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Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects.

Concepcion D, Ross KD, Hutt KR, Yeo GW, Hamilton BA - PLoS Genet. (2015)

Bottom Line: These insertions typically show more modest gene expression changes than de novo mutations, suggesting selection or attenuation.Genome-wide splicing-sensitive microarrays and gene-focused assays confirm specificity of Nxf1 genetic modifier activity for IAP insertion alleles.Strikingly, CRISPR/Cas9-mediated genome editing demonstrates that a single amino acid substitution in Nxf1, E610G, is sufficient to recreate a quantitative genetic modifier in a co-isogenic background.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular and Molecular Medicine, Moores UCSD Cancer Center and Institute for Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, California, United States of America; Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, United States of America.

ABSTRACT
Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes. In mice, Intracisternal A Particles (IAPs) are a frequent source of both new mutations and polymorphism across laboratory strains. Intronic IAPs can induce alternative RNA processing choices, including alternative splicing. We previously showed IAP I∆1 subfamily insertional mutations are suppressed by a wild-derived allele of the major mRNA export factor, Nxf1. Here we show that a wider diversity of IAP insertions present in the mouse reference sequence induce insertion-dependent alternative processing that is suppressed by Nxf1CAST alleles. These insertions typically show more modest gene expression changes than de novo mutations, suggesting selection or attenuation. Genome-wide splicing-sensitive microarrays and gene-focused assays confirm specificity of Nxf1 genetic modifier activity for IAP insertion alleles. Strikingly, CRISPR/Cas9-mediated genome editing demonstrates that a single amino acid substitution in Nxf1, E610G, is sufficient to recreate a quantitative genetic modifier in a co-isogenic background.

No MeSH data available.


Related in: MedlinePlus

Shared sequence features of IAPs suppressed by Nxf1 alleles.Alignment of IAPs whose effects on host gene expression were modified by either congenic or genome edited Nxf1 alleles suggests that most of the IAP sequence is not required for either mutagenic potential or suppression by Nxf1. Shared sequence includes just 837 bp of LTR through 5’ end of the gag gene at Cdh19, ~60 bp in four fragments within pol, and 1108 bp including the RNA transport element (RTE), polypurine tract (ppt) and 3’ LTR.
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pgen.1005123.g007: Shared sequence features of IAPs suppressed by Nxf1 alleles.Alignment of IAPs whose effects on host gene expression were modified by either congenic or genome edited Nxf1 alleles suggests that most of the IAP sequence is not required for either mutagenic potential or suppression by Nxf1. Shared sequence includes just 837 bp of LTR through 5’ end of the gag gene at Cdh19, ~60 bp in four fragments within pol, and 1108 bp including the RNA transport element (RTE), polypurine tract (ppt) and 3’ LTR.

Mentions: As far as we are aware, Nxf1 remains the most highly-connected node for genetic interactions among modifier genes that act on either natural or chemically-induced mutations in mice [19, 42]. The current results add three times as many allele-specific genetic interactions for Mvb1 alleles of Nxf1 (CAST and E610G) as had previously been reported. We previously showed that the most common Mus musculus castaneus allele of Nxf1, containing many polymorphic sites, suppressed the classical vibrator mutation [20] and that a congenic stock including this allele suppressed several other IΔ1 IAP insertional mutations [19]. Our results extend the diversity of IAP insertions susceptible to Nxf1 substantially beyond the IΔ1 subfamily (Fig. 2) and provide further evidence against activity on alternative processing at non-IAP introns (Fig. 3). Alternative events suppressed by Nxf1 alleles include known bleeding exons with alternative termination, such as Slc15a2 [43] and Trpc6 [30], and IAP-dependent alternative splicing, such as Adamts13 [27, 44] and Cpne8, as well as introns for which public transcriptome data do not indicate a predominant alternative variant. Comparison of IAP elements whose effects can be suppressed by Nxf1 alleles further suggests minimum sequence requirements for both mutation and suppression lie in <1 kb in the 5’ end and ~1 kb in the 3’ end of the IAP (Fig. 7), although construction and experimental measurements of a minimal element will be required to test this idea.


Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects.

Concepcion D, Ross KD, Hutt KR, Yeo GW, Hamilton BA - PLoS Genet. (2015)

Shared sequence features of IAPs suppressed by Nxf1 alleles.Alignment of IAPs whose effects on host gene expression were modified by either congenic or genome edited Nxf1 alleles suggests that most of the IAP sequence is not required for either mutagenic potential or suppression by Nxf1. Shared sequence includes just 837 bp of LTR through 5’ end of the gag gene at Cdh19, ~60 bp in four fragments within pol, and 1108 bp including the RNA transport element (RTE), polypurine tract (ppt) and 3’ LTR.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383553&req=5

pgen.1005123.g007: Shared sequence features of IAPs suppressed by Nxf1 alleles.Alignment of IAPs whose effects on host gene expression were modified by either congenic or genome edited Nxf1 alleles suggests that most of the IAP sequence is not required for either mutagenic potential or suppression by Nxf1. Shared sequence includes just 837 bp of LTR through 5’ end of the gag gene at Cdh19, ~60 bp in four fragments within pol, and 1108 bp including the RNA transport element (RTE), polypurine tract (ppt) and 3’ LTR.
Mentions: As far as we are aware, Nxf1 remains the most highly-connected node for genetic interactions among modifier genes that act on either natural or chemically-induced mutations in mice [19, 42]. The current results add three times as many allele-specific genetic interactions for Mvb1 alleles of Nxf1 (CAST and E610G) as had previously been reported. We previously showed that the most common Mus musculus castaneus allele of Nxf1, containing many polymorphic sites, suppressed the classical vibrator mutation [20] and that a congenic stock including this allele suppressed several other IΔ1 IAP insertional mutations [19]. Our results extend the diversity of IAP insertions susceptible to Nxf1 substantially beyond the IΔ1 subfamily (Fig. 2) and provide further evidence against activity on alternative processing at non-IAP introns (Fig. 3). Alternative events suppressed by Nxf1 alleles include known bleeding exons with alternative termination, such as Slc15a2 [43] and Trpc6 [30], and IAP-dependent alternative splicing, such as Adamts13 [27, 44] and Cpne8, as well as introns for which public transcriptome data do not indicate a predominant alternative variant. Comparison of IAP elements whose effects can be suppressed by Nxf1 alleles further suggests minimum sequence requirements for both mutation and suppression lie in <1 kb in the 5’ end and ~1 kb in the 3’ end of the IAP (Fig. 7), although construction and experimental measurements of a minimal element will be required to test this idea.

Bottom Line: These insertions typically show more modest gene expression changes than de novo mutations, suggesting selection or attenuation.Genome-wide splicing-sensitive microarrays and gene-focused assays confirm specificity of Nxf1 genetic modifier activity for IAP insertion alleles.Strikingly, CRISPR/Cas9-mediated genome editing demonstrates that a single amino acid substitution in Nxf1, E610G, is sufficient to recreate a quantitative genetic modifier in a co-isogenic background.

View Article: PubMed Central - PubMed

Affiliation: Department of Cellular and Molecular Medicine, Moores UCSD Cancer Center and Institute for Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, California, United States of America; Department of Medicine, University of California, San Diego School of Medicine, La Jolla, California, United States of America.

ABSTRACT
Endogenous retroviruses and retrotransposons contribute functional genetic variation in animal genomes. In mice, Intracisternal A Particles (IAPs) are a frequent source of both new mutations and polymorphism across laboratory strains. Intronic IAPs can induce alternative RNA processing choices, including alternative splicing. We previously showed IAP I∆1 subfamily insertional mutations are suppressed by a wild-derived allele of the major mRNA export factor, Nxf1. Here we show that a wider diversity of IAP insertions present in the mouse reference sequence induce insertion-dependent alternative processing that is suppressed by Nxf1CAST alleles. These insertions typically show more modest gene expression changes than de novo mutations, suggesting selection or attenuation. Genome-wide splicing-sensitive microarrays and gene-focused assays confirm specificity of Nxf1 genetic modifier activity for IAP insertion alleles. Strikingly, CRISPR/Cas9-mediated genome editing demonstrates that a single amino acid substitution in Nxf1, E610G, is sufficient to recreate a quantitative genetic modifier in a co-isogenic background.

No MeSH data available.


Related in: MedlinePlus