Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.
Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.
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DOI：
10.1371/journal.pgen.1006988
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发表时间：
2017-09
期刊：
影响因子：
4.5
通讯作者：
Murray JAH
中科院分区：
文献类型：
--
作者：
Pass DA;Sornay E;Marchbank A;Crawford MR;Paszkiewicz K;Kent NA;Murray JAH
所有真核生物的基因组都被包装成染色质，DNA与有规则图案的核小体和亚核小体大小的蛋白质结构(如可移动和不稳定转录因子(TF)和起始复合体)交织在一起，共同形成一个动态的染色质景观。虽然以前已经分析了拟南芥中核小体位置的细节，但对它们与更动态的亚核小体颗粒(SubNSP)的关系了解较少，亚核小体粒子被定义为比核小体典型的~150bp更短的保护区。这些亚NSP的全基因组图谱以前还没有在植物中被分析过，这项研究调查了动态结合粒子与转录控制的关系。在这里，我们结合差异微球菌核酸酶(MNase)消化和一种改进的配对末端测序方案来揭示广泛颗粒范围内拟南芥细胞的染色质结构景观。将这些数据与RNAseq表达分析联系起来，可以详细了解已识别的DNA结合颗粒与转录活性的关系。差异消化的使用揭示了敏感的位置，包括位于活性基因转录起始点(TSS)上游的不稳定的-1核小体。我们利用光和暗生长研究了染色质景观对环境条件变化的反应，考虑到这种简单的改变导致了大量的转录变化。由此导致的表达和抑制基因套装的变化与核小体定位的变化几乎没有对应关系，但导致了TSS上游的亚NSP的全球和局部的显著变化。我们检查了先前映射的调控光反应的转录因子PIF3、PIF4和CCA1的位置，发现亚NSP的变化与这些结合位点共同定位。这种细小的颗粒结构只有在低水平的MNase消化时才能检测到，当染色质更完全地消化到核小体时就会消失。我们的结论是，利用差异MNase酶对拟南芥基因组进行广谱分析可以检测到被掩盖的敏感特征，而全基因组亚NSP图谱之间的比较揭示了它们分布的动态变化，特别是在不同的基因组位置(即5‘UTRs)。这里使用的方法允许洞察遗传和外部因素在改变与转录变化相关的亚核小体景观方面的复杂影响。DNA是由蛋白质包装成染色质的，染色质的基本单位是组蛋白蛋白质的复合体，它将大约150bp的DNA包裹到核小体中。用微球菌核酸酶等酶消化染色质，可以切割蛋白质颗粒之间的DNA，通过对切割位置进行测序，可以将它们映射到整个基因组中。虽然核小体是最稳定的特征，但较低强度的消化揭示了更广泛的蛋白质颗粒与DNA结合，特别是最常位于基因上游的小的亚核小体颗粒。在这里，我们展示了这些技术可以在植物拟南芥中使用，以绘制整个基因组中颗粒大小范围的染色质景观。我们首次在多细胞高等真核生物中展示了这种染色质景观是对环境变化的动态响应，在这种情况下是光明或黑暗的生长。虽然核小体的定位没有显著变化，但在这些不同的条件下，我们显示了更小、更不稳定的因素的深刻变化。这些变化在许多情况下与调节基因对光响应的转录因子的已知结合位点相对应，这导致我们提出全谱染色质图谱分析可以直接揭示整个基因组中转录因子复合体结合的变化。
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more complete digestion of chromatin to nucleosomes. We conclude that wide-spectrum analysis of the Arabidopsis genome by differential MNase digestion allows detection of sensitive features hereto obscured, and the comparisons between genome-wide subNSP profiles reveals dynamic changes in their distribution, particularly at distinct genomic locations (i.e. 5’UTRs). The method here employed allows insight into the complex influence of genetic and extrinsic factors in modifying the sub-nucleosomal landscape in association with transcriptional changes. DNA is packaged by proteins into chromatin, of which the fundamental unit is a complex of histone proteins that wraps ~150bp of DNA into a nucleosome. Digestion of chromatin with enzymes such as micrococcal nuclease cuts the DNA between the protein particles, and by sequencing the cut sites, they can be mapped across the entire genome. Whilst nucleosomes are the most stable feature, less intensive digestion reveals a wider range of protein particles bound to DNA, in particular small sub-nucleosomal particles located most frequently upstream of genes. Here we show that these techniques can be used in the plant Arabidopsis to map the chromatin landscape of the range of particles sizes across the genome. We show for the first time in a multicellular higher eukaryote that this chromatin landscape is dynamic in response to environmental changes, in this case light or dark growth. Whereas the nucleosome positioning does not change significantly, we show profound changes in the smaller more labile factors under these different conditions. These changes in many cases correspond to the known binding sites of transcription factors that regulate genes in response to light, leading us to propose that full-spectrum chromatin landscape analysis can reveal directly the changes in transcription factor complex binding across the genome.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
7.4
作者：
Fincher, Justin A.;Vera, Daniel L.;Bass, Hank W.
通讯作者：
Bass, Hank W.
DOI：
10.1073/pnas.1316278111
发表时间：
2014-02-11
影响因子：
11.1
作者：
Franco-Zorrilla, Jose M.;Lopez-Vidriero, Irene;Solano, Roberto
通讯作者：
Solano, Roberto
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
7
作者：
Chen K;Xi Y;Pan X;Li Z;Kaestner K;Tyler J;Dent S;He X;Li W
通讯作者：
Li W