes over developmental time and prepares genes for future expression.

Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J.

Cell Rep. 2012 Dec 27;2(6):1670-83. doi: 10.1016/j.celrep.2012.11.024. Epub 2012 Dec 20.

22.

A computational pipeline for comparative ChIP-seq analyses.

Bardet AF, He Q, Zeitlinger J, Stark A.

Nat Protoc. 2011 Dec 15;7(1):45-61. doi: 10.1038/nprot.2011.420.

PMID:
22179591
23.

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.

He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J.

Nat Genet. 2011 May;43(5):414-20. doi: 10.1038/ng.808. Epub 2011 Apr 10.

PMID:
21478888
24.

Developmental gene regulation in the era of genomics.

Zeitlinger J, Stark A.

Dev Biol. 2010 Mar 15;339(2):230-9. doi: 10.1016/j.ydbio.2009.12.039. Epub 2010 Jan 4. Review.

25.

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.

Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS.

Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7762-7. doi: 10.1073/pnas.0802406105. Epub 2008 May 27.

26.

RNA polymerase is poised for activation across the genome.

Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K.

Nat Genet. 2007 Dec;39(12):1507-11. Epub 2007 Nov 11.

27.

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.

Zeitlinger J, Stark A, Kellis M, Hong JW, Nechaev S, Adelman K, Levine M, Young RA.

Nat Genet. 2007 Dec;39(12):1512-6. Epub 2007 Nov 11.

28.

Connecting up the pathways in Drosophila development.

Riesgo-Escovar JR, Hafen E, Hou XS, Goldstein ES, Perrimon N, Glise B, Noselli S, Kockel L, Zeitlinger J, Staszewski LM, Mlodzik M, Bohmann D.

Trends Cell Biol. 1997 Nov;7(11):421-2. No abstract available.

PMID:
17708993
29.

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.

Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M.

Genes Dev. 2007 Feb 15;21(4):385-90.

30.

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID:
16900145
31.

Activated signal transduction kinases frequently occupy target genes.

Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA.

Science. 2006 Jul 28;313(5786):533-6.

32.

Polycomb complexes repress developmental regulators in murine embryonic stem cells.

Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R.

Nature. 2006 May 18;441(7091):349-53. Epub 2006 Apr 19.

PMID:
16625203
33.

Genome-wide map of nucleosome acetylation and methylation in yeast.

Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, Young RA.

Cell. 2005 Aug 26;122(4):517-27.

34.

Transcriptional regulatory code of a eukaryotic genome.

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA.

Nature. 2004 Sep 2;431(7004):99-104.

35.

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

Zeitlinger J, Simon I, Harbison CT, Hannett NM, Volkert TL, Fink GR, Young RA.

Cell. 2003 May 2;113(3):395-404.

36.

Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.

37.

Serial regulation of transcriptional regulators in the yeast cell cycle.

Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, Wyrick JJ, Zeitlinger J, Gifford DK, Jaakkola TS, Young RA.

Cell. 2001 Sep 21;106(6):697-708.

38.

Parthenogenetic flatworms have more symbionts than their coexisting, sexual conspecifics, but does this support the Red Queen?

Michiels NK, Beukeboom LW, Pongratz N, Zeitlinger J.

J Evol Biol. 2001 Jan 8;14(1):110-119. doi: 10.1046/j.1420-9101.2001.00249.x.

39.

Genome-wide location and function of DNA binding proteins.

Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA.

Science. 2000 Dec 22;290(5500):2306-9.

40.

Thorax closure in Drosophila: involvement of Fos and the JNK pathway.

Zeitlinger J, Bohmann D.

Development. 1999 Sep;126(17):3947-56.

41.

Defective dorsal closure and loss of epidermal decapentaplegic expression in Drosophila fos mutants.

Zeitlinger J, Kockel L, Peverali FA, Jackson DB, Mlodzik M, Bohmann D.

EMBO J. 1997 Dec 15;16(24):7393-401.

42.

Jun in Drosophila development: redundant and nonredundant functions and regulation by two MAPK signal transduction pathways.

Kockel L, Zeitlinger J, Staszewski LM, Mlodzik M, Bohmann D.

Genes Dev. 1997 Jul 1;11(13):1748-58. Erratum in: Genes Dev 1998 Feb 1;12(3):447.

43.

Endogenous retinoids in the zebrafish embryo and adult.

Costaridis P, Horton C, Zeitlinger J, Holder N, Maden M.

Dev Dyn. 1996 Jan;205(1):41-51.

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