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Marck C, et al.  (2006) The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 34(6):1816-35

Abstract: We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic 'p-distance tree' using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes.

Status: Published Type: Journal Article | Research Support, Non-U.S. Gov't | Research Support, U.S. Gov't, Non-P.H.S. PubMed ID: 16600899

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CDC65 EMT1 EMT2 EMT3 EMT4 EMT5 HSX1 IMT1 IMT2 IMT3
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IMT4 RPR1 SCR1 SNR52 SNR6 SOE1 SUF1 SUF10 SUF11 SUF16
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Topics Genes linked to topics (#21 - 30 )
SUF17 SUF2 SUF20 SUF3 SUF4 SUF5 SUF6 SUF7 SUF8 SUF9
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SUP11 SUP16 SUP17 SUP19 SUP2 SUP3 SUP4 SUP5 SUP51 SUP53
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Topics Genes linked to topics (#41 - 50 )
SUP54 SUP56 SUP6 SUP61 SUP7 SUP8 tA(AGC)D tA(AGC)F tA(AGC)G tA(AGC)H
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Topics Genes linked to topics (#51 - 60 )
tA(AGC)J tA(AGC)K1 tA(AGC)K2 tA(AGC)L tA(AGC)M1 tA(AGC)M2 tA(AGC)P tA(UGC)A tA(UGC)E tA(UGC)G
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Topics Genes linked to topics (#61 - 70 )
tA(UGC)L tA(UGC)O tC(GCA)B tC(GCA)G tC(GCA)P1 tC(GCA)P2 tD(GUC)B tD(GUC)D tD(GUC)G1 tD(GUC)G2
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Topics Genes linked to topics (#71 - 80 )
tD(GUC)I1 tD(GUC)I2 tD(GUC)J1 tD(GUC)J2 tD(GUC)J3 tD(GUC)J4 tD(GUC)K tD(GUC)L1 tD(GUC)L2 tD(GUC)M
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Topics Genes linked to topics (#81 - 90 )
tD(GUC)N tD(GUC)O tE(CUC)D tE(CUC)I tE(UUC)B tE(UUC)C tE(UUC)E1 tE(UUC)E2 tE(UUC)E3 tE(UUC)G2
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Topics Genes linked to topics (#91 - 100 )
tE(UUC)G3 tE(UUC)I tE(UUC)J tE(UUC)K tE(UUC)L tE(UUC)M tE(UUC)P tF(GAA)B tF(GAA)D tF(GAA)F
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Topics Genes linked to topics (#101 - 110 )
tF(GAA)G tF(GAA)H1 tF(GAA)H2 tF(GAA)M tF(GAA)N tF(GAA)P1 tF(GAA)P2 TFC1 TFC3 TFC4
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Topics Genes linked to topics (#111 - 120 )
TFC6 TFC7 TFC8 tG(GCC)B tG(GCC)D1 tG(GCC)D2 tG(GCC)E tG(GCC)F2 tG(GCC)G1 tG(GCC)G2
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Topics Genes linked to topics (#121 - 130 )
tG(GCC)J1 tG(GCC)J2 tG(GCC)M tG(GCC)O1 tG(GCC)P1 tG(GCC)P2 tH(GUG)E1 tH(GUG)E2 tH(GUG)G1 tH(GUG)G2
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Topics Genes linked to topics (#131 - 140 )
tH(GUG)H tH(GUG)K tH(GUG)M tI(AAU)B tI(AAU)D tI(AAU)E1 tI(AAU)E2 tI(AAU)G tI(AAU)I1 tI(AAU)I2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#141 - 150 )
tI(AAU)L1 tI(AAU)L2 tI(AAU)N1 tI(AAU)N2 tI(AAU)P1 tI(AAU)P2 tI(UAU)D tI(UAU)L tK(CUU)C tK(CUU)D1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#151 - 160 )
tK(CUU)D2 tK(CUU)E1 tK(CUU)E2 tK(CUU)F tK(CUU)G1 tK(CUU)G2 tK(CUU)G3 tK(CUU)I tK(CUU)J tK(CUU)K
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#161 - 170 )
tK(CUU)M tK(CUU)P tK(UUU)D tK(UUU)G1 tK(UUU)G2 tK(UUU)K tK(UUU)L tK(UUU)O tK(UUU)P tL(CAA)D
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#171 - 180 )
tL(CAA)G1 tL(CAA)G3 tL(CAA)K tL(CAA)L tL(CAA)M tL(CAA)N tL(GAG)G tL(UAA)B1 tL(UAA)B2 tL(UAA)D
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#181 - 190 )
tL(UAA)K tL(UAA)L tL(UAA)N tL(UAG)J tL(UAG)L1 tL(UAG)L2 tM(CAU)C tN(GUU)C tN(GUU)F tN(GUU)G
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#191 - 200 )
tN(GUU)K tN(GUU)L tN(GUU)N1 tN(GUU)N2 tN(GUU)O1 tN(GUU)O2 tN(GUU)P tP(UGG)L tP(UGG)N1 tP(UGG)N2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#201 - 210 )
tP(UGG)O1 tP(UGG)O3 tQ(UUG)B tQ(UUG)C tQ(UUG)D1 tQ(UUG)D2 tQ(UUG)D3 tQ(UUG)E1 tQ(UUG)E2 tQ(UUG)H
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#211 - 220 )
tQ(UUG)L tR(ACG)D tR(ACG)E tR(ACG)J tR(ACG)K tR(ACG)L tR(ACG)O tR(UCU)B tR(UCU)D tR(UCU)E
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#221 - 230 )
tR(UCU)G1 tR(UCU)G2 tR(UCU)G3 tR(UCU)J1 tR(UCU)J2 tR(UCU)K tR(UCU)M1 tR(UCU)M2 TRN1 TRR4
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#231 - 240 )
TRT2 tS(AGA)A tS(AGA)B tS(AGA)D1 tS(AGA)D2 tS(AGA)D3 tS(AGA)E tS(AGA)G tS(AGA)H tS(AGA)J
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#241 - 250 )
tS(AGA)L tS(AGA)M tS(GCU)F tS(GCU)O tT(AGU)B tT(AGU)C tT(AGU)D tT(AGU)H tT(AGU)I1 tT(AGU)I2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#251 - 260 )
tT(AGU)J tT(AGU)N1 tT(AGU)N2 tT(AGU)O1 tT(AGU)O2 tT(UGU)G1 tT(UGU)G2 tT(UGU)H tT(UGU)P tV(AAC)E1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#261 - 270 )
tV(AAC)E2 tV(AAC)G1 tV(AAC)G2 tV(AAC)G3 tV(AAC)H tV(AAC)J tV(AAC)K1 tV(AAC)K2 tV(AAC)L tV(AAC)M1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#271 - 280 )
tV(AAC)M2 tV(AAC)M3 tV(AAC)O tV(CAC)D tV(CAC)H tV(UAC)B tV(UAC)D tW(CCA)G1 tW(CCA)G2 tW(CCA)J
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Evolution blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#281 - 285 )
tW(CCA)K tW(CCA)M tW(CCA)P tX(XXX)D tX(XXX)L
Additional Literature blue ball blue ball blue ball blue ball blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball
Evolution blue ball blue ball blue ball blue ball blue ball
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