Molecular Mechanisms Governing Transcription Factor Search for Enhancers

ZHAO Fengyu; ZHANG Shuoxia; WANG Yaolai

doi:10.12211/2096-8280.2026-013

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Molecular Mechanisms Governing Transcription Factor Search for Enhancers

更新时间：2026-04-27

- Molecular Mechanisms Governing Transcription Factor Search for Enhancers
- Synthetic Biology Journal Pages: 1-13(2026)
- 作者机构：
  
  江南大学数学与数据科学学院，江苏无锡 214122
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2026-013
  CLC： Q786
- Received：04 March 2026，
  
  Revised：2026-04-23，
  
  Online First：27 April 2026，
- 稿件说明：
移动端阅览
赵凤语，张硕霞，王耀来. 转录因子的增强子搜寻机理［J］. 合成生物学， 2026， 7. DOI： 10.12211/2096-8280.2026-013

ZHAO Fengyu， ZHANG Shuoxia， WANG Yaolai. Molecular Mechanisms Governing Transcription Factor Search for Enhancers［J］. Synthetic Biology Journal， 2026， 7. DOI： 10.12211/2096-8280.2026-013
赵凤语，张硕霞，王耀来. 转录因子的增强子搜寻机理［J］. 合成生物学， 2026， 7. DOI： 10.12211/2096-8280.2026-013 DOI：

ZHAO Fengyu， ZHANG Shuoxia， WANG Yaolai. Molecular Mechanisms Governing Transcription Factor Search for Enhancers［J］. Synthetic Biology Journal， 2026， 7. DOI： 10.12211/2096-8280.2026-013 DOI：

摘要

转录因子如何在细胞核中高效搜索并定位增强子，是个看似简单却困扰至今的经典难题。其内在机理的揭示，将为细胞信号转导设计提供不可或缺的理论基础。经典的自由扩散模型和易化扩散模型认为，转录因子在细胞核中自由扩散，可沿DNA滑动、跳跃，并可在不同的DNA链之间跳转。为解决此类模型固有的搜寻低效难题，导向搜索模型提议，细胞核内存在为转录因子提供导航的“路标”。然而，关于“路标”及“导航机制”的研究尚处于初级阶段，未知和困惑远多于已知。转录凝聚体和短串联重复序列的发现，为这一问题的解答提供了新思路。本文在综述现有模型的基础上，概括提出短串联重复序列与转录凝聚体通过“引导与富集—浓缩与催化”的互补机制共同保障转录因子在复杂染色质环境中实现快速而精准的靶点定位。该模型为理解增强子搜寻机理与相关DNA序列设计提供了新视角。

Abstract

It remains elusive how transcription factors (TFs) efficiently search for and localize enhancers. Unraveling the dynamic mechanisms is not only fundamental to understanding gene regulation but also provides a critical theoretical framework for engineering cellular signal transduction pathways. Classical models

including free diffusion model and facilitated diffusion model

posit that TFs diffuse freely through the nucleoplasm

engage in non-specific DNA binding

and navigate the genome via sliding

hopping

or intersegmental transfer until encountering their cognate enhancers. While these theories are well-supported by experimental evidence in prokaryotes

they lack validation in eukaryotes and fail to recapitulate the physicochemical complexity of the eukaryotic nucleus

particularly densely packed chromatin environment. To address the inefficiency inherent to random diffusion

the guided exploration model has emerged

proposing that nuclear "signpost" elements

such as specific chromatin structures or protein assemblies

direct TF trafficking. However

research into the identity of these signposts and the underlying "navigation mechanisms" remains in its infancy

with fundamental questions far outnumbering definitive answers. In recent years

the discovery of transcriptional condensates and short tandem repeats (STRs) inspired new insights. TFs harboring intrinsically disordered regions (IDRs) can undergo liquid-liquid phase separation (LLPS) to form biomolecular condensates. These condensates functionally mimic nuclear signposts

serving as spatial beacons that guide TF search processes and

as supported by emerging evidence

potentiate gene transcriptional activation. Concurrently

STRs are enriched surrounding enhancers

where they directly interact with TFs and play pivotal roles in eukaryotic gene regulation. Here

we review the canonical TF search models

the LLPS-driven formation of transcriptional condensates

and the functional roles of STRs in enhancer biology. We propose an integrated model wherein STRs and transcriptional condensates act in synergy to enable rapid and precise TF targeting within complex chromatin. This complementary mechanism

termed "guidance and enrichment

concentration and catalysis"

resolves key inefficiencies of classical diffusion models and offers a conceptual framework for deciphering enhancer selection and engineering synthetic DNA regulatory sequences.

关键词

Keywords

references

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