PMC

FISH to metaphase chromosomes and nuclei of cells with integrated EBV DNA with the EBV BamHI W DNA probe. (A to C) Hybridization to cytogenetic preparations of Namalwa-Cl8 cells; (D to F) hybridization to LCL IB4-D. (A) Simultaneous hybridization to both viral (EBV BamHI W) DNA and chromosome X in denatured and RNase A-treated samples. Yellow signals (arrow) on each sister chromatid of chromosome X (red) indicates the localization of integrated EBV genomes in the telomeric region of Xp. The chromosome X-painting probe was labeled with Cy3 and the EBV BamHI W DNA was labeled with biotin and detected with FITC-conjugated avidin. Chromosomes were counterstained with DAPI. (B) Track of the EBV BamHI fragment W (BamHI W) RNA (green) within a nondenatured interphase nucleus. The EBV BamHI W DNA was labeled with biotin, and hybridization was detected with FITC-avidin. The nucleus was counterstained with DAPI. (C) Simultaneous hybridization of the BamHI W DNA probe and the chromosome X-specific probe in denatured samples indicates the X chromosome domain (red) and the BamHI W nuclear RNA (green) in a DAPI-stained nucleus. The chromosome X-painting probe was labeled with Cy3, and the EBV BamHI W DNA was labeled with biotin and detected with FITC-conjugated avidin. Note that the RNA track extends from the chromosome X interphase domain into a more peripheral position. (D) Simultaneous hybridization to viral (EBV BamHI W) DNA and chromosome 4 in denatured and RNase A-treated samples. Yellow signals on each sister chromatid on q25 of one chromosome 4 (red) indicate the localization of integrated EBV genomes. The chromosome 4-painting probe was labeled with Cy3, and the EBV BamHI W DNA was labeled with biotin and detected with FITC-conjugated avidin. Chromosomes were counterstained with DAPI. (E) Nuclear RNA from the BamHI W region of EBV (green) in nondenatured preparations. EBV BamHI W DNA was labeled with biotin, and hybridization was detected with FITC-conjugated avidin. The nucleus was counterstained with DAPI. Note the large accumulation of RNA at the end of the track. (F) Simultaneous hybridization of the BamHI W probe and the chromosome 4-specific probe in denatured samples indicate the two chromosome 4 domains (red) and the BamHI W nuclear RNA track (green) in a DAPI-stained nucleus of an IB4-D cell. Note that the RNA track extends from the chromosome 4 interphase domain across almost half of the nucleus.

Chromosome synteny supports multiple gains of a W chromosome from a B chromosome in butterflies and moths. (A) Synteny analysis of the D. iulia W chromosome against the remaining 31 chromosomes (autosomes in gray, Z chromosome shown in orange) indicates a lack of shared sequence homology between the W and Z chromosomes. (B) Synteny between the D. iulia W chromosome and the K. inachus and S. exigua genome assemblies finds no synteny between the W chromosomes despite a high degree of synteny between the autosomes and Z chromosome. (C) A partial phylogeny of Lepidoptera shows our current hypothesis of multiple independent gains of a W chromosome in butterflies and moths. Question marks reflect uncertainty in those branches about the exact time and relationship to more basal clades of W sequence. Divergence times are from .

The nature of the silkworm W chromosome as a source of female-enriched piRNAs. The silkworm W chromosome contributes to production of female-enriched piRNAs. Primary piRNAs can be produced from defective transposon loci in the W chromosome and autosomes. Female-enriched secondary piRNAs can be generated through cleavage of W chromosome-derived sense transposon mRNAs by such primary piRNAs. Female-enriched piRNAs such as Pakurin-derived piRNAs can be produced both from SDR and non-SDR loci in the W chromosome. A set of female-enriched piRNAs such as Judo-derived piRNAs shows a striking enrichment in the SDR.

Repetitive elements underlie the unusual DNA sequence content of the W chromosome. (A) Percent of the genome uniquely mappable with 74 bp sequences shows that the W chromosome is much more repetitive than the autosomal or Z chromosomes. Gray bar marks the mean for autosomal chromosomes. (B) Stacked bar charts with the relative composition of repeat classes on the autosomal, Z, and W chromosomes. Longer repeat classes (LINEs and LTRs) are substantially increased on the W chromosome relative to the other chromosomes. LINEs (C) and LTRs (D) both show an increased divergence from the repeat consensus sequence, consistent with reduced purifying or background selection on the W chromosome. E, GC content on the W chromosome is much higher than expected from the autosomes or the Z chromosome.