Publications
Publications
Supporting the scientific spirit of transparency, the Stowers Institute for Medical Research makes the data underlying its scientific publications freely accessible to the scientific community. Access to original, unprocessed data allows other scientists to validate and extend findings made by Stowers researchers.
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The multi-lineage transcription factor ISLI 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 Rep. [published ahead of print October 21 2023]. 2023.
Short tandem repeats bind transcription factorsto 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, Gordan R, Zeitlinger J, Kundaje A, Fordyce PM. Science. 2023;381:eadd1250.
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;14:5862 doi: 10.1038/s41467-023-41408-1.
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. [published ahead of print August 8 2023]. Dev Cell 2023;58:1-19.
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.
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.
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.
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.
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.
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.
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.
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.
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. doi.org/10.1038/s41422-018-0072-0. Published online July 2018.;28:904-917.
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.
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.
H19 promotes cholestatic liver fibrosis by preventing ZEB1-mediated inhibition of epithelial cell adhesion molecule
Song Y, Liu C, Liu X, Trottier J, Beaudoin M, Zhang L, Pope C, Peng G, Barbier O, Zhong X, Li L, Wang L. Hepatology.2017;66:1183-1196.
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.
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.
Paused RNA polymerase II inhibits new transcriptional initiation
Shao W, Zeitlinger J. Nat Genet.2017;49:1045-1051..
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.
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Emerging questions in transcriptional regulation : What are the sequence rules driving gene regulation?
Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Cell Syst. 2023;14:247-251.
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;299:102760.
Seven myths of how transcription factors read the cis-regulatory code
Zeitlinger J. Curr Opin Syst Biol. 2020;23:22-31.
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.
Osteoblast ablation burns out functional stem cells.
Zhao M, Li L. Blood. 2015;125:2590-2591.
A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis.
Gracz AD, Williamson IA, Roche KC, Johnston MJ, Wang F, Wang Y, Attayek PJ, Balowski J, Liu XF, Laurenza RJ, Gaynor LT, Sims CE, Galanko JA, Li L, Allbritton NL, Magness ST. Nat Cell Biol. 2015;17:340-349.
Homing and migration assays of hematopoietic stem/progenitor cells.
He XC, Li Z, Sugimura R, Ross J, Zhao M, Li L. Methods Mol Biol. 2014;1185:279-284.
RNA polymerase II pausing during development.
Gaertner B, Zeitlinger J. Development. 2014;141:1179-1183.
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.
To be or not to be a stem cell: dissection of cellular and molecular components of haematopoietic stem cell niches.
Perry JM, Li L. EMBO J. 2012;31:1060-1061.
MAPing the role of Kras mutations in hyperplastic polyps.
Barrett T, Li L. Gastroenterology. 2011;141:799-801.
Bone Metastasis Targets The Endosteal Hematopoietic Stem Cell Niche.
Sugimura R, Li L. IBMS BoneKEy. 2011;8:381-384.
Book review of Evolution, Development, and the Predictable Genome by David L. Stern.
Zeitlinger J. Am J Hum Biol. 2011;43:414-420.
Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases.
Sugimura R, Li L. Birth Defects Res C Embryo Today. 2010;90:243-256.
Fountain of Youth: aged blood-forming stem cells could be rejuvenated by young microenvironment.
Yin T, Li L. Cell Res. 2010;20:504-505.
Shifting in balance between osteogenesis and adipogenesis substantially influences hematopoiesis.
Sugimura R, Li L. J Mol Cell Biol. 2010;2:61-62.
Functional assays for hematopoietic stem cell self-renewal.
Perry JM, Li L. Methods Mol Biol. 2010;636:45-54.
Developmental gene regulation in the era of genomics.
Zeitlinger J, Stark A. Dev Biol. 2010;339:230-239.
HSC mobilization: new incites and insights.
Ross J, Li L. Blood. 2009;114:1283-1284.
Visualize eHPCs in different zones.
Yin T, Xie Y, Li L. Blood. 2009;114:230-231.
