Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Sep 9;52(16):9501-9518.
doi: 10.1093/nar/gkae641.

ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection

Berta Eliad  1 , Noa Schneider  1 , Orna Ben-Naim Zgayer  1 , Yarden Amichan  1 , Fabian Glaser  2 , Emily A Erdmann  3 , Suba Rajendren  3 , Heather A Hundley  3 , Ayelet T Lamm  1
Affiliations

ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection

Berta Eliad et al. Nucleic Acids Res. .

Abstract

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans, it is not, making them invaluable for RNA editing research. In C. elegans, ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans. In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.

PubMed Disclaimer

Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Localization of ADR-2 in embryos at different stages of mitosis. (A) Representative immunofluorescence images of DNA (DAPI in blue) and ADR-2 (magenta) in embryos from wild-type (N2), adr-1-/- and adbp-1-/- worms, including adr-2-/- worms as control strain. Their colocalization is shown as the overlap of both images. The surrounding background staining around the embryo in wild-type is probably a staining artifact. (B) Embryos of wild-type (N2), adr-1-/- and adbp-1-/- strains. A representative nucleus from each stage is shown: Int, interphase; Pro, prophase; Meta, metaphase; and Ana, anaphase. Scale bar, 10 μm.
Figure 2.
Figure 2.
Localization of ADR-2 in the hermaphrodite adult gonads, head, body, tail, and sperm. (A) Representative immunofluorescence images of DNA (blue) and ADR-2 (magenta) from wild-type (N2) (top), adbp-1 mutant (middle), and adr-2-/- control (bottom) strains. Their colocalization is shown as the overlap of both images. Scale bar, 30 μm. (B) Representative immunofluorescence images of DNA (blue), ADR-2 (magenta), and MH27 (green) from the head, body, tail, and sperm of wild-type (N2) strain. Their colocalization is shown as the overlap of the three images. Red arrows indicate where ADR-2 is absent. The orange arrow indicates the location of the sperm. Scale bar, 30 μm.
Figure 3.
Figure 3.
Editing sites in adbp-1 mutant worms reside primarily in exons. (A) The bar plot represents known edited sites in the wild-type worms compared to the adbp-1 mutant worms both at the embryo stage and at the L4 larval stage. (B) The bar plot represents known edited sites in adbp-1 mutant worms at the embryo and at the L4 larval stage. (C–F) Pie charts represent the distribution of annotated known editing sites in wild-type worms and the adbp-1 mutant worms in the embryo and L4 stages. In the wild-type embryo worms, we detected 13398 annotated known editing sites (C) and 7908 annotated known editing sites at the L4 stage (D). In the adbp-1 mutant embryo samples, we detected annotated known 188 editing sites (E), while in the adbp-1 mutant L4 worms, we detected 124 annotated known editing sites (F). (G, H) Wild-type worms and adbp-1 mutant worms share significant common edited genes.
Figure 4.
Figure 4.
ADR-2 is enzymatically active in the cytoplasm in adbp-1 mutant, targeting mostly exons. The pie charts describe editing sites in genes found by a pipeline searching for new editing sites in adbp-1 mutant at the embryo (A) and L4 (B) stages. Genes found edited only in the adbp-1 mutant and not in wild-type worms (WT) are represented by the color blue. In contrast, the orange color represents genes in adbp-1 mutant worms that also undergo editing in wild-type worms; however, the edited sites in each gene differ between the strains. Editing sites uniquely found in adbp-1 mutant worms tend to be in exons. (C) Distribution of nucleotides surrounding random adenosine sites and editing sites in wild-type and adbp-1 mutant worms at coding regions, introns, UTRs, and their sums. The x-axis represents the position of the editing site (0) and its surrounding nucleotides. The y-axis represents the probability of finding each nucleotide in each position.
Figure 5.
Figure 5.
Low editing levels impair edited gene expression at the embryo stage. (A–D) The genes expressed in wild-type worms versus adbp-1 mutant worms and the genes expressed in wild-type worms versus ADAR mutant worms, both in the embryo stage, are represented in log scale plots. Each dot represents a gene. Grey dots represent all the genes, blue dots represent edited genes at their 3′UTR, and purple dots represent lncRNAs. The black line is a regression line for all genes, the blue line is the regression line for genes edited at their 3′UTR, and the purple line is the regression line for the lncRNAs. (E, F) The volcano plots describe the log2 fold change versus –log10(P-adjusted) between the genes expressed in wild-type worms to adr-1;adr-2 mutant worms, and wild-type worms to adbp-1 mutant worms at the embryo. Non-significant genes are colored in grey. Differentially expressed genes, which adhere to the following criteria: |log2FoldChange| > 1 and P-adjusted < 0.05, are highlighted in red. Genes with only |log2FoldChange| > 1 are colored green, and genes with only P-adjusted < 0.05 are colored blue.
Figure 6.
Figure 6.
A proposed model of the interaction between ADR-2 and ADBP-1. (A) AlphaFold-Multimer prediction of ADBP-1 and ADR-2. ADBP-1 is green, the ADR-2 deaminase domain is dark yellow, and the rest of the protein is blue. (B) The mutated ADBP-1 has a missing part, noted in gray, while the remaining part is indicated in green. (C) In wild-type worms, ADBP-1 mediated ADR-2 import to the nucleus. Once ADR-2 is in the nucleus, it is adjacent to the chromosomes, where RNA editing occurs co-transcriptionally, regulated by the binding of ADR-1 to ADR-2. (D) In the adbp-1 mutant, ADR-2 remains in the cytoplasm and edits sites randomly in exons. (C and D) were created with BioRender.com.
See this image and copyright information in PMC

Update of

Similar articles

See all similar articles

Cited by

References

    1. Gott J.M., Emeson R.B.. Functions and mechanisms of RNA editing. Annu. Rev. Genet. 2000; 34:499–531. - PubMed
    1. Erdmann E.A., Mahapatra A., Mukherjee P., Yang B., Hundley H.A.. To protect and modify double-stranded RNA - the critical roles of ADARs in development, immunity and oncogenesis. Crit. Rev. Biochem. Mol. Biol. 2021; 56:54–87. - PMC - PubMed
    1. Walkley C.R., Li J.B.. Rewriting the transcriptome: adenosine-to-inosine RNA editing by ADARs. Genome Biol. 2017; 18:205. - PMC - PubMed
    1. Levanon Y.E., Eisenberg E.. A-to-I RNA editing — immune protector and transcriptome diversifier. Nat. Rev. Genet. 2018; 19:473–490. - PubMed
    1. Bass B.L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 2002; 71:817–846. - PMC - PubMed

MeSH terms