Zeitlinger Lab | Publications

Original Research Papers

Short tandem repeats bind transcription factors to tune eukaryotic gene expression.

Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Shrikumar A, Afek A, Greenleaf WJ, Gordân R Zeitlinger J, Kundaje A and Fordyce PM.Science. 2023 Sept 22;381(6664):eadd1250. doi: 10.1126/science.add1250. PMID: 37733848

The multi-lineage transcription factor ISL I controls cardiomyocyte cell fate through interaction with NKX2.5.

Maven BEJ, Gifford CA, Weilert M, Gonzalez-Teran B, Huttenhain R, Pelonero A, Ivey KN, Samse-Knapp K, Kwong W, Gordon D, McGregor M, Nishino T, Okorie E, Rossman S, Costa MW, Krogan NJ, Zeitlinger J, Srivastava D. Stem Cell Reports. 2023 Nov 14;18(11):2138-2153. doi: 10.1016/j.stemcr.2023.09.014. Epub 2023 Oct 19. PMID: 37863045

Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development.

Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Nat Commun. 2023 Sept 21;14(1):5862. doi: 10.1038/s41467-023-41408-1. PMID: 37735176

Original Data

Short tandem repeats bind transcription factors to tune eukaryotic gene expression.

Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greeleaf WJ, Gordan R, Zeitlinger J, Kundaje A, Fordyce PM. Science. 2023 Sept 22;381(6664)eadd1250. doi: 10.1126/science.add1250. PMID: 37733848

Chromatin accessibility in Drosophila embryo is determined by transcription factor pioneering and enhancer activation.

Brennan KJ, Weilert M, Krueger S, Pampari A, Lui HY, Yan AWH, Morrison JA, Hughers TR, Rushlow CA, Kundaje A, Zeitlinger J. Dev Cell. 2023 Aug 3: S1534-5807(23)00347-7. doi: 10.1016/j.devcel.2023.01.001 Online ahead of print. PMID: 37557175

Original Data

De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding.

Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. bioRxiv. 2023;May 11:2023.05.11.540401. doi: 10.1101/2023.05.11.540401. Preprint. PMID: 37214836

Emerging questions in transcriptional regulation

Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Cell Syst. 2023 Apr 19:14(4):247-251. doi:10.1016/j.cels.2023.03.005. PMID: 37080160

Off the deep end: What can deep learning do for the gene expression field?

Raicu AM, Fay JC, Rohner N,Zeitlinger J, Arnosti DN. J Boil Chem. 2023;Jan:299(1):102760. doi: 10.1016/j.jbc.2022.102760. Epub 2022 Nov 30. PMID:36462664

The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters

Soffers JHM, Alcantara SG, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. PLoS Genet. 2021;17:e1009668. doi: 10.1371/journal.pgen.1009668. PMCID:PMC8648115

Original Data

Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec Z, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Nat Genet. 2021;53:354-366. PMID: 33603233

Original Data

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. Mol Syst Biol. 2021;17:e9866. doi: 10.15252/msb.20209866. PMID: 33543829

Original Data

b-Catenin and Associated Proteins Regulate Lineage Differentiation in Ground State Mouse Embryonic Stem Cells

Tao F, Soffers J, Hu D, Chen S, Gao X, Zhang Y, Zhao C, Smith SE, Unruh JR, Zhang D, Tsuchiya D, Venkatraman A, Zhao M, Li Z, Qian P, Parmely T, He XC, Washburn M, Florens L, Perry JM, Zeitlinger J, Workman J, Li L. Stem Cell Rep. 2020;15:662-676. PMID: 32822591

Original Data

An atlas of transcription factors expressed in male pupal terminalia of Drosophila melanogaster

Vincent BJ, Rice GR, Wong GM, Glassford WJ, Downs KI, Shastay JL, Charles-Obi K, Natarajan M, Gogol M, Zeitlinger J, Rebeiz M. G3 (Bethesda). 2019. doi: 10.1534/g3.119.400788. PMID: 31619460.

Original Data

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

Tettey TT, Gao X, Shao W, Story BA, Chitsazan AD, Glaser RL, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. Cell Rep. 2019;27:3770-3779 e7. PMID: 31242411

Original Data

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

Shao W, Alcantara SG, Zeitlinger J. eLife. 2019;8:e41461. doi: 41410.47554/eLife.41461. PMID: 31021316

Original Data

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

Miller DE, Staber C, Zeitlinger J, Hawley RS. G3 (Bethesda). 2018;8:3131-3141. PMID: 30087105

Original Data

Suppression of m(6)A 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. Author Correction: Cell Res 2018:1-14. https://doi.org/10.1038/s41422-018-0072-0. Published online July 2018.;28:904-917.PMID: 30065315

Original Data

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

Papagianni A, Fores M, Shao W, He S, Koenecke N, Andreu MJ, Samper N, Paroush Z, Gonzalez-Crespo S, Zeitlinger J, Jimenez G. Proc Natl Acad Sci U S A.2018;115:1807-1812. PMID: 29432195

Original Data

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;432:151-164. PMID: 28982536

Original Data

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;27:1501-1512. PMID: 28784834

Original Data

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;42:667-680.e4. PMID: 28950103

Paused RNA polymerase II inhibits new transcriptional initiation

Shao W, Zeitlinger J. Nat Genet.2017;49:1045-1051. PMID: 28504701

Original Data

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;27:64-74. PMID: 27979994

Original Data

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;17:196. PMID: 27678375

Original Data

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;25:1703-14. PMID: 26335633

Original Data

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

He Q, Johnston J, Zeitlinger J. Nat Biotechnol. 2015;33:395-401. PMID: 25751057

Original Data

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;28:1550-1555. PMID: 24958592

Original Data

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;31:1375-1390. PMID: 24509725

Original Data

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;29:2705-2713. PMID: 23980024

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;2:e00861. doi: 00810.07554/eLife.00861. PMID: 23951546

Original Data

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;2:1670-1683. PMID: 23260668

Original Data

A computational pipeline for comparative ChIP-seq analyses.

Bardet AF, He Q, Zeitlinger J, Stark A. Nat Protoc. 2012;7:45-61. PMID: 22179591

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;43:414-420. PMID: 21478888

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;105:7762-7767. PMID: 18505835

Reviews, Commentaries, Chapters or Books

Seven myths of how transcription factors read the cis-regulatory code

Zeitlinger J. Curr Opin Syst Biol. 2020;23:22-31. PMID: 33134611

Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis.

Arnosti DN, Fay JC, Zeitlinger J. A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015. BioEssays. 2015;37:1042-1044. PMID: 26354485

RNA polymerase II pausing during development.

Gaertner B, Zeitlinger J. Development. 2014;141:1179-1183. PMID: 24595285

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;153:976-987. PMID: 23706736

Book review of Evolution, Development, and the Predictable Genome by David L. Stern.

Zeitlinger J. Am J Hum Biol. 2011;43:414-420.

Developmental gene regulation in the era of genomics.

Zeitlinger J, Stark A. Dev Biol. 2010;339:230-239. PMID: 20045679

Zeitlinger Lab Publications