Limits...
Domestic chickens activate a piRNA defense against avian leukosis virus

View Article: PubMed Central - PubMed

ABSTRACT

PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious.

Doi:: http://dx.doi.org/10.7554/eLife.24695.001

No MeSH data available.


Related in: MedlinePlus

Ribosome profiling in adult rooster testes.(A) Schematic of ribosome profiling library construction. (B) Length distributions of RPFs mapped to mRNA CDS (black) and ALVE (purple). (C) Metagene plots of RNA-seq (top) and RPF (bottom) at 5´ leader, CDS, and 3´ trailer of mRNAs. The x-axis shows the median length of these regions, and the y-axis represents the mean of normalized abundance. (D) Discrete Fourier transformation of the distance spectrum of 5´ ends of RPFs across mRNA CDSs (black) and ALVE (purple).DOI:http://dx.doi.org/10.7554/eLife.24695.006
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5383398&req=5

fig1s3: Ribosome profiling in adult rooster testes.(A) Schematic of ribosome profiling library construction. (B) Length distributions of RPFs mapped to mRNA CDS (black) and ALVE (purple). (C) Metagene plots of RNA-seq (top) and RPF (bottom) at 5´ leader, CDS, and 3´ trailer of mRNAs. The x-axis shows the median length of these regions, and the y-axis represents the mean of normalized abundance. (D) Discrete Fourier transformation of the distance spectrum of 5´ ends of RPFs across mRNA CDSs (black) and ALVE (purple).DOI:http://dx.doi.org/10.7554/eLife.24695.006

Mentions: To determine whether the observed co-sedimentation with ribosomes reflects the active translation, we performed ribosome profiling using testis lysates from adult White Leghorn. Ribosome profiling is based on the facts that the ribosome-bound fraction of mRNA is protected from RNase digestion in vitro (Steitz, 1969), and that the subsequent genome-wide sequencing of ribosome-protected fragments (RPFs) provides a snapshot of in vivo translation (Ingolia et al., 2009). RNA fragments protected from RNase A and T1 digestion were isolated from 80S fractions and sequenced (Figure 1—figure supplement 3A) (Ricci et al., 2014; Cenik et al., 2015). Similar to reported RPF sizes in mammals, the RPF sizes in chicken from coding DNA sequences (CDS) ranged from 26–32 nt (Figure 1—figure supplement 3B). While RNA-seq reads were distributed throughout the entire set of mRNA transcripts, RPF reads were enriched in CDS regions (Figure 1—figure supplement 3C), and RPFs that mapped to CDS regions accounted for 96% of the RPFs that mapped to entire mRNA transcripts. The RPF reads mapping to open read frames displayed an obvious three-nt periodicity (Figure 1—figure supplement 3D), reflecting the triplet nature of the genetic code during translation elongation. Based on the enrichment of RPFs at CDS regions and the observed codon periodicity of RPFs, we conclude that the ribosome profiling identified RNAs undergoing translation.


Domestic chickens activate a piRNA defense against avian leukosis virus
Ribosome profiling in adult rooster testes.(A) Schematic of ribosome profiling library construction. (B) Length distributions of RPFs mapped to mRNA CDS (black) and ALVE (purple). (C) Metagene plots of RNA-seq (top) and RPF (bottom) at 5´ leader, CDS, and 3´ trailer of mRNAs. The x-axis shows the median length of these regions, and the y-axis represents the mean of normalized abundance. (D) Discrete Fourier transformation of the distance spectrum of 5´ ends of RPFs across mRNA CDSs (black) and ALVE (purple).DOI:http://dx.doi.org/10.7554/eLife.24695.006
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383398&req=5

fig1s3: Ribosome profiling in adult rooster testes.(A) Schematic of ribosome profiling library construction. (B) Length distributions of RPFs mapped to mRNA CDS (black) and ALVE (purple). (C) Metagene plots of RNA-seq (top) and RPF (bottom) at 5´ leader, CDS, and 3´ trailer of mRNAs. The x-axis shows the median length of these regions, and the y-axis represents the mean of normalized abundance. (D) Discrete Fourier transformation of the distance spectrum of 5´ ends of RPFs across mRNA CDSs (black) and ALVE (purple).DOI:http://dx.doi.org/10.7554/eLife.24695.006
Mentions: To determine whether the observed co-sedimentation with ribosomes reflects the active translation, we performed ribosome profiling using testis lysates from adult White Leghorn. Ribosome profiling is based on the facts that the ribosome-bound fraction of mRNA is protected from RNase digestion in vitro (Steitz, 1969), and that the subsequent genome-wide sequencing of ribosome-protected fragments (RPFs) provides a snapshot of in vivo translation (Ingolia et al., 2009). RNA fragments protected from RNase A and T1 digestion were isolated from 80S fractions and sequenced (Figure 1—figure supplement 3A) (Ricci et al., 2014; Cenik et al., 2015). Similar to reported RPF sizes in mammals, the RPF sizes in chicken from coding DNA sequences (CDS) ranged from 26–32 nt (Figure 1—figure supplement 3B). While RNA-seq reads were distributed throughout the entire set of mRNA transcripts, RPF reads were enriched in CDS regions (Figure 1—figure supplement 3C), and RPFs that mapped to CDS regions accounted for 96% of the RPFs that mapped to entire mRNA transcripts. The RPF reads mapping to open read frames displayed an obvious three-nt periodicity (Figure 1—figure supplement 3D), reflecting the triplet nature of the genetic code during translation elongation. Based on the enrichment of RPFs at CDS regions and the observed codon periodicity of RPFs, we conclude that the ribosome profiling identified RNAs undergoing translation.

View Article: PubMed Central - PubMed

ABSTRACT

PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious.

Doi:: http://dx.doi.org/10.7554/eLife.24695.001

No MeSH data available.


Related in: MedlinePlus