Integrative dissection of gene regulatory elements at base resolution

Zeyu Chen; Nauman Javed; Molly Moore; Jingyi Wu; Gary Sun; Michael Vinyard; Alejandro Collins; Luca Pinello; Fadi J Najm; Bradley E Bernstein

doi:10.1016/j.xgen.2023.100318

Integrative dissection of gene regulatory elements at base resolution

Cell Genom. 2023 Apr 28;3(6):100318. doi: 10.1016/j.xgen.2023.100318. eCollection 2023 Jun 14.

Authors

Zeyu Chen^{1

2

3}, Nauman Javed^{1

2

3}, Molly Moore², Jingyi Wu^{1

2

3}, Gary Sun^{1

3}, Michael Vinyard^{2

4

5}, Alejandro Collins², Luca Pinello^{2

4}, Fadi J Najm², Bradley E Bernstein^{1

2

3}

Affiliations

¹ Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
² Gene Regulation Observatory, Broad Institute, Cambridge, MA, USA.
³ Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA.
⁴ Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
⁵ Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Abstract

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 to dissect regulatory sequences within the exemplar immune locus encoding CD69. We converge on a ∼170 base interval within a differentially accessible and acetylated enhancer critical for CD69 induction in stimulated Jurkat T cells. Individual C-to-T base edits within the interval markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on regulatory interactions between the transcriptional activators GATA3 and TAL1 and the repressor BHLHE40. Systematic analysis suggests that the interplay between GATA3 and BHLHE40 plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing regulatory elements in their endogenous chromatin contexts and identifying operative artificial variants.

Keywords: CRISPRi; base editing; immune response; regulatory elements; transcription factor.

Abstract

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