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Integrative dissection of gene regulatory elements at base resolution

Zeyu Chen, Nauman Javed, Molly Moore, Jingyi Wu, Michael Vinyard, View ORCID ProfileLuca Pinello, Fadi J. Najm, Bradley E. Bernstein
doi: https://doi.org/10.1101/2022.10.05.511030
Zeyu Chen
1Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
3Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
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Nauman Javed
1Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
3Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
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Molly Moore
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
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Jingyi Wu
1Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
3Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
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Michael Vinyard
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
4Department of Pathology, Massachusetts General Hospital and Harvard Medical School
5Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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Luca Pinello
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
4Department of Pathology, Massachusetts General Hospital and Harvard Medical School
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  • ORCID record for Luca Pinello
Fadi J. Najm
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
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  • For correspondence: fadinajm@broadinstitute.org bradley_bernstein@dfci.harvard.edu
Bradley E. Bernstein
1Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
2Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA
3Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
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  • For correspondence: fadinajm@broadinstitute.org bradley_bernstein@dfci.harvard.edu
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Summary

Although vast numbers of putative gene regulatory elements have been cataloged, the sequence motifs and individual bases that underlie their functions remain largely unknown. Here we combine epigenetic perturbations, base editing, and deep learning models to dissect regulatory sequences within the exemplar immune locus encoding CD69. Focusing on a differentially accessible and acetylated upstream enhancer, we find that the complementary strategies converge on a ∼170 base interval as critical for CD69 induction in stimulated Jurkat T cells. We pinpoint individual cytosine to thymine base edits that markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on binding competition between the transcriptional activator GATA3 and the repressor BHLHE40. Systematic analysis of GATA and bHLH/Ebox motifs suggests that interplay between these factors plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing gene regulatory elements in their endogenous chromatin contexts and identifying operative artificial variants.

Highlights

  • Base editing screens and deep learning pinpoint sequences and single bases affecting immune gene expression

  • An artificial C-to-T variant in a regulatory element suppresses CD69 expression by altering the balance of transcription factor binding

  • Competition between GATA3 and BHLHE40 regulates inducible immune genes and T cell states

Competing Interest Statement

B.E.B. declares outside interests in Fulcrum Therapeutics, HiFiBio, Arsenal Biosciences, Cell Signaling Technologies, and Chroma Medicine.

Footnotes

  • ↵7 Lead Contact

  • - Expanded introduction, discussion, and references - Included Enformer fine-tuned model references in the text as well as methods. Pertains to Fig S1D, Fig3D. - Added GSE accessions and github link

  • https://github.com/BernsteinLab/BE_CD69_paper_2022

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 08, 2022.
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Integrative dissection of gene regulatory elements at base resolution
Zeyu Chen, Nauman Javed, Molly Moore, Jingyi Wu, Michael Vinyard, Luca Pinello, Fadi J. Najm, Bradley E. Bernstein
bioRxiv 2022.10.05.511030; doi: https://doi.org/10.1101/2022.10.05.511030
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Integrative dissection of gene regulatory elements at base resolution
Zeyu Chen, Nauman Javed, Molly Moore, Jingyi Wu, Michael Vinyard, Luca Pinello, Fadi J. Najm, Bradley E. Bernstein
bioRxiv 2022.10.05.511030; doi: https://doi.org/10.1101/2022.10.05.511030

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