title: The head-regeneration transcriptome of the planarian Schmidtea mediterranea.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. t.sandmann@dkfz.de
authors.forename: Thomas
authors.initials: T
authors.lastname: Sandmann
authors.forename: Matthias C
authors.initials: MC
authors.lastname: Vogg
authors.forename: Suthira
authors.initials: S
authors.lastname: Owlarn
authors.forename: Michael
authors.initials: M
authors.lastname: Boutros
authors.forename: Kerstin
authors.initials: K
authors.lastname: Bartscherer
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000235:genetics; D001921:Brain / Q000254:growth & development; D050657:Core Binding Factor alpha Subunits / Q000235:genetics / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D049751:Genome, Helminth; D006257:Head / Q000254:growth & development; D015801:Helminth Proteins / Q000235:genetics* / Q000378:metabolism; D017403:In Situ Hybridization; D010932:Planarians / Q000235:genetics* / Q000378:metabolism; D034622:RNA Interference; D012038:Regeneration / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D050657:Core Binding Factor alpha Subunits; D015801:Helminth Proteins; D014157:Transcription Factors