RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

By Pascal J. Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke‐Andersen, Marianne S. Christensen, C. K. Mapendano, M. Schierup, T. Jensen. Science, 2008

771 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c22dba2c20cf8015fd8ae70488a16d089ebfb690

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In Molecular Biology

1. Johannes Rinn
2. Howard Y. Chang
3. Ling-Ling Chen
4. John S. Mattick
5. Aviv Regev
6. Claes Wahlestedt
7. David L. Spector
8. J. Wilusz

Citations in the corpus

• Non-coding RNA: what is functional and what is junk? (2015, neutral): “…RNA degradation machinery is either depleted or inhibited (Wyers et al., 2005; Davis and Ares, 2006; Thiebaut et al., 2006; Chekanova et al., 2007; Milligan et al., 2008; Preker et al., 2008; Vasiljeva et al., 2008; Neil et al., 2009; Xu et al., 2009; Tisseur et al., 2011; Tan-Wong et al., 2012).”
• Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. (2011, background): “Unstable, likely noncoding, transcripts can also be derived from divergent (bidirectional) transcription in both yeast and mammals (Core et al. 2008; Preker et al. 2008; Seila et al. 2008).”
• Long non-coding RNAs with enhancer-like function in human (2010, background): “There has also been reports of divergent transcription of short RNAs flanking transcriptional start sites of the active promoters (Core et al., 2008; Preker et al., 2008; Seila et al., 2008).”
• Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer (2016, background): “lncRNAs have been generally thought to be unstable due to their low expression levels and the existence of known classes of unstable transcripts such as the promoter upstream transcripts (PROMPTs) [44].”
• Long Noncoding RNAs: Past, Present, and Future (2013, background): “Fewer of the newly discovered NATs are spliced or polyadenylated when compared to mRNAs or stand-alone lncRNAs, and while the expression of SAS pairs is more intercorrelated (either positively or negatively) than expected by chance alone, whether most NATs have biological function remains to be…”
• Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution (2015, background): “While almost all divergent transcription results in short unstable transcripts [41-43,72,73], we and others have reported over 500 lincRNAs that are transcribed divergently to protein coding genes [9,35,62].”
• Transcriptome analysis by strand-specific sequencing of complementary DNA (2009, background): “Recent sequencing of short RNAs demonstrated that divergent transcription is associated with promoter regions of the majority of active genes in mammals (5,19,20).”
• Long noncoding RNAs: functional surprises from the RNA world. (2009, background): “4-kb antisense ncRNA that is rapidly degraded by the exosome, a phenomenon that has made detecting such unstable transcripts often difficult, except when RNA decay activities are depleted (Wyers et al. 2005; Davis and Ares 2006; Preker et al. 2008).”
• Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions (2012, background): “This non-annotated transcript locates to a highly conserved region and might be classified as PROMPT (28).”
• A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers (2010, background): “However, enhancergenerated transcripts are very unstable, possibly due to a constitutive surveillance by the nuclear exosome [39,40], leading to their complete degradation or the generation of short RNAs [41].”
• Progression through the RNA polymerase II CTD cycle (2009, background): “The fact that at least some of these short transcripts are rapidly degraded by the exosome (Preker et al., 2008) indicates that they are released from the transcription elongation complex, which is to say that they are termination products rather than precursors to full-length transcripts.”
• The rise of regulatory RNA (2014, background): “There are also other reports of less distinct classes of promoter-associated RNAs called PASRs 125 , TSSa-RNAs 126 and PROMPTS 127 , some of which may play a role in RNA-directed transcriptional gene silencing 128 .”
• Regulatory roles of natural antisense transcripts (2009, background): “Moreover, antisense transcripts have been documented for many active promoter”