Fig 1.
Detection of small RNA molecules homologous to AfuSINE sequences.
Total RNAs isolated with Trizol were electrophoresed on 1.5% agarose gels (a). After separation by PEG precipitation, high molecular weight RNAs (HMW RNAs) and low molecular weight RNAs (LMW RNAs) were electrophoresed on 1.5% agarose gels (b). The LMW fractions from 400 ng/μl of total RNA were resolved on 15% (w/v) polyacrylamide Tris-borate-EDTA-urea gels and stained with SYBR Gold Nucleic Acid Gel Stain (c). Northern blot hybridization of small RNAs homologous to AfuSINE sequences in A. fumigatus Af293 (d). LMW RNA fractions were isolated using TRIzol and 5 μg RNA sample was loaded into each well for northern blot analysis. Only small RNAs (<40 nt; arrowed) from the antisense strand were detected.
Table 1.
List of 5 putative 5S rRNA-related SINE sequences (AfuSINE3) and 8 putative tRNA-related SINE sequences (AfuSINE2).
Fig 2.
Consensus sequences of A, IE and C box promoters of type I RNA pol III in 5S rRNA-derived AfuSINE sequences (AfuSINE3s).
Fig 3.
Consensus A and B box promoter sequences of RNA pol III in tRNA-derived AfuSINE sequences (AfuSINE2s).
Fig 4.
Structure of the AfuSINE2-1a tRNA-derived SINE.
Structure of the AfuSINE2-1a tRNA-derived SINE found in A. fumigatus Af293 (a) and the alignment of its 3'-terminus which is related to I-4_AO LINE (b).
Fig 5.
Mapping of SINE-like sequences of the A. fumigatus Af293 genome.
Mapping of SINE-like sequences on eight chromosomes of the A. fumigatus Af293 genome including previously described LINE-like sequences (LLEs; [22]). Chromosome numbers are shown on the left and the size of each chromosome is shown on the right.
Fig 6.
Structure of LINE-like element.
Structure of LINE-like element (LLE#4_3.0; [22]) on A. fumigatus Af293 chromosome 4 showing insertion of the AfuSINE2_4c sequence next to the LLE RT.
Fig 7.
Southern blot hybridization of AfuSINE sequences in the genome of A. fumigatus Af293.
Southern blot hybridization of AfuSINE sequences in the genome of A. fumigatus Af293 (virus-infected strain; indicated by plus sign) and A. fumigatus NK125 (virus-free strain; indicated by minus sign). HindIII-digested DNA of each strain was separated in 1% agarose gels in 1xTAE, denatured and blotted onto nylon membrane. Hyperladder 1 (M; 10 kbp; Bioline) was used as marker.