State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China.
State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China.
Mol Plant. 2017 Jul 5;10(7):962-974. doi: 10.1016/j.molp.2017.05.001. Epub 2017 May 6.
Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are poorly understood. Here, we present genome-wide nucleosome maps of maize shoot and endosperm generated by sequencing the micrococcal nuclease digested nucleosomal DNA. The changes of gene transcriptional status between shoot and endosperm were accompanied by preferential nucleosome loss from the promoters and shifts in the first nucleosome downstream of the transcriptional start sites (+1 nucleosome) and upstream of transcriptional termination sites (-1 nucleosome). Intrinsically DNA-encoded nucleosome organization was largely associated with the capacity of a gene to alter its transcriptional status among different tissues. Compared with tissue-specific genes, constitutively expressed genes showed more pronounced 5' and 3' nucleosome-depleted regions as well as further +1 nucleosome to transcriptional start sites and -1 nucleosome to transcriptional termination sites. Moreover, nucleosome organization was more highly correlated with the plasticity of gene transcriptional status than with its expression level when examined using in vivo and predicted nucleosome data. In addition, the translational efficiencies of tissue-specific genes appeared to be greater than those of constitutively expressed genes. Taken together, our results indicate that intrinsically DNA-encoded nucleosome organization is important, beyond its role in regulating gene expression levels, in determining the plasticity of gene transcriptional status.
核小体是染色质的基本单位，通过调节 DNA 可及性在基因调控中发挥着关键作用。然而，它们在调节组织特异性基因转录中的作用还知之甚少。在这里，我们通过对微球菌核酸酶消化的核小体 DNA 进行测序，生成了玉米茎和胚乳的全基因组核小体图谱。在茎和胚乳之间，基因转录状态的变化伴随着启动子处优先丢失核小体，以及转录起始位点（+1 核小体）下游和转录终止位点（-1 核小体）上游的第一个核小体位置发生改变。内在的 DNA 编码核小体组织在很大程度上与一个基因在不同组织中改变其转录状态的能力有关。与组织特异性基因相比，组成型表达的基因在 5' 和 3' 处具有更明显的核小体缺失区域，并且 +1 核小体更靠近转录起始位点，-1 核小体更靠近转录终止位点。此外，在用体内和预测的核小体数据进行检查时，核小体组织与基因转录状态的可变性比其表达水平具有更高的相关性。此外，组织特异性基因的翻译效率似乎大于组成型表达基因。总之，我们的研究结果表明，内在 DNA 编码核小体组织在决定基因转录状态的可塑性方面很重要，超出了其在调节基因表达水平方面的作用。
