...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Epigenetics & Chromatin >Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize
【24h】

Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize

机译：优化的减少代表性的亚硫酸氢盐测序揭示了玉米中组织特异性的mCHH岛

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Background DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size of ~2.5?Gb. As an alternative, we adapted region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) to survey genome-wide methylation in maize. Results We developed a pipeline for selecting restriction enzymes in silico and experimentally showed that, in the maize genome, MseI - and CviQI -digested fragments are precisely enriched in promoters and gene bodies, respectively. We proceeded with comparisons of epigenomes and transcriptomes between shoots and tassels and found that the occurrences of highly methylated, tissue-specific, mCHH islands upstream of transcription start sites (TSSs) were positively correlated with differential gene expression. Furthermore, 5′ regulatory regions between TSS and mCHH islands often contain putative binding sites of known transcription factors (TFs) that regulate the flowering process and the timing of the transition from the vegetative to the reproductive phase. By integrating MNase-seq and siRNA-seq data, we found that regions of mCHH islands accumulate 21nt-siRNAs in a tissue-specific manner, marking the transition to open chromatin, thereby ensuring the accessibility of TFs for tissue-specific gene regulation. Conclusions Our ROI-directed RRBS pipeline is eminently applicable to DNA methylation profiling of large genomes. Our results provide novel insights into the tissue-specific epigenomic landscapes in maize, demonstrating that DNA methylation and siRNA and chromatin accessibility constitute a critical, interdependent component that orchestrates the transition from the vegetative to the reproductive phase.
机译：背景DNA甲基化在植物的许多调控过程中起着重要作用。考虑到玉米的基因组大小约为2.5？Gb，以单碱基分辨率在玉米中分析全基因组DNA甲基化在经济上是不可行的。作为替代方案，我们调整了目标区域（ROI）导向的减少表达的亚硫酸氢盐测序（RRBS），以调查玉米中的全基因组甲基化。结果我们开发了一种在计算机中选择限制性酶的管道，并通过实验表明，在玉米基因组中，MseI和CviQI消化的片段分别在启动子和基因体中精确富集。我们进行了茎和t之间表观基因组和转录组的比较，发现转录起始位点（TSSs）上游甲基化程度高，组织特异性的mCHH岛的发生与差异基因表达呈正相关。此外，TSS和mCHH岛之间的5'调控区通常包含已知转录因子（TFs）的推定结合位点，该结合位点调节开花过程和从营养期到生殖期的过渡时间。通过整合MNase-seq和siRNA-seq数据，我们发现mCHH岛的区域以组织特异性方式积累21nt-siRNA，标志着向开放染色质的过渡，从而确保TF可用于组织特异性基因调节。结论我们的ROI导向RRBS管道非常适用于大型基因组的DNA甲基化分析。我们的结果提供了对玉米组织特异性表观基因组格局的新颖见解，表明DNA甲基化和siRNA和染色质可及性构成了关键的，相互依赖的组成部分，协调了从营养到生殖阶段的过渡。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号