PDF(Pubmed)
Abstract：
BACKGROUND: SETDB1 (SET domain bifurcated-1) is a histone H3-lysine 9 (H3K9)-specific methyltransferase that mediates heterochromatin formation and repression of target genes. Despite the assumed functional link between DNA methylation and SETDB1-mediated H3K9 trimethylations, several studies have shown that SETDB1 operates autonomously of DNA methylation in a region- and cell-specific manner. This study analyzes SETDB1-null HAP1 cells through a linked methylome and transcriptome analysis, intending to explore genes controlled by SETDB1-involved DNA methylation.
RESULTS: We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1\'s function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells.
CONCLUSIONS: SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
RESULTS: We investigated SETDB1-mediated regulation of DNA methylation and gene transcription in human HAP1 cells using reduced-representation bisulfite sequencing (RRBS) and RNA sequencing. While two-thirds of differentially methylated CpGs (DMCs) in genic regions were hypomethylated in SETDB1-null cells, we detected a plethora of C2H2-type zinc-finger protein genes (C2H2-ZFP, 223 of 749) among the DMC-associated genes. Most C2H2-ZFPs with DMCs in their promoters were found hypomethylated in SETDB1-KO cells, while other non-ZFP genes with promoter DMCs were not. These C2H2-ZFPs with DMCs in their promoters were significantly upregulated in SETDB1-KO cells. Similarly, C2H2-ZFP genes were upregulated in SETDB1-null 293T cells, suggesting that SETDB1\'s function in ZFP gene repression is widespread. There are several C2H2-ZFP gene clusters on chromosome 19, which were selectively hypomethylated in SETDB1-KO cells.
CONCLUSIONS: SETDB1 collectively and specifically represses a substantial fraction of the C2H2-ZFP gene family. Through the en-bloc silencing of a set of ZFP genes, SETDB1 may help establish a panel of ZFP proteins that are expressed cell-type specifically and thereby can serve as signature proteins for cellular identity.
摘要：
背景：SETDB1（SET结构域分叉-1）是一种组蛋白H3-赖氨酸9（H3K9）特异性甲基转移酶，可介导靶基因的异染色质形成和抑制。尽管DNA甲基化和SETDB1介导的H3K9三甲基化之间存在功能联系，一些研究表明，SETDB1以区域和细胞特异性的方式自主操作DNA甲基化。本研究通过连接的甲基化组和转录组分析分析SETDB1-nullHAP1细胞，旨在探索由SETDB1参与的DNA甲基化控制的基因。
结果：我们使用还原代表亚硫酸氢盐测序（RRBS）和RNA测序研究了SETDB1介导的人HAP1细胞中DNA甲基化和基因转录的调控。尽管在SETDB1-null细胞中，基因区域中三分之二的差异甲基化CpG（DMC）被低甲基化，我们检测到过多的C2H2型锌指蛋白基因（C2H2-ZFP，DMC相关基因中的749个中的223个）。在SETDB1-KO细胞中发现大多数具有DMC启动子的C2H2-ZFP低甲基化，而其他具有启动子DMC的非ZFP基因则没有。这些在其启动子中具有DMC的C2H2-ZFP在SETDB1-KO细胞中显著上调。同样，C2H2-ZFP基因在SETDB1-null293T细胞中上调，这表明SETDB1在ZFP基因抑制中的功能是广泛的。19号染色体上有几个C2H2-ZFP基因簇，它们在SETDB1-KO细胞中选择性地低甲基化。
结论：SETDB1共同且特异性地抑制了大部分C2H2-ZFP基因家族。通过一组ZFP基因的整体沉默，SETDB1可以帮助建立一组ZFP蛋白，这些蛋白是特异性表达的细胞类型，从而可以作为细胞身份的特征蛋白。
结果：我们使用还原代表亚硫酸氢盐测序（RRBS）和RNA测序研究了SETDB1介导的人HAP1细胞中DNA甲基化和基因转录的调控。尽管在SETDB1-null细胞中，基因区域中三分之二的差异甲基化CpG（DMC）被低甲基化，我们检测到过多的C2H2型锌指蛋白基因（C2H2-ZFP，DMC相关基因中的749个中的223个）。在SETDB1-KO细胞中发现大多数具有DMC启动子的C2H2-ZFP低甲基化，而其他具有启动子DMC的非ZFP基因则没有。这些在其启动子中具有DMC的C2H2-ZFP在SETDB1-KO细胞中显著上调。同样，C2H2-ZFP基因在SETDB1-null293T细胞中上调，这表明SETDB1在ZFP基因抑制中的功能是广泛的。19号染色体上有几个C2H2-ZFP基因簇，它们在SETDB1-KO细胞中选择性地低甲基化。
结论：SETDB1共同且特异性地抑制了大部分C2H2-ZFP基因家族。通过一组ZFP基因的整体沉默，SETDB1可以帮助建立一组ZFP蛋白，这些蛋白是特异性表达的细胞类型，从而可以作为细胞身份的特征蛋白。
