The chromatin remodeling protein Lsh safeguards accessibility at potential enhancer regions and blocks access to lineage specific transcription factors

Chromatin structure controls access to DNA sequences, facilitates binding of transcription factors at enhancers and controls tissue specific gene expression. Dynamic regulation of chromatin accessibility is a key feature of cellular differentiation, but the factors involved in this process are not fully understood. We identified Lsh as important safeguard of enhancer accessibility. Lsh is a chromatin remodeling protein that controls DNA methylation level during development. Mutation of human Lsh (HELLS) causes the ICF syndrome, a severe human disorder with early lethality. Using MNase-seq we demonstrate specific genome-wide changes of chromatin structure in dependence of Lsh. While short term depletion of Lsh does not affect DNA methylation level, it leads to increased MNase digestibility at transcriptional regulatory elements. Our data suggests that Lsh impedes chromatin access at potential enhancers, which can be predicted based on DNAse hypersensitivity, specific histone modifications (H3K4me1) and based on transcription factor binding motifs. Furthermore, we demonstrate enhanced occupancy of ectopically expressed transcription factors after Lsh depletion attesting improved chromatin accessibility. Our data suggests that Lsh masks transcription factor binding sites and acts as guardian of chromatin accessibility at a subset of enhancers.

染色质结构可调控DNA序列的可及性，促进转录因子在增强子区域的结合，并控制组织特异性基因的表达。染色质可及性的动态调控是细胞分化的核心特征之一，但其相关调控因子尚未完全阐明。我们证实Lsh是增强子可及性的重要守护因子。Lsh是一种染色质重塑蛋白（chromatin remodeling protein），在发育过程中调控DNA甲基化水平。人类Lsh（HELLS）的突变会引发ICF综合征，一种早发致死的严重人类遗传病。我们通过微球菌核酸酶测序（MNase-seq）技术，证实了Lsh依赖性的全基因组染色质结构特异性改变。尽管短期敲低Lsh不会改变DNA甲基化水平，但会使转录调控区域的MNase消化敏感性显著升高。我们的研究数据表明，Lsh会阻碍潜在增强子区域的染色质可及性——这类潜在增强子可通过DNA酶超敏感位点、特异性组蛋白修饰（H3K4me1）以及转录因子结合基序进行预测。此外，我们证实，在Lsh敲低后，异位表达的转录因子的结合占有率显著升高，这直接证明染色质可及性得到了提升。我们的研究数据表明，Lsh会遮蔽转录因子结合位点，并作为一类增强子子集的染色质可及性守护因子发挥作用。