title: Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.
abstract: BACKGROUND
  Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various lncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the lncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of lncRNAs and their secondary structures across the Anopheles genus.
  
  
  RESULTS
  Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 lncRNAs and more than 300 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that lncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles.
  
  
  CONCLUSIONS
  This study offers one of the first lncRNA secondary structure analyses in vector insects. Our description of lncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into lncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.
authors.affiliation: Boston College, Chestnut Hill, MA, 02467, USA. Jenkinad@bc.edu.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Jenkins
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. Robert.waterhouse@gmail.com.|Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland. Robert.waterhouse@gmail.com.|Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA. Robert.waterhouse@gmail.com.|The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA. Robert.waterhouse@gmail.com.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Waterhouse
authors.affiliation: Boston College, Chestnut Hill, MA, 02467, USA. marc.muskavitch@biogen.com.|Biogen Idec, 14 Cambridge Center, Cambridge, MA, 02142, USA. marc.muskavitch@biogen.com.
authors.forename: Marc A T
authors.initials: MA
authors.lastname: Muskavitch
mesh_terms: D000818:Animals; D000852:Anopheles / Q000235:genetics*; D017124:Conserved Sequence; D004331:Drosophila melanogaster / Q000235:genetics; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D009690:Nucleic Acid Conformation; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger