Mechanistic Insights Into NFIX‐Mediated DNA Recognition and Transcriptional Regulation in Skeletal Muscle

TL;DR

This study reveals how the NFIX protein recognizes DNA and regulates genes in skeletal muscle, offering insights into muscle development and disease.

Contribution

The study provides the first high-resolution structural and mechanistic understanding of NFIX's DNA recognition and transcriptional regulation in skeletal muscle.

Findings

NFIX binds DNA as a monomer and recognizes the TGGCA motif through base-specific interactions.

Disrupting NFIX's DNA-binding residues impairs its transcriptional activation in reporter assays.

NFIX regulates genes involved in muscle metabolism, stress responses, and inflammation.

Abstract

Skeletal muscle is essential for voluntary movement and exhibits a remarkable capacity for regeneration following injury. NFIX, a member of the Nuclear Factor I (NFI) family of transcription factors, plays a critical role in both skeletal muscle development and regeneration. Despite its emerging importance, the molecular basis of NFIX‐mediated DNA recognition and transcriptional regulation in skeletal muscle remains poorly defined. Here, we demonstrate that NFIX promotes key cellular processes in skeletal muscle cells, as siRNA‐mediated knockdown of NFIX significantly reduces cell proliferation, increases apoptosis, and impairs differentiation. Transcriptomic analysis revealed that NFIX regulates a network of genes involved in muscle metabolism, stress responses, and immune inflammatory responses. Biophysical characterization showed that NFIX exists as a monomer in solution and binds palindromic DNA with a 1:1 stoichiometry. A high‐resolution crystal structure of the NFIXDBD bound to palindromic DNA reveals a monomeric binding mode driven by base‐specific recognition of the TGGCA motif. Mutations that disrupt key DNA‐contacting residues abolished both DNA binding and transcriptional activation in luciferase reporter assays. Together, these findings define the molecular mechanism of NFIX‐dependent gene regulation in skeletal muscle and establish a structural framework for its function, providing new insights into the potential therapeutic targeting of NFIX in muscle diseases.

An atomic view of the NFIX–DNA complex reveals recognition of the TGGCA motif and links sequence‐specific binding to the transcriptional programs governing skeletal muscle development and disease.

An atomic view of the NFIX–DNA complex uncovers its role in skeletal muscle development and disease.NFIX directs muscle‐related transcriptional programs via sequence‐specific recognition of the TGGCA motif.Integrated biophysical and structural analyses provide the molecular basis of TGGCA major‐groove recognition by NFIX.

An atomic view of the NFIX–DNA complex uncovers its role in skeletal muscle development and disease.

NFIX directs muscle‐related transcriptional programs via sequence‐specific recognition of the TGGCA motif.

Integrated biophysical and structural analyses provide the molecular basis of TGGCA major‐groove recognition by NFIX.

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