Transcriptional interference: an unexpected layer of complexity in gene regulation

Mazo, Alexander; Hodgson, Jacob W.; Petruk, Svetlana; Sedkov, Yurii; Brock, Hugh W.

doi:10.1242/jcs.007633

Cited by 99 publications

(90 citation statements)

References 59 publications

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“…This profile is consistent with the binding of many common transcription factors, including Pol II, at the 3Ј end of many genes (17). Because antisense transcripts are thought to provide some regulatory function to sense transcription, their termination toward the 5Ј end may result from competition with sense transcription as suggested by the polymerase collision model (18). It is yet to be determined whether any detected sense/antisense pairs are subjected to androgen regulation.…”

Section: Resultssupporting

confidence: 69%

Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model

Lovci

Kwon

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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High-throughput sequencing has rapidly gained popularity for transcriptome analysis in mammalian cells because of its ability to generate digital and quantitative information on annotated genes and to detect transcripts and mRNA isoforms. Here, we described a double-random priming method for deep sequencing to profile double poly(A)-selected RNA from LNCaP cells before and after androgen stimulation. From Ϸ20 million sequence tags, we uncovered 71% of annotated genes and identified hormone-regulated gene expression events that are highly correlated with quantitative real time PCR measurement. A fraction of the sequence tags were mapped to constitutive and alternative splicing events to detect known and new mRNA isoforms expressed in the cell. Finally, curve fitting was used to estimate the number of tags necessary to reach a ''saturating'' discovery rate among individual applications. This study provides a general guide for analysis of gene expression and alternative splicing by deep sequencing.alternative splicing ͉ androgen-regulated gene expression in prostate cancer cells ͉ curve regression ͉ high-throughput sequencing M icroarray-based approaches, especially unbiased tiling arrays, suggest that up to 80% of the genome may be transcribed to produce a huge number of uncharacterized transcripts relative to current gene annotation (1-4). In contrast, recent transcriptome analysis by deep sequencing indicates that the vast majority of expressed transcripts in mammalian tissues and cell lines are confined to annotated genes and exons (5, 6). Although microarraybased approaches suffer from a great degree of uncertainty in relating detected hybridization signals to defined transcripts, sequencing-based approaches tend to be overwhelmed by abundant transcripts in the cell. Construction of ''normalized'' libraries for deep sequencing might facilitate the discovery of low abundance transcripts, many of which may act as noncoding, regulatory RNA in mammalian cells.An advantage of transcriptome analysis by deep sequencing is the ability to detect structural variation of individual transcripts. It is well known that different transcripts from the same genes may be generated by differential promoter usage, heterogeneous transcriptional start sites and alternative 3Ј end formation (2). A recent Pol II ChIP-chip study indicates that protein-coding genes may have an average of 3 to 5 promoters in both the mouse and human genomes (7). Further adding to the diversity in the transcriptome is alternative RNA processing of most protein-coding genes as a consequence of alternative 5Ј and 3Ј splice site choices, exon inclusion/ skipping, intron retention, and combinatorial use of alternative exons (8). It is estimated that up to 74% of human genes undergo alternative splicing, which is believed to contribute to the complexity of the proteome in mammalian cells (9).It is striking to note that individual laboratories now have the capacity to generate sequenced tags that are on the same order of sequenced mRNA/ESTs in publicly availab...

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Section: Resultssupporting

confidence: 69%

Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model

Lovci

Kwon

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…34). In such a case, it is not the ncRNA itself but its synthesis and the pausing of RNA polymerase during elongation that prevents activator binding (35).…”

Section: Discussionmentioning

confidence: 99%

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Lardenois

Liu

Walther

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

124

217

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Budding yeast noncoding RNAs (ncRNAs) are pervasively transcribed during mitosis, and some regulate mitotic protein-coding genes. However, little is known about ncRNA expression during meiotic development. Using high-resolution profiling we identified an extensive meiotic ncRNA expression program interlaced with the protein-coding transcriptome via sense/antisense transcript pairs, bidirectional promoters, and ncRNAs that overlap the regulatory regions of genes. Meiotic unannotated transcripts (MUTs) are mitotic targets of the conserved exosome component Rrp6, which itself is degraded after the onset of meiosis when MUTs and other ncRNAs accumulate in successive waves. Diploid cells lacking Rrp6 fail to initiate premeiotic DNA replication normally and cannot undergo efficient meiotic development. The present study demonstrates a unique function for budding yeast Rrp6 in degrading distinct classes of meiotically induced ncRNAs during vegetative growth and the onset of meiosis and thus points to a critical role of differential ncRNA expression in the execution of a conserved developmental program.

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“…(ii) Overlapping transcription is thought to cause transcriptional interference (Martianov et al, 2007;Mazo et al, 2007). Accordingly, initiation of transcription from the downstream L1-ASP may interfere with elongation of the original Met transcript.…”

Section: Discussionmentioning

confidence: 99%

Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription

et al. 2010

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The cytosine analogues 5-azacytidine and 5-aza-2 0 -deoxycytidine are currently the most advanced drugs for epigenetic cancer therapy. Both drugs function as DNA methyltransferase (DNMT) inhibitors and lead to the reactivation of epigenetically silenced tumour suppressor genes. However, not much is known about their target sequence specificity and their possible side effects on normally methylated sequences such as long interspersed nuclear element (LINE)-1 retroelements. It has been shown that demethylation and activation of the LINE-1 antisense promoter can drive the transcription of neighbouring sequences. In this study, we show that demethylation of the colon carcinoma cell line HCT116, either by treatment with DNMT inhibitors or by genetic disruption of the major DNMTs, induces the expression of an illegitimate fusion transcript between an intronic LINE-1 element and the proto-oncogene cMet (L1-cMet). Similar findings were also obtained with myeloid leukaemia cells, an established cellular model for the approved indication of azacytidine and decitabine. Interestingly, upregulation of L1-cMet transcription resulted in reduced cMet expression, which in turn led to decreased cMet receptor signalling. Our results thus provide an important paradigm for demethylation-dependent modulation of gene expression, even if the promoter of the corresponding gene is unmethylated.

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Transcriptional interference: an unexpected layer of complexity in gene regulation

Cited by 99 publications

References 59 publications

Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model

Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Demethylation of a LINE-1 antisense promoter in the cMet locus impairs Met signalling through induction of illegitimate transcription

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