Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
Genome Biol. 2011 Aug 16;12(8):R76. doi: 10.1186/gb-2011-12-8-r76.
Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown.
To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning.
Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.
扁形动物可以在不到一周的时间内再生头部，包括一个功能齐全的大脑。尽管这些动物在医学研究和再生医学方面具有巨大的潜力，但再生的机制和涉及的分子在很大程度上仍是未知的。
为了鉴定在涡虫头部再生早期阶段差异表达的基因，我们从 3 亿多个来自 16 个不同时间点再生头部的涡虫片段的配对末端读数中生成了一个从头转录组组装。该组装产生了 26018 个假定的转录本，包括跨越多个基因组超级基因座的非常长的转录本，以及数千个同工型。使用来自两个平台的短读数据，我们分析了头部再生的前三天的动态基因调控。我们确定了至少五个不同的时间协同表达类，包括在受伤后几个小时内特异性诱导的基因。此外，我们还研究了一个保守的 Runx 转录因子 smed-runt-like1 的作用。对再生视觉系统的 RNA 干扰 (RNAi) 敲低和免疫荧光分析表明，smed-runt-like1 编码了眼睛形态和光感受器模式的转录调控因子。
短读序列的转录组测序允许同时进行转录本的从头组装和差异表达分析，证明了在扁形动物头部再生过程中存在高度动态的调控。
