Libertini Emanuele, Lebreton Alice, Lakisic Goran, Dillies Marie-Agnès, Beck Stephan, Coppée Jean-Yves, Cossart Pascale, Bierne Hélène
Plate-forme Transcriptome et Epigénome, Département Génomes et Génétique, Institut Pasteur Paris, France ; Medical Genomics Group, UCL Cancer Institute, University College London London, UK.
Unité des Interactions Bactéries-Cellules, Institut Pasteur Paris, France ; Institut National de la Santé et de la Recherche Médicale U604 Paris, France ; Institut National de la Recherche Agronomique USC2020 Paris, France.
Front Genet. 2015 Dec 1;6:339. doi: 10.3389/fgene.2015.00339. eCollection 2015.
BAH domain-containing protein 1 (BAHD1) is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi), but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq) to compare the DNA methylation profile of HEK293 cells expressing low levels of BAHD1 (HEK-CT) to that of isogenic cells stably overexpressing BAHD1 (HEK-BAHD1). We show that increasing BAHD1 levels induces de novo DNA methylation on autosomes and a marked hypomethylation on the X chromosome (chrX). We identified 91,358 regions that have different methylation patterns in HEK-BAHD1 compared to HEK-CT cells (termed "BAHD1-DMRs"), of which 83,850 mapped on autosomes and 7508 on the X chromosome (chrX). Autosomal BAHD1-DMRs were predominantly hypermethylated and located to satellites, interspersed repeats, and intergenic regions. In contrast, BAHD1-DMRs on chrX were mainly hypomethylated and located to gene bodies and enhancers. We further found that BAHD1-DMRs display a higher-order organization by being clustered within large chromosomal domains. Half of these "BAHD1-Associated differentially methylated Domains" (BADs) overlapped with lamina-associated domains (LADs). Based on these results, we propose that BAHD1-mediated heterochromatin formation is linked to DNA methylation and may play a role in the spatial architecture of the genome.
含BAH结构域蛋白1（BAHD1）参与人类细胞中的异染色质形成和基因抑制。BAHD1也定位于失活的X染色体（Xi），但这种靶向作用的功能意义尚不清楚。到目前为止，对该蛋白的研究因其内源性丰度低而受到阻碍，其在表观遗传调控中的作用仍未得到充分探索。在这项工作中，我们使用全基因组亚硫酸氢盐测序（BS-seq）来比较低水平表达BAHD1的HEK293细胞（HEK-CT）与稳定过表达BAHD1的同基因细胞（HEK-BAHD1）的DNA甲基化谱。我们发现，增加BAHD1水平会诱导常染色体上的从头DNA甲基化以及X染色体（chrX）上的显著低甲基化。我们鉴定出与HEK-CT细胞相比，HEK-BAHD1中具有不同甲基化模式的91,358个区域（称为“BAHD1-DMRs”），其中83,850个位于常染色体上，7508个位于X染色体（chrX）上。常染色体上的BAHD1-DMRs主要是高甲基化的，位于卫星序列、散布重复序列和基因间区域。相比之下，chrX上的BAHD1-DMRs主要是低甲基化的，位于基因体和增强子区域。我们进一步发现，BAHD1-DMRs通过聚集在大的染色体结构域内而呈现出更高阶的组织形式。这些“BAHD1相关差异甲基化结构域”（BADs）中有一半与核纤层相关结构域（LADs）重叠。基于这些结果，我们提出BAHD1介导的异染色质形成与DNA甲基化有关，并且可能在基因组的空间结构中发挥作用。
