RUNX1 Utilizes Novel 3bp-Spaced Motif Arrays to Regulate Cell-Context-Dependent Function

✍️Author: Shan Liu

📧Email: 3shanliu3@gmail.com

Copyright (c) 2025 YenLab@SKLEH. All rights reserved.

Introduction

The transcription factor RUNX1 orchestrates hematopoietic differentiation but drives leukemogenesis, creating a functional paradox. RUNX1 binds open chromatin via a canonical 12-bp motif but most in vivo targets lack this sequence, challenging conventional TF-DNA interaction models.

To resolve this, we developed TRACE (Tagging and Recovery of Chromatin-associated Elements), a mammalian system employing endogenous DNA libraries to map RUNX1 binding in physiological contexts.

We uncover: 1) Novel motif arrays: RUNX1 targets inaccessible chromatin through novel 3bp-spaced motif arrays, forming alternative binding platforms. 2) Epigenetic plasticity: DNA methylation at motif array regions inversely correlates with differential TET2 expression across HSPC and AML, revealing cell-type-specific epigenetic crosstalk. 3) Functional complexity: Motif arrays regulate both lineage-specific and leukemic programs, connecting architecture to pathological switching.

Integrating TRACE-defined motif arrays with methylation dynamics, we demonstrate how RUNX1 toggles between hematopoiesis and leukemogenesis via a syntax-based mechanism, merging sequence arrangement with epigenetic context.

📁Scripts organization

• Scripts head with 0_ is for general preprocessing NGS data, include

  TRACE, ChIP-seq, CUT&Tag, WGBS, MNase-seq ,RNA-seq

• Script head with series number is pipeline for specific analysis follows the order in the TRACE paper.

  Specifically, the bash script is for processing data and corresponding R scripts is used for downstream analysis, statistics and plotting.

• Published HT-SELEX data was processed using the Inomotif package with modified Python code, as detailed in the directory: Inomotif_modified

• Scripts in the Script_pipeline folder was called by pipelines.