The Air Noncoding RNA: An Imprinted cis-silencing Transcript

Braidotti, Giovanna; Baubec, Tuncay; Pauler, Florian M.; Seidl, Christine; Smrzka, Oskar W.; Stricker, Stefan H.; Yotova, Iveta; Barlow, Denise P.

doi:10.1101/sqb.2004.69.55

Cited by 65 publications

(59 citation statements)

References 72 publications

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“…Consistent with this, Igf2r exhibits allele-specific histone modifications (Fournier et al 2002). However, RNA FISH analysis using specific probes against Air RNA did not show coating by Air RNA of the imprinted chromosomal region (Braidotti et al 2004). …”

Section: Kcnq1 Locusmentioning

confidence: 59%

“…Genomic imprinting was first discovered on the X chromosome, where Sharman and colleagues (Richardson et al 1971;Sharman 1971) described a form of XCI in marsupials in which the paternal X chromosome is preferentially silenced. Other than in mammals, genomic imprinting has also been identified in angiosperm plants and in a few insects (Braidotti et al 2004). Recent studies have shown that >100 genes are imprinted in mammals, either "paternally imprinted" (the gene is silent on the paternal allele) or "maternally imprinted" (the gene is silent on the maternal allele).…”

Section: Roles Of Ncrnas In Genomic Imprinting: One Is Enoughmentioning

confidence: 99%

“…DMR2 resides in a promoter that drives the transcription of a nonprotein-coding antisense transcript, Air, which partially overlaps with Igf2r. Air is an ∼108-kb, capped, polyadenylated, ncRNA and is transcribed exclusively by RNA pol II from the paternal allele (Wutz et al 1997;Braidotti et al 2004;Seidl et al 2006). The majority of Air transcripts evade cotranscriptional splicing resulting in mature unspliced, highly unstable nuclear transcripts (Seidl et al 2006).…”

Section: Kcnq1 Locusmentioning

confidence: 99%

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Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum

Prasanth¹,

Spector²

2007

Genes Dev.

364

305

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A large portion of the eukaryotic genome is transcribed as noncoding RNAs (ncRNAs). While once thought of primarily as "junk," recent studies indicate that a large number of these RNAs play central roles in regulating gene expression at multiple levels. The increasing diversity of ncRNAs identified in the eukaryotic genome suggests a critical nexus between the regulatory potential of ncRNAs and the complexity of genome organization. We provide an overview of recent advances in the identification and function of eukaryotic ncRNAs and the roles played by these RNAs in chromatin organization, gene expression, and disease etiology.

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Section: Kcnq1 Locusmentioning

confidence: 59%

Section: Roles Of Ncrnas In Genomic Imprinting: One Is Enoughmentioning

confidence: 99%

Section: Kcnq1 Locusmentioning

confidence: 99%

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Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum

Prasanth¹,

Spector²

2007

Genes Dev.

364

305

View full text Add to dashboard Cite

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“…The human IGF2R gene shows a polymorphic type of imprinted expression that is limited to embryonic stages, whereas adult tissues have been reported to show only biparental expression (Xu et al 1993;Killian et al 2001). This contrasts to the maintenance of imprinted Igf2r expression in most tissues of the mouse embryo and adult (Braidotti et al 2004). Alternatively, it may be that some types of regulatory element are not conserved in evolution.…”

Section: Evolutionary Conservation Versus Unbiased Approachesmentioning

confidence: 61%

“…Thus, these two DHS show parental-specific regulation that correlates the presence of the DHS with the expressed parental allele. However, the presence of a DHS may not reflect the expression status of these promoters, as the Air promoter DHS9 is also present in a slightly modified form in ES cells, which do not express Air (Braidotti et al 2004). ES cells carry the maternal-specific DNA methylation imprint on the Air promoter (Stoger et al 1993), which indicates that the presence of the DHS on the paternal allele likely correlates with the absence of DNA methylation.…”

Section: Dhs Mapping To Interspersed Repeatsmentioning

confidence: 99%

Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements

Pauler

Stricker²,

Warczok³

et al. 2005

Genome Res.

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Epigenetic mechanisms restrict the expression of imprinted genes to one parental allele in diploid cells. At the Igf2r/Air imprinted cluster on mouse chromosome 17, paternal-specific expression of the Air noncoding RNA has been shown to silence three genes in cis: Igf2r, Slc22a2, and Slc22a3. By an unbiased mapping of DNase I hypersensitive sites (DHS) in a 192-kb region flanking Igf2r and Air, we identified 21 DHS, of which nine mapped to evolutionarily conserved sequences. Based on the hypothesis that silencing effects of Air would be directed towards cis regulatory elements used to activate genes, DHS are potential key players in the control of imprinted expression. However, in this 192-kb region only the two DHS mapping to the Igf2r and Air promoters show parental specificity. The remaining 19 DHS were present on both parental alleles and, thus, have the potential to activate Igf2r on the maternal allele and Air on the paternal allele. The possibility that the Igf2r and Air promoters share the same cis-acting regulatory elements, albeit on opposite parental chromosomes, was supported by the similar expression profiles of Igf2r and Air in vivo. These results refine our understanding of the onset of imprinted silencing at this cluster and indicate the Air noncoding RNA may specifically target silencing to the Igf2r promoter.

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The control of polycomb repressive complexes by long noncoding RNAs

et al. 2021

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The polycomb repressive complexes 1 and 2 (PRCs; PRC1 and PRC2) are conserved histone-modifying enzymes that often function cooperatively to repress gene expression. The PRCs are regulated by long noncoding RNAs (lncRNAs) in complex ways. On the one hand, specific lncRNAs cause the PRCs to engage with chromatin and repress gene expression over genomic regions that can span megabases. On the other hand, the PRCs bind RNA with seemingly little sequence specificity, and at least in the case of PRC2, direct RNA-binding has the effect of inhibiting the enzyme. Thus, some RNAs appear to promote PRC activity, while others may inhibit it. The reasons behind this apparent dichotomy are unclear. The most potent PRC-activating lncRNAs associate with chromatin and are predominantly unspliced or harbor unusually long exons.Emerging data imply that these lncRNAs promote PRC activity through internal RNA sequence elements that arise and disappear rapidly in evolutionary time. These sequence elements may function by interacting with common subsets of RNA-binding proteins that recruit or stabilize PRCs on chromatin.

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The Air Noncoding RNA: An Imprinted cis-silencing Transcript

Cited by 65 publications

References 72 publications

Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum

Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum

Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements

The control of polycomb repressive complexes by long noncoding RNAs

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