Linker Histone H1.0 Couples Cellular Stiffness to Chromatin Structure [RNA-seq]

Eukaryotic nuclei encase the genome and differentially package it for the various needs of distinct cell types. Tuning of genome structure and function is accomplished by chromatin binding proteins, which are responsive to cellular stress, determining the transcriptome and phenotype of the cell. We sought to investigate the connection between extracellular stress and chromatin structure to regulate cellular stiffness. We demonstrate that the linker histone H1.0, which compacts nucleosomes into higher order chromatin fibers, controls genome structure and cellular response to stress. Histone H1.0 has privileged expression in tension-responsive fibroblasts across tissue types in mouse and humans, and is necessary and sufficient to mount a myofibroblast phenotype in these cells. Loss of histone H1.0 prevents transforming growth factor beta (TGF-b)-induced fibroblast contraction, proliferation and migration in an isoform-specific manner via inhibition of a transcriptome targeting extracellular matrix molecules. Histone H1.0 is associated with local regulation of gene expression by chromatin fiber compaction and histone acetylation, rendering the nucleus and cell stiffer in response to cytokine stimulation. Knockdown of H1.0 decreased levels of HDAC1 and the chromatin reader BRD4, thereby preventing transcription of a fibrotic gene program. Transient depletion of histone H1.0 in vivo decompacts chromatin and prevents fibrosis in cardiac muscle, lung, and kidney, thereby linking chromatin structure with fibroblast phenotype in response to extracellular stress. Our work identifies an unexpected role of linker histones to sense and respond to cellular stress, directly coupling cellular tension, nuclear organization and gene transcription. RNA-seq of isolated adult mouse cardiac fibroblasts treated with siRNA against H1.0 or siScramble control, in the presence and absence of TGFb. There are 3 biological replicates per condition.

真核细胞核包裹基因组，并依据不同细胞类型的多样需求对其进行差异化包装。基因组结构与功能的调控由染色质结合蛋白完成，这类蛋白可响应细胞应激，进而决定细胞的转录组与表型。本研究旨在探究细胞外应激与染色质结构之间的关联，以调控细胞刚度。我们证实，连接组蛋白H1.0（linker histone H1.0）可将核小体（nucleosome）压缩为高级染色质纤维（chromatin fiber），其能够调控基因组结构以及细胞对应激的响应。连接组蛋白H1.0在小鼠与人类不同组织中的张力响应性成纤维细胞中呈特异性高表达，且在这些细胞中足以诱导肌成纤维细胞表型（myofibroblast phenotype），同时也是该过程所必需的。连接组蛋白H1.0的缺失会以亚型特异性的方式，通过抑制靶向细胞外基质分子的转录组，阻断转化生长因子β（transforming growth factor beta, TGF-β）诱导的成纤维细胞收缩、增殖与迁移。连接组蛋白H1.0通过染色质纤维压缩与组蛋白乙酰化（histone acetylation）实现基因表达的局部调控，从而使细胞核与细胞在细胞因子刺激下变得更僵硬。敲低H1.0会降低组蛋白去乙酰化酶1（HDAC1）与染色质阅读器BRD4的表达水平，进而阻止纤维化基因程序的转录。在活体中短暂敲低连接组蛋白H1.0可使染色质解压缩，并阻断心脏、肺脏与肾脏的纤维化进程，从而将染色质结构与细胞外应激响应下的成纤维细胞表型关联起来。本研究揭示了连接组蛋白感知并响应细胞应激的意外功能，直接将细胞张力、细胞核组织与基因转录联系在一起。本数据集包含经针对H1.0的小干扰RNA（small interfering RNA, siRNA）或无序对照siRNA（siScramble）处理的分离成年小鼠心脏成纤维细胞的RNA测序（RNA-seq）数据，处理条件分别设置为存在与不存在转化生长因子β，每组设置3个生物学重复。