Intragenic Enhancers Act as Alternative Promoters

Kowalczyk, Monika S.; Hughes, Jim R.; Garrick, David; Lynch, Magnus; Sharpe, Jacqueline A.; Sloane-Stanley, Jackie; McGowan, Simon J.; Gobbi, Marco De; Hosseini, Mona; Vernimmen, Douglas; Brown, Jill M.; Gray, Nicola E.; Collavin, Licio; Gibbons, Richard J.; Flint, Jonathan; Taylor, Stephen; Buckle, Veronica J.; Milne, Thomas A.; Wood, W. G.; Higgs, Douglas R.

doi:10.1016/j.molcel.2011.12.021

Cited by 245 publications

(243 citation statements)

References 38 publications

(55 reference statements)

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“…It is known that RNAPII accumulates at enhancers (19), and it was proposed that intragenic enhancers could act as internal alternative promoters (38). One possibility to explain why AGO1 association to chromatin occurs mostly at active enhancers is that it is due to its interaction with RNAPII.…”

Section: Discussionmentioning

confidence: 99%

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

Alló

Agirre

Bessonov

et al. 2014

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

103

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The roles of Argonaute proteins in cytoplasmic microRNA and RNAi pathways are well established. However, their implication in small RNA-mediated transcriptional gene silencing in the mammalian cell nucleus is less understood. We have recently shown that intronic siRNAs cause chromatin modifications that inhibit RNA polymerase II elongation and modulate alternative splicing in an Argonaute-1 (AGO1)-dependent manner. Here we used chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to investigate the genome-wide distribution of AGO1 nuclear targets. Unexpectedly, we found that about 80% of AGO1 clusters are associated with cell-type-specific transcriptional enhancers, most of them (73%) overlapping active enhancers. This association seems to be mediated by long, rather than short, enhancer RNAs and to be more prominent in intragenic, rather than intergenic, enhancers. Paradoxically, crossing ChIP-seq with RNA-seq data upon AGO1 depletion revealed that enhancer-bound AGO1 is not linked to the global regulation of gene transcription but to the control of constitutive and alternative splicing, which was confirmed by an individual gene analysis explaining how AGO1 controls inclusion levels of the cassette exon 107 in the SYNE2 gene.Argonaute proteins | transcriptional enhancers | alternative splicing A lternative splicing was initially seen as an interesting mechanism to explain protein diversity but affecting a limited number of mammalian genes. The recent development of high-throughput sequencing technologies has dramatically changed this view, generating a renewed interest in alternative splicing. We now know that alternative splicing affects transcripts from more than 90% of human genes (1) and that normal and pathological cell differentiation not only depends on differential gene expression but also on alternative splicing patterns. Mutations in alternative splicing regulatory sequences and factors are involved in the etiology of numerous hereditary diseases, premature aging, and cancer (2).Recently, amid an avalanche of papers reporting various connections between the chromatin context and splicing (3-9), a relationship between splicing and small RNAs has emerged. The convergence of these previously unrelated areas (RNA interference, chromatin, and splicing) has been studied by our laboratory, showing that siRNAs (20-25 nt long) targeting both intronic and exonic regions near the cassette exon 33 (E33, also known as EDI) of the fibronectin gene were able to regulate its alternative splicing by affecting the chromatin context at the target region, with an increase of histone tail modifications associated with gene silencing (H3K9me2 and H3K27me3, i.e., dimethylation of lysine 9 and trimethylation of lysine 27 of histone H3 respectively). Moreover, this effect was shown to be dependent on Argonaute proteins (AGO1 and AGO2) and involves a decrease of RNA polymerase II (RNAPII) elongation, which concomitantly up-regulates E33 inclusion into the mature mRNA (3). More recently, a similar effect was fou...

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Section: Discussionmentioning

confidence: 99%

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

Alló

Agirre

Bessonov

et al. 2014

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

103

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“…a Little or no expression in erythroid cell mRNA.. (107). Rapid advances in genomic technologies, including genomewide association studies, functional genomics, and high throughput gene expression analyses, are increasing our knowledge of gene regulation and its role in determining complex traits (75,108).…”

Section: Discussionmentioning

confidence: 99%

Identification of Biologically Relevant Enhancers in Human Erythroid Cells

Steiner

Bogardus

et al. 2013

Journal of Biological Chemistry

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Background: Programs of cellular development and differentiation are controlled by enhancers. Results: Human erythroid cell type-specific enhancers are marked by p300 and groups of transcription factors. Conclusion: Enhancers are important regulators of species-specific erythroid cell structure and function. Significance: Deciphering how nonpromoter regulatory elements control gene expression in erythroid cells is important for understanding inherited and acquired hematologic disease.

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“…1C). Intragenic enhancers have been shown previously to act as alternative promoters, regulating unidirectional transcription in the direction of the host gene's expression to produce lncRNAs that are abundant, stable (polyadenylated), and spliced (Kowalczyk et al 2012). In the case of the intergenic enhancers studied here, we have no evidence that they produce stable long transcripts.…”

Section: Intergenic Embryonic Enhancers Can Function As Weak Promotersmentioning

confidence: 99%

“…In Caenorhabditis elegans, putative enhancers (intergenic TF-bound regions) have bidirectional eRNA transcription but form longer transcripts in the direction of the closest downstream gene (Chen et al 2013). This resembles some intragenic mammalian enhancers, which also transcribe long noncoding RNA (lncRNA) transcripts in the direction of the gene's transcription (Kowalczyk et al 2012). This suggests that these long unidirectional eRNAs are a different class from short bidirectional unstable eRNAs, or perhaps there is a continuum of eRNA with different lengths and directionality in between.…”

mentioning

confidence: 98%

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

et al. 2018

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Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio-temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.

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Intragenic Enhancers Act as Alternative Promoters

Cited by 245 publications

References 38 publications

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

Identification of Biologically Relevant Enhancers in Human Erythroid Cells

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

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