SATB1介导的MAR元件相互作用参与人β-globin基因簇活性染色质结构的建立
摘要
细胞是一个有序进行各种各样复杂程序的有机统一体,而细胞核则是细胞内部的又一个更小的有机体,基因转录复制等许多重要的与遗传发育紧密相连的生物学过程都离不开细胞核这个微小的细胞器。众所周知,基因的转录之所以能够有条不紊地进行,是因为有许多有序的调节机制存在,一旦正常的调控被打破,细胞进而是机体就会表现出各种异常症状,导致各种疾病的发生。所以说,基因的表达调控机制研究对于人类了解细胞乃至机体的正常新陈代谢,了解各种疾病的发生原理,找寻治疗各种疾病的对症药物具有很重要的意义。
目前,对于基因表达调控的研究主要集中在三个水平上,分别是DNA水平、染色体水平以及细胞核水平,但是我们知道,这三个水平的调控不是单独存在而是互相联系密不可分的。DNA水平上主要包括一些顺式调控元件和反式调控因子的相互作用,而顺式调控元件有很多是位于基因上游很远处的远距离调控元件,它们要近距离的调控基因的表达,必须从很远处来接触基因,那么这就必然涉及到远距离调控元件和相关基因所在的染色质区域在空间上的相互接近,这种相互接近就是染色质水平上的调控。远距离调控元件对于基因簇调控的作用机制一直是分子生物学转录调控领域的重要问题之一。多年来一直有两种理论模型:接触模型(ContactModel)和非接触模型(Non-contact Model)。接触模型中的一个基本模型是成环模型(Looping Model)。它认为:远距离调控元件上结合的反式因子通过形成环状结构克服漫长的空间间隔直接与靶基因的启动子发生接触形成复合物。非接触模型主要是连接模型(Linkage Model),它认为:远距离调控元件并不直接与各基因的启动子相互作用,仅指导转录因子和增强子的辅助因子(Enhancer facilitator)等蛋白因子沿基因座顺序的、发育阶段特异的结合形成染色质元件的阵列从而确定将要转录的结构域。
DNA水平和染色体水平上的调控都是在细胞核内发生的,那么就与核内的复杂结构密不可分。许多重要的调控因子都是核蛋白,它们对于基因的开启表达与失活有很重要的作用。而核这个复杂的结构也为基因表达提供了有序的场所。近来的研究表明,当基因活性表达的时候,该基因所在的染色质片段能环出所在的染色体版图(chromosome territory,CT)。这与染色体间区分布有大量调控基因表达所需的调控机器有关,这就是著名的CT-IC模型的基础理论。因此基因在细胞核内的定位就由原来简单认为的异染色质区和常染色质区发展得更为深入了,基因在细胞核内的定位以及位置的变化与基因表达调控之间的关系也越来越受到重视。
目前的研究表明,基因在染色质水平上的调控,包括染色质空间构象的变化过程,以及基因在核内的定位等都与核内的一类重要的非染色质结构紧密联系,这个结构就是核基质。核基质参与基因表达调控的观点已经被很多人提出并且有一些初步的验证。核基质作为细胞核内重要的结构,募集了大量与调控相关的转录因子和酶,实验结果发现与基因核基质的结合状况与基因活化状况相关。核基质发挥这种功能主要是通过核基质结合蛋白与染色体DNA上的特殊序列,称为核基质结合区(MARs)的结合而发生的。研究表明核基质和MARs的结合也是存在选择性的,这种选择性和基因表达密切相关。而核基质结合蛋白目前研究确认的不是很多,如SATB1,cux,SMAR1,PARP等等。我们对其中的SATB1比较关注,SATB1本身有着自我多聚化的特性,可以形成复杂的空间鸟笼结构为基因表达调控的染色质空间相互作用提供平台。已经有报道SATB1在β珠蛋白基因表达调控中促进e基因而降低γ基因的表达,这种作用和SATB1在β珠蛋白基因簇上的特异MAR区结合密不可分。我们的研究就要探讨SATB1在染色质水平上是如何调控β珠蛋白基因的表达的。
我们首先以一个已知的HS2MAR为固定片段,利用本实验室发展的QACT方法搜寻在空间上可能和HS2MAR相互作用的染色质片段,结果我们发现,在β珠蛋白基因簇上有3个片段以较高的频率被捕获,分别位于HS4和HS5之间的8150(HS4MAR),ε基因上游的HBEMAR,γ~A基因的下游HBGMAR。其中HBEMAR和HBGMAR是已经有线索表明它们确实是MAR区,但是8150是以前没有报道过的。我们首先利用EMSA和ChIP的方法证明了8150确实可以和核抽提物结合并且可以和SATB1蛋白特异结合。然后我们又利用3C的方法证明这两个基因的MAR都可以和调控片段HS2MAR以及8150以较高频率结合并且在hemin诱导细胞分化后,这种相互作用明显加强。说明这些MARs区在空间上能形成相互作用的复杂染色质结构,我们称之为MAR base。然后我们又利用ChIP的方法对这四个位点和SATB1的结合做了分析,结果表明,除了HBGMAR外,其它三个HS2MAR,HBEMAR以及8150都能较强的和SATB1结合,并且这种结合在Hemin诱导细胞分化后,结合有所加强。ChIP-3C的结果又表明SATB1对于HBEMAR,HS2MAR和8150它们之间的相互作用是能够起到一个直接的介导作用的,这些结果表明SATB1能介导β珠蛋白基因簇内存在的MARs区的相互作用特别是ε基因所在的染色质片段和其调控区域所在的染质体片段之间的相互作用。也就是说SATB1参与ε基因和相应的调控区域之间的MARbase的形成。
为了验证SATB1对于这种相互作用是否是必需的,我们利用RNA干扰的技术将内源的SATB1干扰掉之后,首先检测红系相关的珠蛋白基因的表达发现,发现在β珠蛋白基因簇而言,ε基因的表达急剧下降,可达60%左右,而β基因的表达不受影响,一个出乎意料的现象是,γ基因的表达也有约20%左右的下降,这个和文献报道SATB1表达降低后,γ基因的表达上升相反,因为我们所用的细胞是一种发育早期的K562细胞,与文献报道所用的发育后期的K562细胞不同,在发育早期的K562细胞里,当hemin诱导时ε和γ基因的表达都是上调的,所以这种结果也是苻合细胞特性的。接下来我们检测了红系特异转录因子,如GATA1/2,EKLF,CTCF,NFE2等等的表达,结果表明,这些转录因子的表达基本没有什么变化。接着我们用ChIP的方法检测了在这些位点上,SATB1的结合变化情况,结果表明对于HS2MAR,HBEMAR和8150而言,它们和SATB1的结合明显下降,而对于HBGMAR而言,仍旧是很低的结合。我们又用3C的方法来检测这些MARs区域之间的相互作用,结果表明HBEMAR和HS2MAR以及8150之间的相互作用明显减弱,而对于HBGMAR和HS2MAR以及8150之间的相互作用而言,并没有明显的变化,同时我们还检测了HS2核心序列和ε基因以及γ基因的启动子之间的相互作用,发现HS2核心序列和ε基因的启动子之间的相互作用减弱很多而HS2核心序列和γ基因的启动子之间的相互作用只有很微弱的变化。由此我们推断SATB1确实对于ε基因以及它的MARbase的形成而言是一个必需的蛋白因子,而对于γ基因的影响只是由于SATB1影响了调控元件从而间接的影响到了该基因的表达。
接着我们又分析了在Hemin诱导前后SATB1本身的修饰情况的变化,结果发现在诱导分化后,SATB1的乙酰化减弱,有文献表明,乙酰化修饰减弱能够使SATB1和DNA的结合变强,说明由SATB1介导所形成的MARbase由于SATB1的修饰变化有一个动态的调节从而对基因表达变化起到动态的调节。最后我们利用免疫荧光,GFP-SATB1融合蛋白原位观察以及ChIP的方法证明SATB1和上述的MARs区的结合在细胞分裂时期的染色体上并不是完全解离的,而是有部分的保留,这种保留对于下一轮细胞周期时,活性base以及活性染色质构象的重建可能起到很重要的作用。
综上所述,我们的研究表明SATB1能通过介导ε基因以及其调控区的MARs之间的相互作用形成MARbase的方式从而调控活性染色质结构的形成以及基因表达,同时SATB1本身的修饰变化情况能动态的调节base的形成,并且这种base的结构在细胞分裂时期是有一定程度的保留,以有利于下一轮细胞周期活性结构的重建。
Cell and cell nucleus are both well-organized. Many important biological processes including gene transcription, DNA replication happen in the nucleus. As we have known, gene transcriptionis is exquisitely regulated. Disturbance of the gene regulation frequently results in severe diseases. In depth study of the mechanisms of gene regulation will provide the clues to know the mechanisms of many diseases, which will help to design effective drugs.
Gene expression can be regulated at three levels including DNA, chromatin and nuclear level. As we have known, the three levels of regulation are interrelated to each other. The interaction between cis-regulatory elements and trans-regulatory factors reflects DNA level regulation. Many regulatory elements are far away from genes and they can contact genes by chromatin folding. The contacting and folding is chromatin level regulation. A basic and important question is how the remote regulatory elements bypass the long-range distance and regulate gene expression. Two models have been proposed, that is, the Contact Model and Non-contact model. A basic model in Contact-Model is Looping Model, which describes that the trans-factors binding to long-range enhancing elements can contact the target gene promoters through the formation of looping structure to overcome the spatial distance between them. Non-contact Model is represented by the Linking Model ,which suggests that LCR can not contact genes' promoters directly but direct transcriptional factors and enhancer facilitators to bind chromatin elements along with the gene locus.
The regulation at both DNA level and chromatin level happen in the nucleus and are closely related to the nuclear structure. Many regulatory proteins are nuclear proteins and they have important roles in the initiation and termination of gene expression. The nucleus provides the space for the gene expression. Many studies suggested that the chromatin fragment can loop out of its chromosome territory (CT) when the gene actively expresses, which is associated with regulation machinery distributed in the interval of chromosomes. This is the famous CT-IC model. Since then, the gene localization has developed from simply being described as at the euchromatin region and heterochromatin region to more complicated nuclear localization. Therefore, the gene regulation attracted more attention now.
Recent studies have showed that nuclear matrix is an important non-chromatin structure in the nucleus and the nuclear matrix can have influence on the gene expression, chromatin conformation and gene localization by recruiting the transcriptional factors and enzymes. Some studies have suggested that the binding between nuclear matrix and gene can affect the gene expression. A group of important proteins, called the matrix binding proteins can mediate the binding between the nuclear matrix and chromatin fragments. The DNA elements that associate with nuclear matrix were named matrix attachment regions (MAR). The binding between MARs and matrix is selective and the selectivity is related with the gene expression. MARs binding proteins have been confirmed including SATBl, cux, SMAR1 and PARP. We have studied the function of SATBl in regulating gene expression. The characteristic self-association of SATBl lead to the formation of a birdcage structure which provides a platform for gene expression regulation and chromatin fragments crosstalking. A previous report has confirmed that SATBl can up-regulate the expression ofε-globin gene and down-regulate the expression ofγ-globin gene. The regulation is related to the binding of SATBl to special MARs. In this study, we have explored the regulatory function of SATBl toβ-globin gene cluster at chromatin level.
We used the QACT to capture possible associated fragments with a known MAR element in HS2 ofβ-globin LCR (HS2MAR, the leader). The results showed that there are three HS2MAR associated chromatin fragments including 8150 , a privously unknown element locates between HS4 and HS5, HBEMAR that locates upstream ofεgene promoter, HBGMAR that locates upstream ofγ~A gene promoter. HBEMAR and HBGMAR have been confirmed to be MARs. Our EMSA and ChIP results had suggested that 8150 is a potential MAR. 3C assay had showed that HBEMAR and HBGMAR can associated with HS2MAR and 8150 elements; also, the associations can be strengthened after induction of the cells by Hemin. These data indicated that a MAR base structon may exist. Our ChIP assay showed that HS2MAR、8150 and HBEMAR can bind SATB1 and the binding increase after Hemin induction . The ChIP-3C results showed that SATB1 can bind to HBEMAR、HS2MAR and 8150 in vivo and mediated the associations among these MARs in theβ-globin gene cluster, especially the association between HBEMAR and upstream regulatory fragments. We presumed that SATB1 function as core of the MARbase. To explore if SATB1 is necessary for the MARbase, RNA interference was used to knock down SATB1 expression in K562 cells . Expression assay of globin genes showed that embryonic gene likeεandζgenes were substantially decreased. For the fetal and adult stage globin genes, while the expression ofβ-globin gene showed no obvious change,γandαglobin genes been decreased upon STAB1 down-regulation, which is not consistent with previously reported results. We reasoned that this may result from cell differences. Our K562 cell is an early passage K562 cells that is different from the late passage K562 cells used in that the above mentioned report. Our K562 cells can be induced by Hemin into the erythroid direction with the up-regulation of bothεandγglobin genes. In the case of late passage K562 cells, the expression ofεglobin gene is down-regulated and the expression ofγgene is up-regulated with Hemin induction. Our results also showed that the expression of erythroid specific transcriptional factors had no obvious change. The ChIP assay showed that the binding of SATB1 to these MARs reduced . The 3C assay showed that the associations between HBEMAR and HS2MAR/8150 decreased substantially, but not the associations between HBGMAR and HS2MAR/8150. Another 3C assay showed that the association between HS2 core sequence and HBE gene promoter had also been reduced in the SATB1 RNAi cells. We concluded that SATB1 is necessary for theεspecific MARbase formation, forγspecific MARbase, SATB1 is not necessary and the influence onγ-globin gene expression may result from indirect effects .
We next analyzed the acetylation status of SATB1 after hemin induction of the K562 cells. We found that the acetylation of SATB1 had been reduced after induction. A previous paper had showed that the acetylation of SATB1 can reduce the binding of SATB1 to DNA, so that the acetylation change of SATB1 can serve as a dynamic regulator of the MARbase. Finally, immunofluorenscence assay、GFP-SATB1 fusion protein localization analysis and ChIP assay were used to show that the binding of SATB1 to these MARs can be partially maintained on mitotic chromosome.
Our results indicated that SATB1 can mediate the formation of aεgene specific MARbase to regulate the high-order chromatin structure ofβ-globin gene cluster and that the acetylation state of SATB1 may serve as a dynamic regulator of the MARbase. Meanwhile, the MARbase may be maintained to some degree during cell mitosis and facilitate the reestablishment of active chromatin structure in the next cell cycle.
目前,对于基因表达调控的研究主要集中在三个水平上,分别是DNA水平、染色体水平以及细胞核水平,但是我们知道,这三个水平的调控不是单独存在而是互相联系密不可分的。DNA水平上主要包括一些顺式调控元件和反式调控因子的相互作用,而顺式调控元件有很多是位于基因上游很远处的远距离调控元件,它们要近距离的调控基因的表达,必须从很远处来接触基因,那么这就必然涉及到远距离调控元件和相关基因所在的染色质区域在空间上的相互接近,这种相互接近就是染色质水平上的调控。远距离调控元件对于基因簇调控的作用机制一直是分子生物学转录调控领域的重要问题之一。多年来一直有两种理论模型:接触模型(ContactModel)和非接触模型(Non-contact Model)。接触模型中的一个基本模型是成环模型(Looping Model)。它认为:远距离调控元件上结合的反式因子通过形成环状结构克服漫长的空间间隔直接与靶基因的启动子发生接触形成复合物。非接触模型主要是连接模型(Linkage Model),它认为:远距离调控元件并不直接与各基因的启动子相互作用,仅指导转录因子和增强子的辅助因子(Enhancer facilitator)等蛋白因子沿基因座顺序的、发育阶段特异的结合形成染色质元件的阵列从而确定将要转录的结构域。
DNA水平和染色体水平上的调控都是在细胞核内发生的,那么就与核内的复杂结构密不可分。许多重要的调控因子都是核蛋白,它们对于基因的开启表达与失活有很重要的作用。而核这个复杂的结构也为基因表达提供了有序的场所。近来的研究表明,当基因活性表达的时候,该基因所在的染色质片段能环出所在的染色体版图(chromosome territory,CT)。这与染色体间区分布有大量调控基因表达所需的调控机器有关,这就是著名的CT-IC模型的基础理论。因此基因在细胞核内的定位就由原来简单认为的异染色质区和常染色质区发展得更为深入了,基因在细胞核内的定位以及位置的变化与基因表达调控之间的关系也越来越受到重视。
目前的研究表明,基因在染色质水平上的调控,包括染色质空间构象的变化过程,以及基因在核内的定位等都与核内的一类重要的非染色质结构紧密联系,这个结构就是核基质。核基质参与基因表达调控的观点已经被很多人提出并且有一些初步的验证。核基质作为细胞核内重要的结构,募集了大量与调控相关的转录因子和酶,实验结果发现与基因核基质的结合状况与基因活化状况相关。核基质发挥这种功能主要是通过核基质结合蛋白与染色体DNA上的特殊序列,称为核基质结合区(MARs)的结合而发生的。研究表明核基质和MARs的结合也是存在选择性的,这种选择性和基因表达密切相关。而核基质结合蛋白目前研究确认的不是很多,如SATB1,cux,SMAR1,PARP等等。我们对其中的SATB1比较关注,SATB1本身有着自我多聚化的特性,可以形成复杂的空间鸟笼结构为基因表达调控的染色质空间相互作用提供平台。已经有报道SATB1在β珠蛋白基因表达调控中促进e基因而降低γ基因的表达,这种作用和SATB1在β珠蛋白基因簇上的特异MAR区结合密不可分。我们的研究就要探讨SATB1在染色质水平上是如何调控β珠蛋白基因的表达的。
我们首先以一个已知的HS2MAR为固定片段,利用本实验室发展的QACT方法搜寻在空间上可能和HS2MAR相互作用的染色质片段,结果我们发现,在β珠蛋白基因簇上有3个片段以较高的频率被捕获,分别位于HS4和HS5之间的8150(HS4MAR),ε基因上游的HBEMAR,γ~A基因的下游HBGMAR。其中HBEMAR和HBGMAR是已经有线索表明它们确实是MAR区,但是8150是以前没有报道过的。我们首先利用EMSA和ChIP的方法证明了8150确实可以和核抽提物结合并且可以和SATB1蛋白特异结合。然后我们又利用3C的方法证明这两个基因的MAR都可以和调控片段HS2MAR以及8150以较高频率结合并且在hemin诱导细胞分化后,这种相互作用明显加强。说明这些MARs区在空间上能形成相互作用的复杂染色质结构,我们称之为MAR base。然后我们又利用ChIP的方法对这四个位点和SATB1的结合做了分析,结果表明,除了HBGMAR外,其它三个HS2MAR,HBEMAR以及8150都能较强的和SATB1结合,并且这种结合在Hemin诱导细胞分化后,结合有所加强。ChIP-3C的结果又表明SATB1对于HBEMAR,HS2MAR和8150它们之间的相互作用是能够起到一个直接的介导作用的,这些结果表明SATB1能介导β珠蛋白基因簇内存在的MARs区的相互作用特别是ε基因所在的染色质片段和其调控区域所在的染质体片段之间的相互作用。也就是说SATB1参与ε基因和相应的调控区域之间的MARbase的形成。
为了验证SATB1对于这种相互作用是否是必需的,我们利用RNA干扰的技术将内源的SATB1干扰掉之后,首先检测红系相关的珠蛋白基因的表达发现,发现在β珠蛋白基因簇而言,ε基因的表达急剧下降,可达60%左右,而β基因的表达不受影响,一个出乎意料的现象是,γ基因的表达也有约20%左右的下降,这个和文献报道SATB1表达降低后,γ基因的表达上升相反,因为我们所用的细胞是一种发育早期的K562细胞,与文献报道所用的发育后期的K562细胞不同,在发育早期的K562细胞里,当hemin诱导时ε和γ基因的表达都是上调的,所以这种结果也是苻合细胞特性的。接下来我们检测了红系特异转录因子,如GATA1/2,EKLF,CTCF,NFE2等等的表达,结果表明,这些转录因子的表达基本没有什么变化。接着我们用ChIP的方法检测了在这些位点上,SATB1的结合变化情况,结果表明对于HS2MAR,HBEMAR和8150而言,它们和SATB1的结合明显下降,而对于HBGMAR而言,仍旧是很低的结合。我们又用3C的方法来检测这些MARs区域之间的相互作用,结果表明HBEMAR和HS2MAR以及8150之间的相互作用明显减弱,而对于HBGMAR和HS2MAR以及8150之间的相互作用而言,并没有明显的变化,同时我们还检测了HS2核心序列和ε基因以及γ基因的启动子之间的相互作用,发现HS2核心序列和ε基因的启动子之间的相互作用减弱很多而HS2核心序列和γ基因的启动子之间的相互作用只有很微弱的变化。由此我们推断SATB1确实对于ε基因以及它的MARbase的形成而言是一个必需的蛋白因子,而对于γ基因的影响只是由于SATB1影响了调控元件从而间接的影响到了该基因的表达。
接着我们又分析了在Hemin诱导前后SATB1本身的修饰情况的变化,结果发现在诱导分化后,SATB1的乙酰化减弱,有文献表明,乙酰化修饰减弱能够使SATB1和DNA的结合变强,说明由SATB1介导所形成的MARbase由于SATB1的修饰变化有一个动态的调节从而对基因表达变化起到动态的调节。最后我们利用免疫荧光,GFP-SATB1融合蛋白原位观察以及ChIP的方法证明SATB1和上述的MARs区的结合在细胞分裂时期的染色体上并不是完全解离的,而是有部分的保留,这种保留对于下一轮细胞周期时,活性base以及活性染色质构象的重建可能起到很重要的作用。
综上所述,我们的研究表明SATB1能通过介导ε基因以及其调控区的MARs之间的相互作用形成MARbase的方式从而调控活性染色质结构的形成以及基因表达,同时SATB1本身的修饰变化情况能动态的调节base的形成,并且这种base的结构在细胞分裂时期是有一定程度的保留,以有利于下一轮细胞周期活性结构的重建。
Cell and cell nucleus are both well-organized. Many important biological processes including gene transcription, DNA replication happen in the nucleus. As we have known, gene transcriptionis is exquisitely regulated. Disturbance of the gene regulation frequently results in severe diseases. In depth study of the mechanisms of gene regulation will provide the clues to know the mechanisms of many diseases, which will help to design effective drugs.
Gene expression can be regulated at three levels including DNA, chromatin and nuclear level. As we have known, the three levels of regulation are interrelated to each other. The interaction between cis-regulatory elements and trans-regulatory factors reflects DNA level regulation. Many regulatory elements are far away from genes and they can contact genes by chromatin folding. The contacting and folding is chromatin level regulation. A basic and important question is how the remote regulatory elements bypass the long-range distance and regulate gene expression. Two models have been proposed, that is, the Contact Model and Non-contact model. A basic model in Contact-Model is Looping Model, which describes that the trans-factors binding to long-range enhancing elements can contact the target gene promoters through the formation of looping structure to overcome the spatial distance between them. Non-contact Model is represented by the Linking Model ,which suggests that LCR can not contact genes' promoters directly but direct transcriptional factors and enhancer facilitators to bind chromatin elements along with the gene locus.
The regulation at both DNA level and chromatin level happen in the nucleus and are closely related to the nuclear structure. Many regulatory proteins are nuclear proteins and they have important roles in the initiation and termination of gene expression. The nucleus provides the space for the gene expression. Many studies suggested that the chromatin fragment can loop out of its chromosome territory (CT) when the gene actively expresses, which is associated with regulation machinery distributed in the interval of chromosomes. This is the famous CT-IC model. Since then, the gene localization has developed from simply being described as at the euchromatin region and heterochromatin region to more complicated nuclear localization. Therefore, the gene regulation attracted more attention now.
Recent studies have showed that nuclear matrix is an important non-chromatin structure in the nucleus and the nuclear matrix can have influence on the gene expression, chromatin conformation and gene localization by recruiting the transcriptional factors and enzymes. Some studies have suggested that the binding between nuclear matrix and gene can affect the gene expression. A group of important proteins, called the matrix binding proteins can mediate the binding between the nuclear matrix and chromatin fragments. The DNA elements that associate with nuclear matrix were named matrix attachment regions (MAR). The binding between MARs and matrix is selective and the selectivity is related with the gene expression. MARs binding proteins have been confirmed including SATBl, cux, SMAR1 and PARP. We have studied the function of SATBl in regulating gene expression. The characteristic self-association of SATBl lead to the formation of a birdcage structure which provides a platform for gene expression regulation and chromatin fragments crosstalking. A previous report has confirmed that SATBl can up-regulate the expression ofε-globin gene and down-regulate the expression ofγ-globin gene. The regulation is related to the binding of SATBl to special MARs. In this study, we have explored the regulatory function of SATBl toβ-globin gene cluster at chromatin level.
We used the QACT to capture possible associated fragments with a known MAR element in HS2 ofβ-globin LCR (HS2MAR, the leader). The results showed that there are three HS2MAR associated chromatin fragments including 8150 , a privously unknown element locates between HS4 and HS5, HBEMAR that locates upstream ofεgene promoter, HBGMAR that locates upstream ofγ~A gene promoter. HBEMAR and HBGMAR have been confirmed to be MARs. Our EMSA and ChIP results had suggested that 8150 is a potential MAR. 3C assay had showed that HBEMAR and HBGMAR can associated with HS2MAR and 8150 elements; also, the associations can be strengthened after induction of the cells by Hemin. These data indicated that a MAR base structon may exist. Our ChIP assay showed that HS2MAR、8150 and HBEMAR can bind SATB1 and the binding increase after Hemin induction . The ChIP-3C results showed that SATB1 can bind to HBEMAR、HS2MAR and 8150 in vivo and mediated the associations among these MARs in theβ-globin gene cluster, especially the association between HBEMAR and upstream regulatory fragments. We presumed that SATB1 function as core of the MARbase. To explore if SATB1 is necessary for the MARbase, RNA interference was used to knock down SATB1 expression in K562 cells . Expression assay of globin genes showed that embryonic gene likeεandζgenes were substantially decreased. For the fetal and adult stage globin genes, while the expression ofβ-globin gene showed no obvious change,γandαglobin genes been decreased upon STAB1 down-regulation, which is not consistent with previously reported results. We reasoned that this may result from cell differences. Our K562 cell is an early passage K562 cells that is different from the late passage K562 cells used in that the above mentioned report. Our K562 cells can be induced by Hemin into the erythroid direction with the up-regulation of bothεandγglobin genes. In the case of late passage K562 cells, the expression ofεglobin gene is down-regulated and the expression ofγgene is up-regulated with Hemin induction. Our results also showed that the expression of erythroid specific transcriptional factors had no obvious change. The ChIP assay showed that the binding of SATB1 to these MARs reduced . The 3C assay showed that the associations between HBEMAR and HS2MAR/8150 decreased substantially, but not the associations between HBGMAR and HS2MAR/8150. Another 3C assay showed that the association between HS2 core sequence and HBE gene promoter had also been reduced in the SATB1 RNAi cells. We concluded that SATB1 is necessary for theεspecific MARbase formation, forγspecific MARbase, SATB1 is not necessary and the influence onγ-globin gene expression may result from indirect effects .
We next analyzed the acetylation status of SATB1 after hemin induction of the K562 cells. We found that the acetylation of SATB1 had been reduced after induction. A previous paper had showed that the acetylation of SATB1 can reduce the binding of SATB1 to DNA, so that the acetylation change of SATB1 can serve as a dynamic regulator of the MARbase. Finally, immunofluorenscence assay、GFP-SATB1 fusion protein localization analysis and ChIP assay were used to show that the binding of SATB1 to these MARs can be partially maintained on mitotic chromosome.
Our results indicated that SATB1 can mediate the formation of aεgene specific MARbase to regulate the high-order chromatin structure ofβ-globin gene cluster and that the acetylation state of SATB1 may serve as a dynamic regulator of the MARbase. Meanwhile, the MARbase may be maintained to some degree during cell mitosis and facilitate the reestablishment of active chromatin structure in the next cell cycle.
引文
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