Domestic chickens activate a piRNA defense against avian leukosis virus
- University of Rochester Medical Center, United States
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, United States
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, United States
- University of Manitoba, Canada
Figures
Figure 1 with 4 supplements
Active ERVs in White Leghorn testis.
(A) A254 absorbance profile of 10% to 50% sucrose density gradients of testis lysates from adult rooster. From top to bottom, plots show the relative abundance of 18S rRNA, β-ACTIN mRNA, CILI mRNA, C…
Figure 1—figure supplement 1
Tissue distribution of ERVs and piRNA pathway genes.
(A) Box plots show the abundance of ERV families in different chicken tissues measured by RNA-seq data. (B) Expression of A-MYB, CILI, and CIWI in each tissue measured by RNA-seq data.
Figure 1—figure supplement 2
PIWI proteins are conserved between mammals and birds.
Phylogenetic tree of PIWI proteins, including four human PIWI proteins, three mouse PIWI proteins, and two chicken PIWI proteins.
Figure 1—figure supplement 3
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´ …
Figure 1—figure supplement 4
A recent ALVE insertion in the SOX5 gene detected by genome-resequencing of White Leghorn.
From top to bottom, the genomic location of the insertion, the genome resequencing signals mapping to Crick strand and Watson strand, Ref-Seq track showing the first intron of SOX5, RepeatMasker …
Figure 2 with 2 supplements
Three groups of TEs based on TE expression and piRNA expression.
(A) Scatter plots of TE transcript abundance versus TE piRNA abundance. Each filled circle represents a TE family. Here and in Figure 2—figure supplements 1 and 2, young TE in purple, medium TE in …
Figure 2—figure supplement 1
piRNA-mediated TE suppression in rooster testes.
(A) Length distributions of testis small RNAs that map to TE regions. Blue represents sense mapping piRNAs; Red represents anti-sense mapping piRNAs. (B) Scatter plots of piRNA abundance in total …
Figure 2—figure supplement 2
Medium TE piRNAs are authentic piRNAs.
(A) Length distributions of testis small RNAs that map to young TEs (left) and medium TEs (right). (B) Sequence logo showing the nucleotide composition of Young TE piRNA species (left) and Medium TE …
Figure 3
ALVE piRNA acquisition.
(A) Length distributions of testis small RNAs mapping to ALVE. Blue represents sense mapping piRNAs; Red represents anti-sense mapping piRNAs. (B) Sequence logo showing the nucleotide composition of …
Figure 4 with 2 supplements
ALVE6 is the primary piRNA-producing locus for viral piRNAs.
(A) Cumulative distributions for all piRNAs (Blue) and for uniquely mapping piRNAs (Red) on the 1633 piRNA loci in White Leghorn. (B) An example of conserved piRNA-producing loci, Cluster33, in …
Figure 4—figure supplement 1
Divergent transcription of piRNA clusters.
(A) Scatter plots of Watson-strand piRNA abundance versus Crick-strand piRNA abundance (left); scatter plots of Watson-strand piRNA precursor abundance versus Crick-strand piRNA precursor abundance …
Figure 4—figure supplement 2
ALVE6 existed in chicken genome prior domestication.
(A) From top to bottom, the genomic location of Cluster719, White Leghorn genomic re-sequencing signals mapping to Crick strand and Watson strand, Ref-Seq track showing depletion of annotated gene, …
Additional files
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Supplementary file 1
Detailed information and statistics for the sequencing data used in this study.
(A) Ribosome profiling sequencing statistics: reads and species. (B) Small RNA sequencing statistics: reads and species. (C) RNA-Seq statistics: reads and species. (D) 200 TE families. (E) TE insertions defined by TEMP. (F) Genome coordinates for the 1633 rooster piRNA-producing loci defined in this study are provided in UCSC BED format (i.e., 0-based) for galGal5. (G) Primers used in this study for qRT-PCR and genomic PCR.
- https://doi.org/10.7554/eLife.24695.015
