2011
DOI: 10.1073/pnas.1106630108
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Abstract: Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) promoters in mouse embryonic stem cells (mESCs), and this activity correlates with CpG islands. Here we report the characterization of upstream antisense transcription in regions encoding transcription start site associated RNAs (TSSa-RNAs) at four divergent CpG island promoters: Isg20l1, Tcea1, Txn1, and Sf3b1. We find that upstream antisense RNAs (uaRNAs) have distinct capped 5′ termini and heterogeneous nonpolyadenylated 3′ ends. u… Show more

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Cited by 168 publications
(167 citation statements)
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“…39,46,47 Even more unsettling is the fact that most of these non-consensus promoters support bidirectional initiation of transcription (reviewed in ref. 48). A major challenge for the future will be determining the applicability of the known set of GTFs and the current models of PIC assembly to the most common class of RNP II promoters.…”
Section: The Role Of Tfiif Within the Pre-initiation Complexmentioning
confidence: 99%
“…39,46,47 Even more unsettling is the fact that most of these non-consensus promoters support bidirectional initiation of transcription (reviewed in ref. 48). A major challenge for the future will be determining the applicability of the known set of GTFs and the current models of PIC assembly to the most common class of RNP II promoters.…”
Section: The Role Of Tfiif Within the Pre-initiation Complexmentioning
confidence: 99%
“…For example, in yeast and mammalian cells, it has been observed that transcription at protein-coding promoters often initiates bidirectionally, whereas bidirectional transcription is infrequent in Drosophila (Core et al 2008;Neil et al 2009;Seila et al 2009;Xu et al 2009;Nechaev et al 2010;Flynn et al 2011;Kharchenko et al 2011;Wei et al 2011). How bidirectional transcription initiation drives productive transcription elongation primarily in the coding direction is not well understood (Seila et al 2008(Seila et al , 2009Flynn et al 2011), but a recent report has suggested that gene loops can play a role (Tan-Wong et al 2012). In addition, it has been shown that mammalian enhancer regions are transcribed, but transcription initiation within enhancer regions has not been well characterized (De Santa et al 2010;Kim et al 2010;Melgar et al 2011;Ong and Corces 2011;Preker et al 2011;Wang et al 2011).…”
mentioning
confidence: 99%
“…The mechanisms that regulate transcription start site (TSS)-associated ncRNA expression have recently been examined by several groups (Huang and Workman 2013). In mammalian cells, cotranscriptional and post-transcriptional mechanisms that mediate early termination of antisense ncRNAs and degradation by the RNA exosome complex combine to limit the abundance of TSS-associated RNAs relative to messenger RNAs (mRNAs) initiating from the same promoters (Arigo et al 2006;Thiebaut et al 2006; Thompson and Parker 2007;Preker et al 2008;Flynn et al 2011;Almada et al 2013;Ntini et al 2013). Furthermore, a recent study in yeast has shown that the chromatin assembly complex CAF-1 represses divergent (antisense) transcription at promoters (Marquardt et al 2014).…”
mentioning
confidence: 99%