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一种自动化的ATAC-seq方法揭示了开放染色质中转录因子剂量反应的序列决定因素。

An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin.

作者信息

Liu Betty B, Shimasawa Masaru, Vermeulen Sidney, Kim Samuel H, Iremadze Nika, Lipson Doron, Shipony Zohar, Greenleaf William J

出版信息

bioRxiv. 2025 Jul 27:2025.07.24.666684. doi: 10.1101/2025.07.24.666684.


DOI:10.1101/2025.07.24.666684
PMID:40777328
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12330524/
Abstract

Transcription factor (TF) dosage is a critical determinant of cellular identity. However, the quantitative relationship between TF dosage and its regulation of chromatin accessibility and gene expression remains poorly understood. To address this, we developed RoboATAC, a scalable, automated ATAC-seq platform for high-throughput accessibility profiling. We then systematically profiled genome-wide chromatin accessibility and gene expression changes induced by graded overexpression of 22 TFs in HEK293T cells (246 total samples), observing dose-dependent changes in accessibility and aggregate TF footprints. Modeling accessibility as a function of sequence and chromatin states revealed that DNA sequence alone accurately predicts dosage sensitivity at elements that become accessible, with low-affinity motifs requiring higher TF levels to induce accessibility. Interpretable deep learning models revealed contributions of motif orientation, spacing, and flanking bases to accessibility, both recapitulating known motifs and nominating novel dosage-sensitive motif arrangements. Nucleosome positioning analysis uncovered two distinct, TF identity dependent patterns by which accessibility is established by changing nucleosome position and occupancy.

摘要

转录因子(TF)剂量是细胞特性的关键决定因素。然而,TF剂量与其对染色质可及性和基因表达的调控之间的定量关系仍知之甚少。为了解决这个问题,我们开发了RoboATAC,这是一个用于高通量可及性分析的可扩展自动化ATAC测序平台。然后,我们系统地分析了HEK293T细胞中22种TF的分级过表达(共246个样本)所诱导的全基因组染色质可及性和基因表达变化,观察到可及性和聚集TF足迹的剂量依赖性变化。将可及性建模为序列和染色质状态的函数表明,仅DNA序列就能准确预测可及元件的剂量敏感性,低亲和力基序需要更高的TF水平来诱导可及性。可解释的深度学习模型揭示了基序方向、间距和侧翼碱基对可及性的贡献,既概括了已知基序,又确定了新的剂量敏感基序排列。核小体定位分析发现了两种不同的、依赖于TF身份的模式,通过改变核小体位置和占有率来建立可及性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/4db13ef09be6/nihpp-2025.07.24.666684v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/bcb59fe1edec/nihpp-2025.07.24.666684v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/dba1a314651b/nihpp-2025.07.24.666684v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/640fc880c574/nihpp-2025.07.24.666684v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/10cfacc31914/nihpp-2025.07.24.666684v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/8c8250d93610/nihpp-2025.07.24.666684v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/4db13ef09be6/nihpp-2025.07.24.666684v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/bcb59fe1edec/nihpp-2025.07.24.666684v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/dba1a314651b/nihpp-2025.07.24.666684v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/640fc880c574/nihpp-2025.07.24.666684v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/10cfacc31914/nihpp-2025.07.24.666684v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/8c8250d93610/nihpp-2025.07.24.666684v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4d3/12330524/4db13ef09be6/nihpp-2025.07.24.666684v1-f0006.jpg

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本文引用的文献

[1]
Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage.

Cell Genom. 2025-3-12

[2]
Single-molecule states link transcription factor binding to gene expression.

Nature. 2024-12

[3]
Genome access is transcription factor-specific and defined by nucleosome position.

Mol Cell. 2024-9-19

[4]
Pioneer factors: nature or nurture?

Crit Rev Biochem Mol Biol. 2024

[5]
Affinity-optimizing enhancer variants disrupt development.

Nature. 2024-2

[6]
Epigenetic pioneering by SWI/SNF family remodelers.

Mol Cell. 2024-1-18

[7]
Pioneer factors: roles and their regulation in development.

Trends Genet. 2024-2

[8]
Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency.

Structure. 2023-11-2

[9]
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation.

Dev Cell. 2023-10-9

[10]
DNA selection by the master transcription factor PU.1.

Cell Rep. 2023-7-25

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