Publications & Protocols

2026

Cooperativity enables widespread role of low-affinity motifs in chromatin accessibility and increases regulatory potential
Weilert M, Brennan KJ, Dalal K, Krueger S, Jiang H, Martinez-Corral R, Zeitlinger J. Cell Genom. 2026 Aug 25:101339. doi: 10.1016/j.xgen.2026.101339. Online ahead of print.

Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models 
McAnany CE, Weilert M, Mehta G, Kamulegeya F, Gardner JM, Schreiber J, Kundaje A, Zeitlinger J. Nat Commun. 2026. doi: 10.1038/s41467-026-74807-1.

2025

[preprint] High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo
Alcantara SG, Bourdareau S, Weilert M, Zeitlinger J. Res Sq 2026 Jan 30:rs.3.rs-8428476. doi: 10.21203/rs.3.rs-8428476/v1.

[preprint] Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Weilert M, Brennan KJ, Dalal K, Krueger S, Jiang H, Martinez-Corral R, Zeitlinger J. bioRxiv 2025 Nov 19:2025.11.18.685822. doi: 10.1101/2025.11.18.685822.

Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model
Dalal K, McAnany C, Weilert M, McKinney MC, Krueger S, Zeitlinger J. Cell Genom. 2025 Apr 9;5(4):100821. doi: 10.1016/j.xgen.2025.100821. Epub 2025 Apr 1.

[preprint] PISA: a versatile interpretation tool for visualizing cis-regulatory rules in genomic data
McAnany CE, Weilert M, Mehta G, Kamulegeya F, Gardner JM, Schreiber J, Kundaje A, Zeitlinger J. bioRxiv 2025 Apr 7. doi: 10.1101/2025.04.07.647613

2024

Co-option of the trichome-forming network initiated the evolution of a morphological novelty in Drosophila eugracilis
Rice G, Gaitán-Escudero T, Charles-Obi K, Zeitlinger J, Rebeiz M. Curr Biol. 2024 Nov 18;34(22):5284-5294.e3. doi: 10.1016/j.cub.2024.09.073. Epub 2024 Oct 25.  

2023

***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 Sep 21;14(1):5862. doi: 10.1038/s41467-023-41408-1.

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 Biol Chem. 2023 Jan;299(1):102760. doi: 10.1016/j.jbc.2022.102760. Epub 2022 Nov 30.  

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.  

The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5
Maven BEJ, Gifford CA, Weilert M, Gonzalez-Teran B, Hüttenhain 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.  

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, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Science. 2023 Sep 22;381(6664):eadd1250. doi: 10.1126/science.add1250. Epub 2023 Sep 22.  

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation
Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Dev Cell. 2023 Oct 9;58(19):1898-1916.e9. doi: 10.1016/j.devcel.2023.07.007. Epub 2023 Aug 8.

[preprint] 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.  

2021

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 Nov 22;17(11):e1009668. doi: 10.1371/journal.pgen.1009668. eCollection 2021 Nov.  

TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. Mol Syst Biol. 2021 Feb;17(2):e9866. doi: 10.15252/msb.20209866.  

Evaluation of facial aesthetics by laypersons in patients undergoing intraoral quadrangular Le Fort II osteotomy compared with conventional Le Fort I osteotomy
Cede J, Graf A, Zeitlinger J, Wagner F, Willinger K, Klug C. Int J Oral Maxillofac Surg. 2021 Sep;50(9):1210-1218. doi: 10.1016/j.ijom.2021.01.013. Epub 2021 Feb 16.  

***Base-resolution models of transcription-factor binding reveal soft motif syntax
Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Nat Genet. 2021 Mar;53(3):354-366. doi: 10.1038/s41588-021-00782-6. Epub 2021 Feb 18.

2020

Seven myths of how transcription factors read the cisregulatory code
Zeitlinger J. Curr Opin Syst Biol. 2020 Oct;23:22-31. doi: 10.1016/j.coisb.2020.08.002. Epub 2020 Sep 4.  

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 Reports. 2020 Sep 8;15(3):662-676. doi: 10.1016/j.stemcr.2020.07.018. Epub 2020 Aug 20.  

2019

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 Dec 3;9(12):3961-3972. doi: 10.1534/g3.119.400788.  

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing
Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. Cell Rep. 2019 Jun 25;27(13):3770-3779.e7. doi: 10.1016/j.celrep.2019.05.099.  

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:e41461. doi: 10.7554/eLife.41461.  

2018

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.  

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.  

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.  

2017

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.  

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.  

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.  

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.  

***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.  

2016

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
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. doi: 10.1186/s13059-016-1057-2.

2015

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.

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.

2014

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.

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.

RNA polymerase II pausing during development
Gaertner B, Zeitlinger J. Development. 2014 Mar;141(6):1179-83. doi: 10.1242/dev.088492.

2013

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.

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.

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.

2012

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.

2011

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.

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.

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.

2008

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

*** email lab to obtain PDF