美国麻省理工学院和哈佛大学布罗德研究所Jason D. Buenrostro团队近期取得重要工作进展。他们研究通过多尺度足迹揭示顺式调控元件的组织架构。相关研究成果2025年1月22日在线发表于《自然》杂志上。

据介绍，顺式调控元件（CRE）控制着基因表达，其结构和功能具有动态性，反映了不同效应蛋白组成随时间的变化。然而，目前用于测量全基因组范围内顺式调控元件上效应蛋白组织情况的方法有限，这阻碍了将顺式调控元件的结构与其在细胞命运和疾病中的功能联系起来的研究工作。

研究人员开发了PRINT这一计算方法，它能够从批量和单细胞染色质可及性数据中识别跨多种蛋白质大小尺度的DNA-蛋白质相互作用足迹。利用这些多尺度足迹，研究人员创建了seq2PRINT框架，该框架借助深度学习实现对转录因子和核小体结合情况的精确推断，并阐释顺式调控元件处的调控逻辑。将seq2PRINT应用于人类骨髓的单细胞染色质可及性数据时，研究人员观察到在造血过程中，以先驱因子为中心的顺式调控元件会依次形成并扩展。

此外，研究人员还发现了小鼠造血干细胞中顺式调控元件结构随年龄变化的情况，包括核小体足迹的广泛减少以及新鉴定出的Ets复合基序的增加。

总之，研究人员建立了一种从染色质可及性数据中深入了解DNA结合蛋白动态变化的方法，并揭示了在细胞分化和衰老过程中调控元件的架构。

附：英文原文

Title: Multiscale footprints reveal the organization of cis-regulatory elements

Author: Hu, Yan, Horlbeck, Max A., Zhang, Ruochi, Ma, Sai, Shrestha, Rojesh, Kartha, Vinay K., Duarte, Fabiana M., Hock, Conrad, Savage, Rachel E., Labade, Ajay, Kletzien, Heidi, Meliki, Alia, Castillo, Andrew, Durand, Neva C., Mattei, Eugenio, Anderson, Lauren J., Tay, Tristan, Earl, Andrew S., Shoresh, Noam, Epstein, Charles B., Wagers, Amy J., Buenrostro, Jason D.

Issue&Volume: 2025-01-22

Abstract: Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time1. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size. Using these multiscale footprints, we created the seq2PRINT framework, which uses deep learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centred on pioneer factors across haematopoiesis. We further discover age-associated alterations in the structure of CREs in murine haematopoietic stem cells, including widespread reduction of nucleosome footprints and gain of de novo identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data, and reveal the architecture of regulatory elements across differentiation and ageing.

DOI: 10.1038/s41586-024-08443-4

Source: https://www.nature.com/articles/s41586-024-08443-4