title: The Long Noncoding RNA Transcriptome ofDictyostelium discoideumDevelopment.
abstract: Dictyostelium discoideumlive in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) inD. discoideumTo characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by whichD. discoideumcompensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030 rafael@genialis.com gadi@bcm.edu.
authors.forename: Rafael D
authors.initials: RD
authors.lastname: Rosengarten
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030.
authors.forename: Balaji
authors.initials: B
authors.lastname: Santhanam
authors.affiliation: Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030.
authors.forename: Janez
authors.initials: J
authors.lastname: Kokosar
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030 rafael@genialis.com gadi@bcm.edu.
authors.forename: Gad
authors.initials: G
authors.lastname: Shaulsky
mesh_terms: D000926:Anticodon / Q000235:genetics; D004023:Dictyostelium / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D008928:Mitochondria / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D000926:Anticodon; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D012343:RNA, Transfer
keywords: Dictyostelium discoideum; development; noncoding RNA; ribosomal RNA depletion; slime mold; transcriptome time course