@article{SiegelHonZhangetal.2014,
  author    = {Siegel, T. Nicolai and Hon, Chung-Chau and Zhang, Qinfeng and Lopez-Rubio, Jose-Juan and Scheidig-Benatar, Christine and Martins, Rafeal M. and Sismeiro, Odile and Copp{\´e}e, Jean-Yves},
  title     = {Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum},
  series = {BMC Genomics},
  volume    = {15},
  journal   = {BMC Genomics},
  doi       = {10.1186/1471-2164-15-150},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-119892},
  pages     = {150},
  year      = {2014},
  abstract  = {Background Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of organisms, where these transcripts have been shown to play important roles in the regulation of gene expression. Likewise, the existence of NATs has been observed in Plasmodium but our understanding towards their genome-wide distribution remains incomplete due to the limited depth and uncertainties in the level of strand specificity of previous datasets. Results To gain insights into the genome-wide distribution of NATs in P. falciparum, we performed RNA-ligation based strand-specific RNA sequencing at unprecedented depth. Our data indicate that 78.3\% of the genome is transcribed during blood-stage development. Moreover, our analysis reveals significant levels of antisense transcription from at least 24\% of protein-coding genes and that while expression levels of NATs change during the intraerythrocytic developmental cycle (IDC), they do not correlate with the corresponding mRNA levels. Interestingly, antisense transcription is not evenly distributed across coding regions (CDSs) but strongly clustered towards the 3′-end of CDSs. Furthermore, for a significant subset of NATs, transcript levels correlate with mRNA levels of neighboring genes. Finally, we were able to identify the polyadenylation sites (PASs) for a subset of NATs, demonstrating that at least some NATs are polyadenylated. We also mapped the PASs of 3443 coding genes, yielding an average 3′ untranslated region length of 523 bp. Conclusions Our strand-specific analysis of the P. falciparum transcriptome expands and strengthens the existing body of evidence that antisense transcription is a substantial phenomenon in P. falciparum. For a subset of neighboring genes we find that sense and antisense transcript levels are intricately linked while other NATs appear to be regulated independently of mRNA transcription. Our deep strand-specific dataset will provide a valuable resource for the precise determination of expression levels as it separates sense from antisense transcript levels, which we find to often significantly differ. In addition, the extensive novel data on 3′ UTR length will allow others to perform searches for regulatory motifs in the UTRs and help understand post-translational regulation in P. falciparum.},
  language  = {en}
}
@article{VieiraJonesDanonetal.2012,
  author    = {Vieira, Jacqueline and Jones, Alex R. and Danon, Antoine and Sakuma, Michiyo and Hoang, Nathalie and Robles, David and Tait, Shirley and Heyes, Derren J. and Picot, Marie and Yoshii, Taishi and Helfrich-F{\"o}rster, Charlotte and Soubigou, Guillaume and Coppee, Jean-Yves and Klarsfeld, Andr{\´e} and Rouyer, Francois and Scrutton, Nigel S. and Ahmad, Margaret},
  title     = {Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability},
  series = {PLoS One},
  volume    = {7},
  journal   = {PLoS One},
  number    = {3},
  doi       = {10.1371/journal.pone.0031867},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134513},
  pages     = {e31867},
  year      = {2012},
  abstract  = {Cryptochromes are conserved flavoprotein receptors found throughout the biological kingdom with diversified roles in plant development and entrainment of the circadian clock in animals. Light perception is proposed to occur through flavin radical formation that correlates with biological activity in vivo in both plants and Drosophila. By contrast, mammalian (Type II) cryptochromes regulate the circadian clock independently of light, raising the fundamental question of whether mammalian cryptochromes have evolved entirely distinct signaling mechanisms. Here we show by developmental and transcriptome analysis that Homo sapiens cryptochrome - 1 (HsCRY1) confers biological activity in transgenic expressing Drosophila in darkness, that can in some cases be further stimulated by light. In contrast to all other cryptochromes, purified recombinant HsCRY1 protein was stably isolated in the anionic radical flavin state, containing only a small proportion of oxidized flavin which could be reduced by illumination. We conclude that animal Type I and Type II cryptochromes may both have signaling mechanisms involving formation of a flavin radical signaling state, and that light independent activity of Type II cryptochromes is a consequence of dark accumulation of this redox form in vivo rather than of a fundamental difference in signaling mechanism.},
  language  = {en}
}