Transcriptional Landscape of the Human and Fly Genomes: Nonlinear and Multifunctional Modular Model of Transcriptomes

Willingham, Aarron; Dike, Sujit; Cheng, Jill; Manak, J. Robert; Bell, Ian; Cheung, E.; Drenkow, Jörg; Dumais, Erica; Duttagupta, Radharani; Ganesh, Madhavan; Ghosh, Srinka; Helt, Gregg; Nix, David A.; Piccolboni, Antonio; Sementchenko, Victor; Tammana, Hari; Kapranov, Philipp; Gingeras, T

doi:10.1101/sqb.2006.71.068

Cited by 15 publications

(13 citation statements)

References 36 publications

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“…In addition to nested protein-coding genes, animal genomes contain numerous complex arrangements, including incomplete overlaps of protein coding regions and their untranslated regions and various RNA genes [2–6,25]. In particular, a substantial fraction of microRNA and small nucleolar RNA genes are either fully contained within introns of protein-coding genes or overlap with protein-coding exons [14].…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Nested genes and increasing organizational complexity of metazoan genomes

et al. 2008

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The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.

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Section: Conclusion and Perspectivementioning

confidence: 99%

Nested genes and increasing organizational complexity of metazoan genomes

et al. 2008

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“…In humans, such conventional genes account for less than 2% of the genome, yet ~90% of the genome is transcribed (Kapranov et al, 2007; Prasanth and Spector, 2007; Willingham et al, 2006). Much of the noncoding RNA (ncRNA) pool corresponds to intergenic sequences or antisense transcripts of unknown function.…”

Section: Introductionmentioning

confidence: 99%

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

Wierzbicki

Haag

Pikaard

2008

Cell

632

786

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Nuclear transcription is not restricted to genes, but occurs throughout the intergenic and noncoding space of eukaryotic genomes. The functional significance of this widespread noncoding transcription is mostly unknown. We show that Arabidopsis RNA Polymerase IVb/Pol V, a multi-subunit nuclear enzyme required for siRNA-mediated gene silencing of transposons and other repeats, transcribes intergenic and noncoding sequences, thereby facilitating heterochromatin formation and silencing of overlapping and adjacent genes. Pol IVb/Pol V transcription requires the chromatin remodeling protein, DRD1 but is independent of siRNA biogenesis. However, Pol IVb/Pol V transcription and siRNA production are both required to silence transposons, suggesting that Pol IVb/Pol V generates RNAs or chromatin structures that serve as scaffolds for siRNA-mediated heterochromatin forming complexes. Pol IVb/Pol V function provides a solution to a paradox of epigenetic control: the need for transcription in order to transcriptionally silence the same region.

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“…The Drosophila melanogaster genome has been estimated to encode >100 lncRNAs (Tupy et al 2005; Willingham et al 2006; Graveley et al 2011). Many of these lncRNA genes are transcribed during embryogenesis and display spatially restricted expression, with predominant RNA accumulation in the developing central and peripheral nervous system (Inagaki et al 2005; Li et al 2009).…”

mentioning

confidence: 99%

A Conserved Long Noncoding RNA Affects Sleep Behavior inDrosophila

Soshnev¹,

Ishimoto²,

McAllister³

et al. 2011

Genetics

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Metazoan genomes encode an abundant collection of mRNA-like, long noncoding (lnc)RNAs. Although lncRNAs greatly expand the transcriptional repertoire, we have a limited understanding of how these RNAs contribute to developmental regulation. Here, we investigate the function of the Drosophila lncRNA called yellow-achaete intergenic RNA (yar). Comparative sequence analyses show that the yar gene is conserved in Drosophila species representing 40–60 million years of evolution, with one of the conserved sequence motifs encompassing the yar promoter. Further, the timing of yar expression in Drosophila virilis parallels that in D. melanogaster, suggesting that transcriptional regulation of yar is conserved. The function of yar was defined by generating null alleles. Flies lacking yar RNAs are viable and show no overt morphological defects, consistent with maintained transcriptional regulation of the adjacent yellow (y) and achaete (ac) genes. The location of yar within a neural gene cluster led to the investigation of effects of yar in behavioral assays. These studies demonstrated that loss of yar alters sleep regulation in the context of a normal circadian rhythm. Nighttime sleep was reduced and fragmented, with yar mutants displaying diminished sleep rebound following sleep deprivation. Importantly, these defects were rescued by a yar transgene. These data provide the first example of a lncRNA gene involved in Drosophila sleep regulation. We find that yar is a cytoplasmic lncRNA, suggesting that yar may regulate sleep by affecting stabilization or translational regulation of mRNAs. Such functions of lncRNAs may extend to vertebrates, as lncRNAs are abundant in neural tissues.

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Transcriptional Landscape of the Human and Fly Genomes: Nonlinear and Multifunctional Modular Model of Transcriptomes

Cited by 15 publications

References 36 publications

Nested genes and increasing organizational complexity of metazoan genomes

Nested genes and increasing organizational complexity of metazoan genomes

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

A Conserved Long Noncoding RNA Affects Sleep Behavior inDrosophila

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