Zeitlinger Lab Publicaitons

Zeitlinger Lab Publications


Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S. Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A.*, Zeitlinger, J.* (2021) Base-resolution models of transcription factor binding reveal soft motif syntax. Nat Genet (epub ahead of print) * co-corresponding authors. Data | PAPER

Ramalingam, V., Natarajan, M., Johnson, J., Zeitlinger, J. (2021) TATA and paused promoters active in differentiated tissues have distinct expression characteristics. Mol Syst Biol. Feb 17; (2):e9866. Data | PAPER

Zeitlinger, J. (2020) Seven myths of how transcription factors read the cis-regulatory code. Curr Opin Syst Biol. Oct 23; 22-31. PAPER

Tao, F., Soffers, J., Hu, D., Chen, S., Gao, X., Zhang, Y., Zhao, C., Smith, S.E., Unruh, J.R., Zhang, D., Tsuchiya, D., Venkatraman, A., Zhao, M., Li, Z., Qian, P., Parmely, T., He, X.C., Washburn, M., Florens, L., Perry, J.M., Zeitlinger, J., Workman, J., and Li, L. (2020) β-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells. Stem Cell Reports. Sept 8; 15(3):662-676. PAPER

Vincent, B.J., Rice, G.R., Wong, G.M., Glassford, W.J., Downs, K.I., Shastay, J.L., Charles-Obi, K., Natarajan, M., Gogol, M., Zeitlinger, J., and Rebeiz, M. (2019) An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogasterG3. Dec 3; 9(12):3961-3972.  PAPER

Tettey, T.T., Gao, X., Shao, W., Li, H., Story, B.A., Chitsazan, A.D., Glaser, R.L., Goode, Z.H., Seidel, C.W., Conaway, R.C., Zeitlinger, J., Blanchette, M., and Conaway, J.W. (2019) A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Rep. June 25; 27 (13):3770-3779.e7. PAPER

Shao, W., G-M Alcantara, S., and Zeitlinger, J. (2019) Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing. eLife. April 25; 8. Data | PAPER

Miller, D.E., Staber, C., Zeitlinger, J., and Hawley, R.S. (2018) GENOME REPORT: Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing. G3. Oct 3;8(10):3131-3141. PAPER

Li, Z., Qian, P., Shao, W., Shi, H., He, X.C., Gogal, M., Yu, Z., Wang, Y., Qi, M., Zhu, Y., Perry, J.M., 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, J.S., Parmely, T., Li, H., Shen, B., Zeitlinger, J., He, C., and Li, L. (2018) Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion. Cell Research. Sep;28(9):904-917. PAPER

Papagianni, A., Forés, M., Shao, W., He, S., Koenecke, N., José Andreu, M., Samper, N., Paroush, Z., González-Crespo, S., Zeitlinger, J., and Jiménez, G. (2018)
Capicua controls ToII/IL-1 signaling targets independently of RTK regulation.
PNAS, Feb 20;115(8):1807-1812. PAPER

De Kumar, B., Parker, H.J., Paulson, A., Parrish M.E., Zeitlinger, J., and Krumlauf, R. (2017)
Hoxa1 targets signaling pathways during neural differentation of ES cells and mouse embryogenesis.
Developmental Biology, Dec 1;432(1):151-164. PAPER

De Kumar, B., Parker, H.J., Paulson, A., Parrish M.E., Pushel, I., Singh, N.P., Zhang, Y., Slaughter, B.D., Unruh, J.R., Florens, L., Zeitlinger, J., and Krumlauf, R. (2017)
HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.
Genome Research, Sep; 27(9):1501-1512. PAPER

Pascual, J., Jacobs, J., Sansores-Garcia, L., Natarajan, M., Zeitlinger, J., Aerts, S., Halder, G. and Hamaratoglu, F. (2017)
Hippo Reprograms the Transcriptional Response to Ras Signaling.
Developmental Cell, Sep 25;42(6):667-680.e4. Data | PAPER

Shao, W., and Zeitlinger, J. (2017)
Paused RNA polymerase II inhibits new transcriptional initiation.
Nature Genetics, July:49(7): 1045-1051. Data | PAPER

Koenecke, N., Johnston, J., He, Q., Meier, S., and Zeitlinger, J. (2017)
Drosophila poised enhancers are generated during tissue patterning with the help of repression.
Genome Research, Jan; 27(1):64-74. Data | PAPER

Koenecke, N., Johnston, J., Gaertner, B., Natarajan, M., and Zeitlinger, J. (2016)
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis.
Genome Biology, Sep 27;17(1):196. Data | PAPER

Sun, Y., Nien, C.Y., Chen, K., Liu, H.Y., Johnston, J., Zeitlinger, J., and Rushlow, C. (2015)
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.
Genome Research, Nov;25(11):1703-14. PAPER

He, Q., Johnston, J., and Zeitlinger, J. (2015) 
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. 
Nature Biotechnology, April;33(4):395-401. PAPER | Data | Abstract | Original Data

Wang, Y.L., Duttke, S.H., Chen, K., Johnston, J., Kassavetis, G.A., Zeitlinger, J., and Kadonaga, J.T. (2014)
TRF2, but not TBP, mediates the transcription of ribosomal protein genes.
Genes & Development, July;28(14):1550-1555. PAPER | Abstract | Original Data

Ikmi, A., Gaertner, B., Seidel, C., Srivastava, M., Zeitlinger, J., and Gibson, M.C. (2014)
Molecular evolution of the yap/yorkie proto-oncogene and elucidation of its core transcriptional program.
Molecular Biology and Evolution, Jun;31(6):1375-90. PAPER |  Abstract | Original Data

Chen, K., Johnston, J., Wanqing, S., Meier, S., Staber, C., and Zeitlinger, J. (2013)
A global change in RNA Polymerase II pausing during the Drosophila mid bastula transition.
eLife Aug 13;2:e00861. Data | PAPER

Bardet, A.F., Steinmann, J., Bafna, S., Knoblich, J.A., Zeitlinger, J., and Stark, A. (2013)
Identification of transcription factor binding sites from ChIP-seq data at high-resolution. 
Bioinformatics, Nov 1;29(21):2705-13. PAPER

Lagha, M., Bothma, J.P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D.S., Zeitlinger, J., and Levine, M.S. (2013)
Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.
Cell, May 23;153(5):976-87. PAPER

Gaertner, B.*, Johnston, J.*, Chen, K., Wallaschek, N., Paulson, A., Garruss, A.S., Gaudenz, K., De Kumar, B., Krumlauf, R., and Zeitlinger, J. (2012)
Poised RNA Polymerase II changes over developmental time and prepares genes for future expression.
Cell Reports, Dec 27;2(6):1670-1683. PAPER | Data | Raw Sequencing Data at Geo

Bardet, A.F., He, Q., Zeitlinger, J. and Stark, A. (2011)
A computational pipeline for comparative ChIP-seq analyses.
Nature Protocols, Dec 15;7(1):45-61. PAPER

He, Q.*, Bardet, A.*, Patton, B., Purvis, J., Johnston, J., Paulson, A., Gogol, M., Stark, A., and Zeitlinger, J. (2011)
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.
Nature Genetics, May;43(5):414-421. PAPER

Zeitlinger, J. (2011)
Book review of Evolution, Development, and the Predictable Genome, by David L. Stern. 
American Journal of Human Biology, 23(2):234-236.

Zeitlinger, J. and Stark, A. (2010)
Developmental gene regulation in the era of genomics.
Developmental Biology, Mar 15;339(2):230-239. PAPER

Hendrix, D., Hong, J.W., Zeitlinger J., Rokhsar, D.S., and Levine M. (2008)
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.
Proceedings of the National Academy of Sciences, Jun 3;105(22):7762-7767. PAPER

Zeitlinger, J., Stark, A., Kellis, M., Hong, J.W., Nechaev, S., Adelman, K., Levine, M. and Young, R.A. (2007) 
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. 
Nature Genetics, Dec;39(12):1512-1516. PAPER

Muse, G.W., Gilchrist, D.A., Nechaev, S., Shah, R., Parker, J.S., Grissom, S.F., Zeitlinger J., and Adelman, K. (2007) 
RNA polymerase is poised for activation across the genome. 
Nature Genetics, Dec;39(12):1507-1511. PAPER

Zeitlinger, J., Zinzen, R., Stark, A., Kellis, M., Zhang, H., Young, R.A., and Levine, M. (2007)
Whole-genome ChIP-chip analysis of Dorsal, Twist and Snail suggests integration of diverse patterning processes in the Drosophila embryo. 
Genes & Development, Feb 15;21(4):385-390. PAPER

Qi, Y., Rolfe, A., MacIsaac, K.D., Gerber, G.K., Pokholok, D., Zeitlinger, J., Danford, T., Dowell, R.D., Fraenkel, E., Jaakkola, T.S., Young, R.A., and Gifford, D.K. (2006)
High-resolution computational models of genome binding events.
Nature Biotechnology, Aug;24(8):963-970. PAPER

Zeitlinger, J.*, Pokholok, D.K.* , Hannett, N.M., Reynolds, D.B., and Young, R.A. (2006)
Activated signal transduction kinases frequently occupy target genes. 
Science, July 28;313(5786):533-536. PAPER

Boyer, L.A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L.A., Lee, T.I., Levine, S.S., Wernig, M., Tajonar, A., Ray, M.K., Bell, G.W., Otte, A.P., Vidal, M., Gifford, D.K., Young, R.A., and Jaenisch, R. (2006)
Polycomb complexes repress developmental regulators in murine embryonic stem cells. 
Nature, May 18;441(7091):349-353. PAPER

Pokholok, D.K., Harbison, C.T., Levine, S., Cole, M., Hannett, N.H., Lee, T.I., Walker, K., Lewitter, F., Rolfe, P.A., Herbolsheimer, E., Bell, G.W., Zeitlinger, J., Gifford, D.K. and Young, R.A. (2005) 
Genome-wide map of nucleosome acetylation and methylation in yeast.
Cell, Aug 26;122(4):517-227. PAPER

Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N.J., Macisaac, K.D., Danford, T.W., Hannett, N.M., Tagne, J.-B., Reynolds, D.B., Yoo, J., Jennings, E.G., Zeitlinger, J., Pokholok, D.K., Kellis, M., Rolfe, A., Takusagawa, K.T., Lander, E.S., Gifford, D.K., Fraenkel, E. and Young, R.A. (2004) 
Transcriptional regulatory code of a eukaryotic genome. 
Nature, Sept 2;431(7004):99-104. PAPER

Zeitlinger, J., Simon, I., Harbison, C.T., Hannett, N.M., Volkert, T.L., Fink, G.F. and Young, R.A. (2003) 
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. 
Cell, May 2;113(3):395-404. PAPER

Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K. and Young, R.A. (2002) 
Transcriptional regulatory networks in Saccharomyces cerevisiae
Science, Oct 25;298(5594):799-804. PAPER

Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S. and Young, R.A. (2001) 
Serial regulation of transcriptional regulators in the yeast cell cycle. 
Cell, Sept 21;106(6):697-708. PAPER

Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T.L., Wilson, C.J., Bell, S.P. and Young, R.A. (2000) 
Genome-wide location and function of DNA binding proteins. 
Science, Dec 22;290(5500):2306-2309. PAPER

Zeitlinger, J. and Bohmann, D. (1999) 
Thorax closure in Drosophila: involvement of Fos and the JNK pathway. 
Development, Sept;126(17):3947-3956. PAPER

Zeitlinger, J., Kockel, L., Peverali, F.A., Jackson, D.B., Mlodzik, M. and Bohmann, D. (1997) 
Defective dorsal closure and loss of epidermal decapentaplegic expression in Drosophila fos mutants. 
EMBO Journal, Dec 15;16(24):7393-7401. PAPER

Kockel, L., Zeitlinger, J., Staszewski, L.M., Mlodzik, M. and Bohmann, D. (1997) 
Jun in Drosophila development: redundant and nonredundant functions and regulation by two MAPK signal transduction pathways. 
Genes & Development, July 1;11(13):1748-1758. PAPER

Costaridis, P., Horton, C., Zeitlinger, J., Holder, N. and Maden, M. (1996) 
Endogenous retinoids in the zebrafish embryo and adult. 
Developmental Dynamics, Jan;205(1):41-51. PAPER


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