RNA-DNA Differences Are Generated in Human Cells within Seconds after RNA Exits Polymerase II

Wang, Isabel X.; Core, Leighton J.; Kwak, Ho Young; Brady, Lauren; Bruzel, Alan; McDaniel, Lee; Richards, Allison L.; Wu, Ming‐Chi; Grunseich, Christopher; Lis, John T.; Cheung, Vivian G.

doi:10.1016/j.celrep.2014.01.037

Cited by 52 publications

(52 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Altogether, we identified about 80,000 to approximately 367,000 editing sites per fraction, with an average of 83% comprising A-to-I and C-to-U types (Supplemental Table S2). It should be noted that ChA − had the most non-A-to-G or non-Cto-T types, which may reflect existence of unknown biology (Wang et al 2014). Among all the A-to-G sites identified (440,821 in total), 64% and 75% were included in the RADAR (Ramaswami and Li 2014) and REDIportal (Picardi et al 2017) databases, respectively.…”

Section: Subcellular Rna-seq and Rna Editingmentioning

confidence: 99%

RNA editing in nascent RNA affects pre-mRNA splicing

et al. 2018

View full text Add to dashboard Cite

In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood. By sequencing the RNA of different subcellular fractions, we examined the timing of adenosine-to-inosine (A-to-I) RNA editing and its impact on alternative splicing. We observed that >95% A-to-I RNA editing events occurred in the chromatin-associated RNA prior to polyadenylation. We report about 500 editing sites in the 3 ′ acceptor sequences that can alter splicing of the associated exons. These exons are highly conserved during evolution and reside in genes with important cellular function. Furthermore, we identified a second class of exons whose splicing is likely modulated by RNA secondary structures that are recognized by the RNA editing machinery. The genome-wide analyses, supported by experimental validations, revealed remarkable interplay between RNA editing and splicing and expanded the repertoire of functional RNA editing sites.

show abstract

Section: Subcellular Rna-seq and Rna Editingmentioning

confidence: 99%

RNA editing in nascent RNA affects pre-mRNA splicing

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Because RDDs are found so soon after transcription, we posited that R-loops that often occur outside of the polymerase complex may be involved in RDD formation. Results from studying human cells with a gain-of-function mutation in senataxin (L389S) that leads to juvenile amyotrophic lateral sclerosis showed lower RDD frequency, consistent with the involvement of R-loops (Wang et al 2014).…”

Section: Rdds Are Dependent On R-loop Formationmentioning

confidence: 94%

“…Previously, we showed RDDs do not arise during RNA synthesis by RNA Polymerase II nor as a direct consequence of incorporation of modified bases; rather, we showed that RDDs begin to occur in nascent RNA chains ∼55 nt from the RNA Polymerase II active site (Wang et al 2014). Because RDDs are found so soon after transcription, we posited that R-loops that often occur outside of the polymerase complex may be involved in RDD formation.…”

Section: Rdds Are Dependent On R-loop Formationmentioning

confidence: 98%

“…RNA-DNA sequence differences were identified as previously described with some modifications (Li et al 2011;Wang et al 2013Wang et al , 2014. In DNA-seq data, we required a minimum coverage of 10 reads at a given site, and the DNA sequence at this site to be 100% concordant (no reads containing alternate alleles).…”

Section: Rdd Identificationmentioning

confidence: 99%

“…Furthermore, we and others have found that there are other types of RNA-DNA sequence differences (RDDs) that are unlikely to be mediated by these deaminases (Li et al 2011;Bahn et al 2012;Bar-Yaacov et al 2013;Rubio et al 2013;Turner et al 2015). These events are found in normal cells, and altered patterns of RDDs were found in neurologic diseases (van Leeuwen et al 1998;Silberberg et al 2012;Krestel et al 2013;Wang et al 2014) and in cancers (Klimek-Tomczak et al 2006;Martinez et al 2008;Lee et al 2013;Avesson and Barry 2014;Han et al 2014;Niavarani et al 2015). Although differences between RNA and their corresponding DNA templates were known for many years, their discoveries in human beyond the editing events mediated by ADAR and APOBEC families of deaminases were debated.…”

mentioning

confidence: 99%

See 2 more Smart Citations

RNA–DNA sequence differences in Saccharomyces cerevisiae

et al. 2016

Self Cite

View full text Add to dashboard Cite

Alterations of RNA sequences and structures, such as those from editing and alternative splicing, result in two or more RNA transcripts from a DNA template. It was thought that in yeast, RNA editing only occurs in tRNAs. Here, we found that Saccharomyces cerevisiae have all 12 types of RNA-DNA sequence differences (RDDs) in the mRNA. We showed these sequence differences are propagated to proteins, as we identified peptides encoded by the RNA sequences in addition to those by the DNA sequences at RDD sites. RDDs are significantly enriched at regions with R-loops. A screen of yeast mutants showed that RDD formation is affected by mutations in genes regulating R-loops. Loss-of-function mutations in ribonuclease H, senataxin, and topoisomerase I that resolve RNA-DNA hybrids lead to increases in RDD frequency. Our results demonstrate that RDD is a conserved process that diversifies transcriptomes and proteomes and provide a mechanistic link between R-loops and RDDs.

show abstract

Transcription factor binding at Ig enhancers is linked to somatic hypermutation targeting

et al. 2019

View full text Add to dashboard Cite

Secondary diversification of the Ig repertoire occurs through somatic hypermutation (SHM), gene conversion (GCV), and class switch recombination (CSR)—three processes that are initiated by activation‐induced cytidine deaminase (AID). AID targets Ig genes at orders of magnitude higher than the rest of the genome, but the basis for this specificity is poorly understood. We have previously demonstrated that enhancers and enhancer‐like sequences from Ig genes are capable of stimulating SHM of neighboring genes in a capacity distinct from their roles in increasing transcription. Here, we use an in vitro proteomics approach to identify E‐box, MEF2, Ets, and Ikaros transcription factor family members as potential binders of these enhancers. ChIP assays in the hypermutating Ramos B cell line confirmed that many of these factors bound the endogenous Igλ enhancer and/or the IgH intronic enhancer (Eμ) in vivo. Further investigation using SHM reporter assays identified binding sites for E2A and MEF2B in Eμ and demonstrated an association between loss of factor binding and decreases in the SHM stimulating activity of Eμ mutants. Our results provide novel insights into trans‐acting factors that dictate SHM targeting and link their activity to specific DNA binding sites within Ig enhancers.

show abstract

RNA-DNA Differences Are Generated in Human Cells within Seconds after RNA Exits Polymerase II

Cited by 52 publications

References 56 publications

RNA editing in nascent RNA affects pre-mRNA splicing

RNA editing in nascent RNA affects pre-mRNA splicing

RNA–DNA sequence differences in Saccharomyces cerevisiae

Transcription factor binding at Ig enhancers is linked to somatic hypermutation targeting

Contact Info

Product

Resources

About