Biology:Aspergillus fumigatus non-coding RNAs
Aspergillus fumigatus is a pathogenic filamentous fungus and is responsible for more infections worldwide than any other mould. Studies of the small non-coding RNA transcriptome of this fungus under a variety of different conditions and the subsequent generation of cDNA libraries from size selected small RNA species, identified several non-coding RNAs (ncRNA) within the fungal genome.[1] The ncRNAs identified were further classified as small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) or novel ncRNAs. The expression of these ncRNAs was also shown to be influenced by developmental stages of the fungus and environmental conditions. Comparative genomics showed that the snoRNAs present within A. fumigatus are conserved across other strains of fungus. This study also identified several partial tRNA sequences within the cDNA libraries which corresponded to either the 5’ or 3’ halves of tRNA molecules. These partial tRNAs are thought to have been created by enonuclolytic cleavage within the anti-codon loop. It has been suggested that these partial tRNA stall protein synthesis however, further studies are required to determine their exact function. The table below summarised the type, genome location and corresponding target sites of the ncRNAs identified in A. fumigatus.
Non-Coding RNAs present in A. fumigatus
| Name | Size | Genome Location | Target | Type | Accession number |
|---|---|---|---|---|---|
| U1-1 | 132 | Intergenic; Afu1g06980/Afu1g07000 | snRNA | AM921915 | |
| U1-2 | 132 | Intergenic; Afu4g12490/Afu4g12500 | snRNA | AM921916 | |
| U5 | 99 | Intergenic; Afu6g12670/Afu6g12680 | snRNA | AM921917 | |
| U6 | 50 | Intergenic; Afu4g12500/Afu4g12520 Intergenic; Afu2g10150/Afu2g10160 | snRNA | AM921918 | |
| Afu-191 | 92 | Intergenic; Afu1g10270/Afu1g10280 | Gm75 in 5.8S and Am32 in U2 | C/D box snoRNA | AM921920 |
| Afu-190 | 107 | Intergenic; Afu4g11320/Afu4g11330 | Gm557 in 18S | C/D box snoRNA | AM921921 |
| Afu-198 | 130 | Intergenic; Afu1g02700/Afu1g02680 | Cm2856 and Um 2859 in 26S | C/D box snoRNA | AM921922 |
| Afu-294 | 85 | Intergenic; Afu1g09750/Afu1g09760 | Cm1851 in 26S; Am43 in 5.8S | C/D box snoRNA | AM921923 |
| Afu-264 | 103 | Intergenic; Afu7g05290/Afu7g05300 | Gm2770 and Gm2773 in 26S; | C/D box snoRNA | AM921924 |
| Afu-277 | 100 | Intergenic; Afu1g09740/Afu1g09760 | Um2706 in 26S; Am97 in 18S; Cm47 in 5.8S | C/D box snoRNA | AM921925 |
| Afu-188 | 84 | Intergenic; Afu4g11310/Afu4g11320 | Am25 and Um26 in 18S | C/D box snoRNA | AM921927 |
| Afu-304 | 106 | Intron 2 (sense); Afu1g09800 | Cm2925 in 26S | C/D box snoRNA | AM921929 |
| Afu-380 | 87 | Intergenic; Afu4g06780/Afu4g06770 | Um2701 in 26S | C/D box snoRNA | AM921930 |
| Afu-513 | 129 | Intergenic; Afu4g11310/Afu4g11320 | Gm1338 and Gm3719 in 26S | C/D box snoRNA | AM921931 |
| Afu-328 | 75 | Intron 2 (sense); Afu6g04570 | Gm2792 in 26S | C/D box snoRNA | AM921932 |
| Afu-335 | 97 | Intron 2 (sense); Afu1g04840 | Cm2316 in 26S | C/D box snoRNA | AM921933 |
| Afu-438 | 83 | Intergenic; Afu2g15980/Afu2g15970 | Am2877 in 26S | C/D box snoRNA | AM921934 |
| Afu-455 | 92 | Intergenic; Afu1g09760/Afu1g09740 | Gm1122 in 18S | C/D box snoRNA | AM921935 |
| Afu-40 | 90 | Intergenic; Afu4g11310/Afu4g11320 | C/D box snoRNA | AM921936 | |
| Afu-514 | 105 | Intergenic; Afu6g03830/Afu6g03840 | C/D box snoRNA | AM921937 | |
| Afu-515 | 89 | Intergenic; Afu4g11310/Afu4g11320 | C/D box snoRNA | AM921938 | |
| Afu-199 | 79 | Intron 1 (sense); Afu7g02320 | C/D box snoRNA | AM921939 | |
| Afu-298 | 93 | Intergenic; Afu1g05080/Afu1g05100 | C/D box snoRNA | AM921940 | |
| Afu-300 | 88 | Intergenic; Afu4g11310/Afu4g11320 | C/D box snoRNA | AM921941 | |
| Afu-215 | 24 | Intergenic; Afu5g12870/Afu5g12880 | C/D box snoRNA | AM921942 | |
| Afu-511 | 164 | Intergenic; Afu1g03400/Afu1g03410 | C/D box snoRNA | AM921943 | |
| Afu-210 | 24 | Intron 2 (sense); Afu2g03610 | C/D box snoRNA | AM921944 | |
| Afu-265 | 23 | Intergenic; Afu3g02340/Afu3g02370 | C/D box snoRNA | AM921945 | |
| Afu-182 | 219 | Intergenic; Afu4g07680/Afu4g07690 | novel | AM921946 | |
| Afu-202 | 266 | Intergenic; Afu1g10420/Afu1g10430 | SRP RNA | AM921947 | |
| Afu-254 | 163 | Intergenic; Afu7g04110/Afu7g04120 | novel | AM921949 | |
| Afu-203 | 111 | Intron 1 (sense); Afu3g14240 | novel | AM921950 | |
| Afu-309 | 318 | Intergenic; Afu4g10430/Afu4g10420 | novel | AM921953 |
References
- ↑ chl C; Rederstorff M; Jö Hertel J et al. (May 2008). "Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis". Nucleic Acids Res. 36 (8): 2677–2689. doi:10.1093/nar/gkn123. PMID 18346967.
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