In The News
06 September 2022
Smart software untangles gene regulation in cells
We seek to understand how different stretches of DNA provide information for gene transcription, expression, and regulation by developing computational tools for analyzing vast quantities of genetic information.
Genetics and Genomics, Development and Regeneration, Molecular and Cell Biology, Systems Biology
Mice, Fruit flies
The Zeitlinger Lab focuses on how DNA sequence information in the genome controls gene regulation in Drosophila and mice to gain insight that can be applied to the human genome in development and disease.
Gene regulation is the process by which a cell determines which genes to turn on and off and when to create specific cells in the body. The Zeitlinger Lab analyzes whole genomes to predict the fate of cells.
Zeitlinger discovered that paused RNA polymerase II is found genome-wide. RNA polymerase II starts the transcription process - producing RNA messages from DNA - but then pauses, as if waiting for a signal to proceed. If paused polymerase is present, the gene is more likely to be activated in the future.
The Zeitlinger Lab develops genomic techniques, including ChIP-nexus, that allow researchers to collect information from vast amounts of cells — sometimes numbering in the millions — to provide an accurate picture of how genes are regulated. They also apply deep learning to ChIP-nexus data from different cell types and stages to better understand the cis-regulatory code (how regulatory DNA sequences affect neighboring genes) and how this code changes during development. Additional technology developed is ChIP-next that allows deciphering of cis-regulatory information, stretches of non-coding DNA that regulate gene expression, from many fewer cells.
Stowers Institute for Medical Research
Julia Zeitlinger, Ph.D., is a developmental and computational biologist where she serves as an Investigator at the Stowers Institute.
Zeitinger and her team developed ChIP-nexus, an innovative technique described in Nature Biotechnology in 2015, which gives investigators an accurate high-resolution map of transcription binding sites.
22 February 2022
12 August 2021
Kristin Watt, Curtis Bacon, Jasmin Camacho receive notification of funding.
19 February 2021
Opening the black box to uncover the rules of the genome’s regulatory code
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.
Seven myths of how transcription factors read the cis-regulatory code
Zeitlinger J. Curr Opin Syst Biol. 2020;23:22-31.
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.
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.
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.