Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P., 250004, India.
Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India.
Plant Mol Biol. 2020 Sep;104(1-2):113-136. doi: 10.1007/s11103-020-01029-4. Epub 2020 Jul 5.
Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.
本研究揭示了组蛋白 H3 甲基化（通过 H3K4/K27me3 标记检测）、胞嘧啶 DNA 甲基化和小麦 Lr28 介导的叶锈抗性过程中差异基因表达之间的复杂关系。在本研究中，在一对近等基因系（NIL）（背景中含有或不含有 Lr28，品系为 HD2329）中检查了全基因组组蛋白修饰。使用的两种组蛋白标记包括 H3K4me3（激活标记）和 H3K27me3（抑制标记）。将结果与使用相同 NIL 获得的表达水平（使用 RNA-seq）和 DNA 甲基化（MeDIP）数据进行比较。本研究的一些突出特点包括：（i）仅在易感品种中可获得大量差异结合位点（DBS），而在其抗性 NIL 中可获得 H3K4me3 和 H3K27me3 的 DBS；（ii）H3K27me3 标记的 DBS 主要富集在基因间区（>80%），而 H3K4me3 的 DBS 分布在所有基因组区域，包括外显子、内含子、基因间区、TTS（转录终止位点）和启动子；（iii）与 DBS 相关的 14 个基因显示出两个标记的共定位；（iv）与 DBS 相关的基因中只有一小部分（H3K4me3 为 7%，H3K27me3 为 12%）与从 RNA-seq 数据推断的基因表达水平相匹配；（v）使用 qRT-PCR 对 26 个选定的代表性基因进行了验证研究；仅验证了 11 个基因的结果。参与促进感染的重要基因编码的蛋白质通常包含 R 基因蛋白携带的结构域，如 Mlo 样蛋白、蛋白激酶和紫色酸性磷酸酶。同样，参与抗性的基因编码的蛋白质包含携带凝集素激酶、R 基因、天冬氨酸蛋白酶等结构域的蛋白质。总体而言，研究结果表明，在亲和和不亲和互作过程中，下游基因表达存在非常复杂的网络；本研究中鉴定的一些基因可能用于未来涉及 RNAi/过表达方法的验证研究。
