Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.
Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.
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KAP1结合的全基因组分析表明KRAB-ZNF的自动调节。
DOI：
10.1371/journal.pgen.0030089
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发表时间：
2007-06
期刊：
影响因子：
4.5
通讯作者：
Farnham, Peggy J.
中科院分区：
文献类型：
--
作者：
O'Geen, Henriette;Squazzo, Sharon L.;Iyengar, Sushma;Blahnik, Kim;Rinn, John L.;Chang, Howard Y.;Green, Roland;Farnham, Peggy J.
我们进行了基因组规模的染色质免疫沉淀（ChIP）芯片比较两种修饰（赖氨酸9 [H3 me 3 K9]和赖氨酸27 [H3 me 3 K27]的三甲基化）组蛋白H3在Ntera 2睾丸癌细胞和三种不同解剖来源的原代人成纤维细胞。我们发现，在每种细胞类型中，两种修饰在两种最大类别的转录因子的启动子处差异富集。具体地，锌指（ZNF）基因由H3 me 3 K9结合，同源异型盒基因由H3 me 3 K27结合。我们先前已经表明，Polycomb抑制复合物2负责介导人类癌细胞中组蛋白H3的赖氨酸27的三甲基化。相比之下，H3 me 3 K9靶标和Polycomb阻遏复合物2的组分之间几乎没有重叠，这表明不同的组蛋白甲基转移酶负责H3 me 3 K9修饰。先前的研究表明，SETDB 1可以三甲基化赖氨酸9上的H3，使用体外或人工拴系测定。SETDB 1被认为是通过含有KAP 1辅阻遏物的复合物募集到染色质中。为了确定含有KAP 1的复合物是否介导所鉴定的H3 me 3 K9靶的三甲基化，我们进行了ChIP芯片测定，并使用人5-kb启动子阵列鉴定了KAP 1靶基因。我们发现，在正常细胞和癌细胞中，ZNF转录因子的大量基因被KAP 1和H3 me 3 K9结合。为了扩展我们对KAP 1的研究，我们接下来使用38阵列平铺集对KAP 1结合进行了完整的基因组分析，确定了约7，000个KAP 1结合位点。鉴定的KAP 1靶标高度富集C2 H2 ZNF，特别是含有Krüppel相关框（KRAB）结构域的那些。有趣的是，尽管大多数KAP 1结合位点位于核心启动子区域内，但ZNF基因附近的结合位点在靶基因的转录区域内大大富集。由于KAP 1通过与KRAB-ZNF蛋白相互作用被募集到DNA中，因此我们认为KRAB-ZNF基因的表达可能通过涉及KAP 1的自动调节机制来控制。组蛋白H3的赖氨酸9或27（分别为H3 me 3 K9或H3 me 3 K27）的甲基化与沉默的染色质相关。然而，尚未对这两种类型的修饰组蛋白H3结合的基因组区域进行全面比较。因此，我们比较了H3 me 3 K9和H3 me 3 K27在四个不同细胞群中约26，000个人类启动子处的结合模式。我们的研究表明，这两种标记与两种最常见的转录调节因子分离差异; H3 me 3 K27高度富集在同源盒基因和H3 me 3 K9高度富集在锌指基因（ZNF）。我们发现许多与H3 me 3 K9结合的启动子也与辅阻遏物KAP 1结合。KAP 1靶基因的全基因组筛选揭示了ZNF基因中KAP 1结合位点与其他靶基因的位置差异。一般而言，KAP 1结合位点定位于核心启动子区域。然而，与ZNF基因相关的KAP 1结合位点位于编码区的3′端附近。我们的研究结果表明，KRAB-ZNF家族成员参与了一个自动调节环，涉及KAP 1蛋白与ZNF靶基因的3′端结合，导致H3 K9的三甲基化和转录抑制。
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Specifically, zinc finger (ZNF) genes were bound by H3me3K9 and homeobox genes were bound by H3me3K27. We have previously shown that the Polycomb repressive complex 2 is responsible for mediating trimethylation of lysine 27 of histone H3 in human cancer cells. In contrast, there is little overlap between H3me3K9 targets and components of the Polycomb repressive complex 2, suggesting that a different histone methyltransferase is responsible for the H3me3K9 modification. Previous studies have shown that SETDB1 can trimethylate H3 on lysine 9, using in vitro or artificial tethering assays. SETDB1 is thought to be recruited to chromatin by complexes containing the KAP1 corepressor. To determine if a KAP1-containing complex mediates trimethylation of the identified H3me3K9 targets, we performed ChIP-chip assays and identified KAP1 target genes using human 5-kb promoter arrays. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. To expand our studies of KAP1, we next performed a complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ~7,000 KAP1 binding sites. The identified KAP1 targets were highly enriched for C2H2 ZNFs, especially those containing Krüppel-associated box (KRAB) domains. Interestingly, although most KAP1 binding sites were within core promoter regions, the binding sites near ZNF genes were greatly enriched within transcribed regions of the target genes. Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1. Methylation of lysines 9 or 27 of histone H3 (H3me3K9 or H3me3K27, respectively) has been associated with silenced chromatin. However, a comprehensive comparison of the regions of the genome bound by these two types of modified histone H3 has not been performed. Therefore, we compared the binding patterns of H3me3K9 and H3me3K27 at ~26,000 human promoters in four different cell populations. Our studies indicated that the two marks segregate differentially with the two most common types of transcriptional regulators; H3me3K27 is highly enriched at homeobox genes and H3me3K9 is highly enriched at zinc-finger genes (ZNFs). We showed that many of the promoters bound by H3me3K9 are also bound by the corepressor KAP1. A genome-wide screen for KAP1 target genes revealed a difference in the location of KAP1 binding sites in the ZNF genes versus other targets. In general, KAP1 binding sites were localized to core promoter regions. However, KAP1 binding sites associated with ZNF genes are near the 3′ end of the coding region. Our results suggest that the KRAB-ZNF family members participate in an autoregulatory loop involving binding of the KAP1 protein to the 3′ end of the ZNF target genes, resulting in trimethylation of H3K9 and transcriptional repression.
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影响因子：
64.5
作者：
Cawley, S;Bekiranov, S;Gingeras, TR
通讯作者：
Gingeras, TR
影响因子：
7
作者：
Bieda, M;Xu, XQ;Farnham, PJ
通讯作者：
Farnham, PJ
DOI：
10.1073/pnas.041616998
发表时间：
2001-02-13
影响因子：
11.1
作者：
Abrink, M;Ortiz, JA;Losson, R
通讯作者：
Losson, R
影响因子：
10.5
作者：
Friedman, JR;Fredericks, WJ;Rauscher, FJ
通讯作者：
Rauscher, FJ
影响因子：
11.4
作者：
Martens, JHA;O'Sullivan, RJ;Jenuwein, T
通讯作者：
Jenuwein, T