Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq.. Glycine max

In order to dissect the gene regulatory network during the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue, we constructed ChIP-Seq libraries for NAC and YABBY transcription factors using pooled cotyledons from seedling developmental stage 4 and stage 5. Millions of raw reads obtained from ChIP-Seq libraries were aligned to the reference soybean genome using the ultrafast Bowtie aligner to obtain quantitative data for genome matched reads. MACS software was used to call peaks representing enriched binding sites for NAC and YABBY transcription factors. Based on our ChIP-Seq data, we identified 72 genes are potentially regulated by NAC transcription factor and 96 genes by YABBY transcription factor. The motif analysis using MEME discovered three separate motifs for the NAC and YABBY transcription factors. For the NAC transcription factor, three commonly found motifs were G[AT]G[AG]G[AG]GA, C[AC]C[GA][TC][GA]CC and TGGGCC . The first one matched to a known zinc finger motif and the last two were identified as leucine zippers in the database of plant transcription factor binding motifs, JASPAR CORE plants. Similarly the three most commonly found motifs for YABBY transcription factors are CC [CA][TC]C[TA][CT]C, GA[AG]AGAAA and CCCCAC . The first two motifs matched to a known zinc finger motif and the last one was an AP2 MBD-like motif. Overall design: Construction of ChIP-Seq libraries for NAC and YABBY transcription factors using germinating cotyledons from seedling developmental stages

为解析子叶从非光合贮藏组织向代谢活跃的光合组织功能转变过程中的基因调控网络，我们使用幼苗发育第4期和第5期的混合子叶，构建了NAC与YABBY转录因子的染色质免疫共沉淀测序（ChIP-Seq）文库。从ChIP-Seq文库获得的数百万条原始读段，采用超快速Bowtie比对工具比对至参考大豆基因组，以获取基因组匹配读段的定量数据。使用MACS软件识别NAC与YABBY转录因子富集结合位点的峰。基于本研究的ChIP-Seq数据，我们鉴定出72个潜在受NAC转录因子调控的基因，以及96个潜在受YABBY转录因子调控的基因。使用MEME软件开展基序分析，共发现针对NAC与YABBY转录因子的3种独立基序：针对NAC转录因子，其三种常见基序分别为G[AT]G[AG]G[AG]GA、C[AC]C[GA][TC][GA]CC与TGGGCC，其中第一种基序与已知的锌指基序匹配，后两种基序在植物转录因子结合基序数据库JASPAR CORE plants中被鉴定为亮氨酸拉链基序；同样地，YABBY转录因子的三种最常见基序为CC[CA][TC]C[TA][CT]C、GA[AG]AGAAA与CCCCAC，其中前两种基序与已知的锌指基序匹配，最后一种基序属于AP2 MBD类基序。实验整体设计：采用幼苗发育阶段的萌发子叶，构建NAC与YABBY转录因子的ChIP-Seq文库。