The Reality of Pervasive Transcription

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
PLoS Biology (Impact Factor: 9.34). 07/2011; 9(7):e1000625; discussion e1001102. DOI: 10.1371/journal.pbio.1000625
Source: PubMed


Despite recent controversies, the evidence that the majority of the human genome is transcribed into RNA remains strong.

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    • "For example, ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are universally used in protein synthesis , small nuclear RNAs (snRNAs) catalyze pre-mRNA splicing, and telomerase RNA ensures that no genetic information is lost from the ends of eukaryotic chromosomes. With the recent realization that transcription is pervasive across eukaryotic genomes [1] [2], it is now clear that these classic " housekeeping " noncoding RNAs represent only the tip of the iceberg. As most (~75%) of the human genome is transcribed, each of our cells likely generates tens of thousands of additional transcripts with little or no predicted protein-coding capacity [3–7]. "
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    ABSTRACT: Most of the human genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs. Many of these transcripts have a 5' cap and a poly(A) tail, yet some of the most abundant long noncoding RNAs are processed in unexpected ways and lack these canonical structures. Here, I highlight the mechanisms by which several of these well-characterized noncoding RNAs are generated, stabilized, and function. The MALAT1 and MEN β (NEAT1_2) long noncoding RNAs each accumulate to high levels in the nucleus, where they play critical roles in cancer progression and the formation of nuclear paraspeckles, respectively. Nevertheless, MALAT1 and MEN β are not polyadenylated as the tRNA biogenesis machinery generates their mature 3' ends. In place of a poly(A) tail, these transcripts are stabilized by highly conserved triple helical structures. Sno-lncRNAs likewise lack poly(A) tails and instead have snoRNA structures at their 5' and 3' ends. Recent work has additionally identified a number of abundant circular RNAs generated by the pre-mRNA splicing machinery that are resistant to degradation by exonucleases. As these various transcripts use non-canonical strategies to ensure their stability, it is becoming increasingly clear that long noncoding RNAs may often be regulated by unique post-transcriptional control mechanisms. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy. Copyright © 2015. Published by Elsevier B.V.
    Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 06/2015; DOI:10.1016/j.bbagrm.2015.06.003
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    • "Overall, 11710 transcripts were detected in the two cell types, representing 70% of the expected Ectocarpus transcriptome. Moreover, another third of the reads mapped onto intergenic regions, a result that could reflect pervasive transcription (Clark et al., 2011). Analysis of those reads will likely unravel interesting features of this yet mysterious characteristic of eukaryotic genomes. "
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    ABSTRACT: Laser capture microdissection (LCM) facilitates the isolation of individual cells from tissue sections, and when combined with RNA amplification techniques, it is an extremely powerful tool for examining genome-wide expression profiles in specific cell-types. LCM has been widely used to address various biological questions in both animal and plant systems, however, no attempt has been made so far to transfer LCM technology to macroalgae. Macroalgae are a collection of widespread eukaryotes living in fresh and marine water. In line with the collective effort to promote molecular investigations of macroalgal biology, here we demonstrate the feasibility of using LCM and cell-specific transcriptomics to study development of the brown alga Ectocarpus siliculosus. We describe a workflow comprising cultivation and fixation of algae on glass slides, laser microdissection, and RNA amplification. To illustrate the effectiveness of the procedure, we show qPCR data and metrics obtained from cell-specific transcriptomes generated from both upright and prostrate filaments of Ectocarpus.
    Frontiers in Plant Science 02/2015; 6(54). DOI:10.3389/fpls.2015.00054
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    • "We used the standard genome annotation as provided by Ensembl to assign alternative transcripts to genes and to divide exons into constitutive (defined as the exons that form part of all possible alternative transcripts of the same gene) and alternative (those forming part of only a subset of a gene's transcripts). In this sense our analysis was entirely based on transcripts instead of genes, which are for that matter to be seen as much more complex entities from which a great number of transcripts may originate (Clark et al., 2011). Exons were enumerated according to the order with which they appear in a given transcript, and exon counts were deduced from transcript instead of gene structures. "
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    ABSTRACT: Genomic sequences exhibit self-organization properties at various hierarchical levels. One such is the gene structure of higher eukaryotes with its complex exon/intron arrangement. Exon sizes and exon numbers in genes have been shown to conform to a law derived from statistical linguistics and formulated by Menzerath and Altmann, according to which the mean size of the constituents of an entity is inversely related to the number of these constituents. We herein perform a detailed analysis of this property in the complete exon set of the mouse genome in correlation to the sequence conservation of each exon and the transcriptional complexity of each gene locus. We show that extensive linear fits, representative of accordance to Menzerath–Altmann law are restricted to a particular subset of genes that are formed by exons under low or intermediate sequence constraints and have a small number of alternative transcripts. Based on this observation we propose a hypothesis for the law of Menzerath–Altmann in mammalian genes being predominantly due to genes that are more versatile in function and thus, more prone to undergo changes in their structure. To this end we demonstrate one test case where gene categories of different functionality also show differences in the extent of conformity to Menzerath–Altmann law.
    Computational Biology and Chemistry 12/2014; 53. DOI:10.1016/j.compbiolchem.2014.08.018
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