bioRxiv : the preprint server for biologyOct 25, 2026

Mapping DNA regions that activate, silence, or organize genes using precise deletion editing

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗OA ↗

Updated Oct 26, 2026

Abstract

Swap-seq enables the systematic deletion of hundreds of regulatory sequences to measure their effects on gene expression.

Noncoding regulatory elements in the human genome can function as enhancers, silencers, or topological elements.
The method evaluates the regulatory elements influencing the expression of the gene PPIF in THP-1 monocytes.
Quantitative analysis reveals effects from distal and intronic enhancers, as well as the characterization of CTCF insulators.
A silencer identified regulates distal genes through a process involving histone deacetylase (HDAC)-mediated repression of nearby enhancers.
Many genomic elements exhibit similar chromatin signatures and transcription factor binding sites, indicating a broader class of repressive elements.
Sequence-to-function models often accurately represent the local activity of regulatory elements but do not consistently connect them to distant target genes.

Simplified

Noncoding regulatory elements in the human genome can control gene expression through distinct mechanisms, including acting as enhancers, silencers, or topological elements. However, we lack tools to identify all such classes systematically and quantify their effects on gene expression in an endogenous genomic context. Here we develop Swap-seq, a method that combines pooled twin prime editing with flow-sorting to delete hundreds of endogenous regulatory sequences and measure their quantitative effects on the expression of a nearby gene. We apply Swap-seq to dissect the regulatory elements that control PPIF expression in THP-1 monocytes. We quantify the effects of distal and intronic enhancers, characterize CTCF insulators, and discover a silencer that regulates distal genes through histone deacetylase (HDAC)-mediated repression of neighboring enhancers. Hundreds of other genomic elements share its chromatin signatures and transcription factor binding sites, suggesting that this silencer represents a broader class of repressive elements. We leverage Swap-seq data to benchmark sequence-to-function models and show that they often capture the local activity of regulatory elements but fail to link them to distal target genes. Swap-seq thus provides a generalizable tool to discover regulatory elements across mechanistic classes, characterize their effects on gene expression, and generate large-scale datasets for evaluating sequence-to-function models.

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Mapping DNA regions that activate, silence, or organize genes using precise deletion editing

Abstract

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