Basis of specificity for a conserved and promiscuous chromatin remodeling protein.
Basis of specificity for a conserved and promiscuous chromatin remodeling protein.
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DOI：
10.7554/elife.64061
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发表时间：
2021-02-12
期刊：
影响因子：
7.7
通讯作者：
McKnight JN
中科院分区：
文献类型：
--
作者：
Donovan DA;Crandall JG;Truong VN;Vaaler AL;Bailey TB;Dinwiddie D;Banks OG;McKnight LE;McKnight JN
真核生物的基因组是通过核小体的重新定位而动态组织起来的。Isw 2是一种酶，以前被定义为全基因组的非特异性核小体间隔因子。在这里，我们表明，Isw 2，而不是作为一个专性靶向核小体重塑体内通过物理相互作用与序列特异性因子。我们证明了Isw 2招募因子使用小的和以前未表征的表位，其通过Isw 2辅助蛋白Itc 1中高度保守的酸性残基指导Isw 2活性。这种相互作用将Isw 2定向在靶核小体上，从而允许核小体精确定位在靶位点。最后，我们表明，这些关键的酸性残基已经失去了果蝇血统，可能解释不一致的Isw 2样蛋白的功能。总而言之，这些数据表明了一个“相互作用的屏障模型”，其中Isw 2与序列特异性因子相互作用，以准确和可重复地定位单个靶向核小体，以定义定相染色质阵列的精确边界。DNA将生命的遗传指令编码在一条长而灵活的分子链中，分子链被整齐地包装起来，以适应细胞内的环境。DNA的短片段缠绕在蛋白质周围形成称为核小体的束，然后旋转成染色质纤维，一种更紧凑的DNA形式。虽然核小体是这种节省空间的包装过程的基本组成部分，但它们也在基因表达中起着关键的调节作用，基因表达是基因被解码成工作蛋白质的地方。将核小体以规则的间隔沿着DNA放置总是控制着DNA的哪些部分--以及哪些基因--细胞的机器可以访问和“读取”来制造蛋白质。但是核小体的位置并不是固定的，基因的表达是一个动态的过程。细胞经常解开并重新包装其DNA，而称为染色质重塑蛋白质的分子马达使核小体上下移动DNA，暴露一些基因并阻碍其他基因。一组染色质重塑蛋白被称为模仿开关（ISWI）复合物。长期以来，人们一直认为这些复合物对核小体的定位与潜在的DNA序列或编码的基因无关，也就是说，以非特异性的方式。然而，这一理论尚未得到彻底的检验。ISWI复合物实际上可能在生物体发育的特定时间或响应其他环境因素将核小体置于DNA的某些部分。但如何达到这样的精确度仍然是未知的。为了验证核小体定位的替代理论，Donovan等人研究了普通面包酵母中的ISWI蛋白和核小体。这涉及系统地去除ISWI蛋白质的部分，以观察复合物是否仍然可以定位核小体，以及蛋白质的哪些部分对这项工作至关重要。通过这样做，Donovan等人鉴定了多种“靶向”蛋白，这些蛋白与ISWI蛋白结合并将复合物递送到DNA的特定靶序列。从那里，复合物重塑核小体，将其定位在距离DNA着陆点特定距离处，如进一步的实验所示。这项研究为解释核小体如何定位包装DNA和控制基因表达提供了一个新的模型。Donovan等人已经确定了核小体和ISWI种类的染色质重塑蛋白之间相互作用的新机制。随着进一步的研究，可能会发现更多的这种相互作用。
Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, nonspecific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodeler in vivo through physical interactions with sequence-specific factors. We demonstrate that Isw2-recruiting factors use small and previously uncharacterized epitopes, which direct Isw2 activity through highly conserved acidic residues in the Isw2 accessory protein Itc1. This interaction orients Isw2 on target nucleosomes, allowing for precise nucleosome positioning at targeted loci. Finally, we show that these critical acidic residues have been lost in the Drosophila lineage, potentially explaining the inconsistently characterized function of Isw2-like proteins. Altogether, these data suggest an ‘interacting barrier model,’ where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays. DNA encodes the genetic instructions for life in a long, flexible molecular chain that is packaged up neatly to fit inside cells. Short sections of DNA are wound around proteins to form bundles called nucleosomes, and then spun into chromatin fibres, a more compact form of DNA. While nucleosomes are a fundamental part of this space-saving packaging process, they also play a key regulatory role in gene expression, which is where genes are decoded into working proteins. Placing nucleosomes at regular intervals along DNA invariably controls which parts of the DNA – and which genes – the cell’s machinery can access and ‘read’ to make proteins. But the nucleosomes’ positions are not fixed, and gene expression is a dynamic process. The cell often uncoils and repackages its DNA while molecular motors called chromatin remodelling proteins move nucleosomes up and down the DNA, exposing some genes and obstructing others. One group of chromatin remodelling proteins are called Imitation Switch (ISWI) complexes. It has long been thought that these complexes position nucleosomes with little regard to the underlying DNA sequence or the genes encoded, that is to say in a non-specific way. However, this theory has not been thoroughly tested. It is possible that ISWI complexes actually place nucleosomes on certain parts of DNA at particular times in an organism’s development, or in response to other environmental factors. Except how such precision is achieved remains unknown. To test this alternative theory of nucleosome positioning, Donovan et al. studied ISWI proteins and nucleosomes in common baker’s yeast. This involved systematically removing sections of ISWI proteins to see whether the complexes could still position nucleosomes, and which parts of the proteins where essential for the job. By doing so, Donovan et al. identified multiple ‘targeting’ proteins that bind to ISWI proteins and deliver the complexes to specific target sequences of DNA. From there, the complex remodels the nucleosome, positioning it at a specific distance from its landing site on DNA, as further experiments showed. This research provides a new model for explaining how nucleosomes are positioned to package DNA and control gene expression. Donovan et al. have identified a new mechanism of interaction between nucleosomes and chromatin remodelling proteins of the ISWI variety. It is possible that more interactions of this kind will be discovered with further research.