A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing

An RNA editing fingerprint of cancer stem cell reprogramming

BACKGROUND

Deregulation of RNA editing by adenosine deaminases acting on dsRNA (ADARs) has been implicated in the progression of diverse human cancers including hematopoietic malignancies such as chronic myeloid leukemia (CML). Inflammation-associated activation of ADAR1 occurs in leukemia stem cells specifically in the advanced, often drug-resistant stage of CML known as blast crisis. However, detection of cancer stem cell-associated RNA editing by RNA sequencing in these rare cell populations can be technically challenging, costly and requires PCR validation. The objectives of this study were to validate RNA editing of a subset of cancer stem cell-associated transcripts, and to develop a quantitative RNA editing fingerprint assay for rapid detection of aberrant RNA editing in human malignancies.

METHODS

To facilitate quantification of cancer stem cell-associated RNA editing in exons and intronic or 3'UTR primate-specific Alu sequences using a sensitive, cost-effective method, we established an in vitro RNA editing model and developed a sensitive RNA editing fingerprint assay that employs a site-specific quantitative PCR (RESSq-PCR) strategy. This assay was validated in a stably-transduced human leukemia cell line, lentiviral-ADAR1 transduced primary hematopoietic stem and progenitor cells, and in primary human chronic myeloid leukemia stem cells.

RESULTS

In lentiviral ADAR1-expressing cells, increased RNA editing of MDM2, APOBEC3D, GLI1 and AZIN1 transcripts was detected by RESSq-PCR with improved sensitivity over sequencing chromatogram analysis. This method accurately detected cancer stem cell-associated RNA editing in primary chronic myeloid leukemia samples, establishing a cancer stem cell-specific RNA editing fingerprint of leukemic transformation that will support clinical development of novel diagnostic tools to predict and prevent cancer progression.

CONCLUSIONS

RNA editing quantification enables rapid detection of malignant progenitors signifying cancer progression and therapeutic resistance, and will aid future RNA editing inhibitor development efforts.

Does RNA editing compensate for Alu invasion of the primate genome?

One of the distinctive features of the primate genome is the Alu element, a repetitive short interspersed element, over a million highly similar copies of which account for >10% of the genome. A direct consequence of this feature is that primates' transcriptome is highly enriched in long stable dsRNA structures, the preferred target of adenosine deaminases acting on RNAs (ADARs), which are the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, there are few essential editing sites conserved across mammals that have maintained their editing level despite the radical change in ADAR target landscape. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which might have contributed to the accelerated evolution of the primates.

Reovirus-mediated induction of ADAR1 (p150) minimally alters RNA editing patterns in discrete brain regions

Transcripts encoding ADAR1, a double-stranded, RNA-specific adenosine deaminase involved in the adenosine-to-inosine (A-to-I) editing of mammalian RNAs, can be alternatively spliced to produce an interferon-inducible protein isoform (p150) that is up-regulated in both cell culture and in vivo model systems in response to pathogen or interferon stimulation. In contrast to other tissues, p150 is expressed at extremely low levels in the brain and it is unclear what role, if any, this isoform may play in the innate immune response of the central nervous system (CNS) or whether the extent of editing for RNA substrates critical for CNS function is affected by its induction. To investigate the expression of ADAR1 isoforms in response to viral infection and subsequent alterations in A-to-I editing profiles for endogenous ADAR targets, we used a neurotropic strain of reovirus to infect neonatal mice and quantify A-to-I editing in discrete brain regions using a multiplexed, high-throughput sequencing strategy. While intracranial injection of reovirus resulted in a widespread increase in the expression of ADAR1 (p150) in multiple brain regions and peripheral organs, significant changes in site-specific A-to-I conversion were quite limited, suggesting that steady-state levels of p150 expression are not a primary determinant for modulating the extent of editing for numerous ADAR targets in vivo.

Genome-wide analysis of Alu editability

A-to-I RNA editing is apparently the most abundant post-transcriptional modification in primates. Virtually all editing sites reside within the repetitive Alu SINEs. Alu sequences are the dominant repeats in the human genome and thus are likely to pair with neighboring reversely oriented repeats and form double-stranded RNA structures that are bound by ADAR enzymes. Editing levels vary considerably between different adenosine sites within Alu repeats. Part of the variability has been explained by local sequence and structural motifs. Here, we focus on global characteristics that affect the editability at the Alu level. We use large RNA-seq data sets to analyze the editing levels in 203 798 Alu repeats residing within human genes. The most important factor affecting Alu editability is its distance to the closest reversely oriented neighbor-average editability decays exponentially with this distance, with a typical distance of ∼800 bp. This effect alone accounts for 28% of the total variance in editability. In addition, the number of Alu repeats of the same and reverse strand in the genomic vicinity, the expressed strand of the Alu, Alu's length and subfamily and the occurrence of reversely oriented neighbor in the same intron\exon all contribute, to a lesser extent, to the Alu editability.

The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome

Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the theoretically catalytically inactive ADR-1. Using high-throughput RNA sequencing of wild-type and adr mutant worms, we expand the repertoire of C. elegans edited transcripts over 5-fold and confirm that ADR-2 is the only active deaminase in vivo. Despite lacking deaminase function, ADR-1 affects editing of over 60 adenosines within the 3' UTRs of 16 different mRNAs. Furthermore, ADR-1 interacts directly with ADR-2 substrates, even in the absence of ADR-2, and mutations within its double-stranded RNA (dsRNA) binding domains abolish both binding and editing regulation. We conclude that ADR-1 acts as a major regulator of editing by binding ADR-2 substrates in vivo. These results raise the possibility that other dsRNA binding proteins, including the inactive human ADARs, regulate RNA editing through deaminase-independent mechanisms.

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and contributes to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in mRNA editing and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high-confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity.

RNA-Seq analysis identifies a novel set of editing substrates for human ADAR2 present in Saccharomyces cerevisiae

ADAR2 is a member of a family of RNA editing enzymes found in metazoa that bind double helical RNAs and deaminate select adenosines. We find that when human ADAR2 is overexpressed in the budding yeast Saccharomyces cerevisiae it substantially reduces the rate of cell growth. This effect is dependent on the deaminase activity of the enzyme, suggesting yeast transcripts are edited by ADAR2. Characterization of this novel set of RNA substrates provided a unique opportunity to gain insight into ADAR2's site selectivity. We used RNA-Seq. to identify transcripts present in S. cerevisiae subject to ADAR2-catalyzed editing. From this analysis, we identified 17 adenosines present in yeast RNAs that satisfied our criteria for candidate editing sites. Substrates identified include both coding and noncoding RNAs. Subsequent Sanger sequencing of RT-PCR products from yeast total RNA confirmed efficient editing at a subset of the candidate sites including BDF2 mRNA, RL28 intron RNA, HAC1 3'UTR RNA, 25S rRNA, U1 snRNA, and U2 snRNA. Two adenosines within the U1 snRNA sequence not identified as substrates during the original RNA-Seq. screen were shown to be deaminated by ADAR2 during the follow-up analysis. In addition, examination of the RNA sequence surrounding each edited adenosine in this novel group of ADAR2 sites revealed a previously unrecognized sequence preference. Remarkably, rapid deamination at one of these sites (BDF2 mRNA) does not require ADAR2's dsRNA-binding domains (dsRBDs). Human glioma-associated oncogene 1 (GLI1) mRNA is a known ADAR2 substrate with similar flanking sequence and secondary structure to the yeast BDF2 site discovered here. As observed with the BDF2 site, rapid deamination at the GLI1 site does not require ADAR2's dsRBDs.

Deciphering the functions and regulation of brain-enriched A-to-I RNA editing

Adenosine-to-inosine (A-to-I) RNA editing, in which genomically encoded adenosine is changed to inosine in RNA, is catalyzed by adenosine deaminase acting on RNA (ADAR). This fine-tuning mechanism is critical during normal development and diseases, particularly in relation to brain functions. A-to-I RNA editing has also been hypothesized to be a driving force in human brain evolution. A large number of RNA editing sites have recently been identified, mostly as a result of the development of deep sequencing and bioinformatic analyses. Deciphering the functional consequences of RNA editing events is challenging, but emerging genome engineering approaches may expedite new discoveries. To understand how RNA editing is dynamically regulated, it is imperative to construct a spatiotemporal atlas at the species, tissue and cell levels. Future studies will need to identify the cis and trans regulatory factors that drive the selectivity and frequency of RNA editing. We anticipate that recent technological advancements will aid researchers in acquiring a much deeper understanding of the functions and regulation of RNA editing.

Spatio-temporal profiling of Filamin A RNA-editing reveals ADAR preferences and high editing levels outside neuronal tissues

RNA editing by ADARs can change the coding potential of protein-coding mRNAs. So far, this type of RNA editing has mainly been shown to affect RNAs expressed in the nervous system with much lower editing levels being observed in other tissues.

The actin crosslinking proteins filamin α and filamin β are widely expressed in most tissues. The mRNAs encoding either protein are edited at the same position leading to a conserved Q to R exchange in both proteins. Using bar-coded next generation sequencing, we show that editing of filamin α is most abundant in the gastrointestinal tract and only to a lesser extent in the nervous system. Using knockout mice, we show that ADARB1 (ADAR2) is responsible for the majority of FLNA editing, while ADAR1 can edit filamin α mRNA in some tissues quite efficiently. Interestingly, editing levels of filamin α and β do not follow the same trend across tissues, suggesting a substrate-specific regulation of editing.