Role of alternative polyadenylation in epigenetic silencing and antisilencing

Ma, Liuyin; Guo, Cheng; Li, Qingshun Quinn

doi:10.1073/pnas.1321025111

Cited by 28 publications

(21 citation statements)

References 21 publications

(30 reference statements)

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“…In previous studies, we identified two chromatin regulators, ASI1 and EMD2, that are required to promote distal polyadenylation so that full-length transcripts can accumulate (19,22). It has been hypothesized that ASI1 and EDM2 may function together and interact through an unknown factor (32). In this study, we found that EDM2 can be copurified with ASI1, although the two proteins do not interact directly (Fig.…”

Section: Aipp1 Is An Antisilencing Factor That Affects Gene Body Chgmentioning

confidence: 54%

A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis

Duan

Wang

Zhang

et al. 2017

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

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In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Here we report that ASI1 and EDM2 form a protein complex in vivo via a bridge protein, ASI1-Immunoprecipitated Protein 1 (AIPP1), which is another RNA recognition motif-containing protein. The complex also may contain the Pol II CTD phosphatase CPL2, the plant homeodomain-containing protein AIPP2, and another BAH domain protein, AIPP3. As is the case with dysfunction of ASI1 and EDM2, dysfunction of AIPP1 impedes the use of distal polyadenylation sites at tested intronic HC-containing genes, such as the histone demethylase gene, resulting in a lack of functional full-length transcripts. A mutation in causes silencing of the transgene and genome-wide CHG hypermethylation at gene body regions, consistent with the lack of full-length functional transcripts in the mutant. Interestingly, compared with, , and mutations, mutations in ,, and cause the opposite effects on the expression of intronic HC-containing genes and other genes, suggesting that CPL2, AIPP2, and AIPP3 may form a distinct subcomplex. These results advance our understanding of the interplay between heterochromatic epigenetic modifications and RNA processing in higher eukaryotes.

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Section: Aipp1 Is An Antisilencing Factor That Affects Gene Body Chgmentioning

confidence: 54%

A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis

Duan

Wang

Zhang

et al. 2017

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

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“…As the intronic polyadenylation site is located within the TE‐containing region, the modification of TE elements might control the use of such intronic polyadenylation and therefore regulate the choice of polyadenylation site. In this study we investigated all intronic polyadenylation and found that Gypsy/Copia from retrotransposons and MuDR from transposons made up the majority of TEs located in the long intron, including polyadenylation; this might be related to DNA methylation, as previously reported (Wang et al ., ; Lei et al ., ; Ma et al ., ). More DNA methylation and histone modification data from bamboo will reveal the interplay between epigenetics and polyadenylation in future.…”

Section: Discussionmentioning

confidence: 97%

Comprehensive profiling of rhizome‐associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)

et al. 2017

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Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to its well-developed rhizome system. However, the post-transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and identify genome-wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis-annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron-containing full-length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome-root system were identified. Taken together, these results suggest that post-transcriptional regulation may potentially have a vital role in the underground rhizome-root system.

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“…Quantity and quality measurements were taken using a NanoDrop spectrophotometer. Arabidopsis poly(A) tags (PATs) were generated with 1 mg of total RNA or 0.5 mg of polysomal RNA using Method B1 as described (Ma et al, 2014). The quality of the PAT library was checked with a Bioanalyzer using Agilent High Sensitivity DNA chips (Agilent Technologies), and concentrations were measured with a Qubit fluorometer and a Qubit dsDNA HS assay kit (Life Technologies).…”

Section: Poly(a) Tag Library Preparation and Sequencingmentioning

confidence: 99%

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

et al. 2017

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Stresses from various environmental challenges continually confront plants, and their responses are important for growth and survival. One molecular response to such challenges involves the alternative polyadenylation of mRNA. In plants, it is unclear how stress affects the production and fate of alternative mRNA isoforms. Using a genome-scale approach, we show that in Arabidopsis thaliana, hypoxia leads to increases in the number of mRNA isoforms with polyadenylated 39 ends that map to 59-untranslated regions (UTRs), introns, and protein-coding regions. RNAs with 39 ends within protein-coding regions and introns were less stable than mRNAs that end at 39-UTR poly(A) sites. Additionally, these RNA isoforms were underrepresented in polysomes isolated from control and hypoxic plants. By contrast, mRNA isoforms with 39 ends that lie within annotated 59-UTRs were overrepresented in polysomes and were as stable as canonical mRNA isoforms. These results indicate that the generation of noncanonical mRNA isoforms is an important feature of the abiotic stress response. The finding that several noncanonical mRNA isoforms are relatively unstable suggests that the production of non-stop and intronic mRNA isoforms may represent a form of negative regulation in plants, providing a conceptual link with mechanisms that generate these isoforms (such as alternative polyadenylation) and RNA surveillance.

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Role of alternative polyadenylation in epigenetic silencing and antisilencing

Cited by 28 publications

References 21 publications

A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis

A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis

Comprehensive profiling of rhizome‐associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

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