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Giuliodori S, et al.  (2003) A composite upstream sequence motif potentiates tRNA gene transcription in yeast. J Mol Biol 333(1):1-20

Abstract: Transcription of eukaryotic tRNA genes relies on the TFIIIC-dependent recruitment of TFIIIB on a approximately 50 bp region upstream of the transcription start site (TSS). TFIIIC specifically interacts with highly conserved, intragenic promoter elements, while the contacts between TFIIIB and the upstream DNA have long been considered as largely non-specific. Through a computer search procedure designed to detect shared, yet degenerate sequence features, we have identified a conserved sequence pattern upstream of Saccharomyces cerevisiae tDNAs. This pattern consists of four regions in which particular sequences are over-represented. The most downstream of these regions surrounds the TSS, while the other three districts of sequence conservation (appearing as a centrally located TATA-like sequence flanked by T-rich elements on both sides) are located across the DNA region known to interact with TFIIIB. Upstream regions whose sequence conforms to this pattern were found to potentiate tRNA gene transcription, both in vitro and in vivo, by enhancing TFIIIB binding. A conserved pattern of DNA bendability was also revealed, with peaks of bending propensity centered on the TATA-like and the TSS regions. Sequence analysis of other eukaryotic genomes further revealed the widespread occurrence of conserved sequence patterns upstream of tDNAs, with striking lineage-specific differences in the number and sequence of conserved motifs. Our data strongly support the notion that tRNA gene transcription in eukaryotes is modulated by composite TFIIIB binding sites that may confer responsiveness to variation in TFIIIB activity and/or concentration.

Status: Published Type: Journal Article | Research Support, Non-U.S. Gov't PubMed ID: 14516739

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BRF1 CDC65 EMT1 EMT2 EMT3 EMT4 EMT5 HSX1 IMT1 IMT2
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IMT3 IMT4 SOE1 SUF1 SUF10 SUF11 SUF16 SUF17 SUF2 SUF20
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Topics Genes linked to topics (#21 - 30 )
SUF3 SUF4 SUF5 SUF6 SUF7 SUF8 SUF9 SUP11 SUP16 SUP17
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Topics Genes linked to topics (#31 - 40 )
SUP19 SUP2 SUP3 SUP4 SUP5 SUP51 SUP53 SUP54 SUP56 SUP6
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Topics Genes linked to topics (#41 - 50 )
SUP61 SUP7 SUP8 tA(AGC)D tA(AGC)F tA(AGC)G tA(AGC)H tA(AGC)J tA(AGC)K1 tA(AGC)K2
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Topics Genes linked to topics (#51 - 60 )
tA(AGC)L tA(AGC)M1 tA(AGC)M2 tA(AGC)P tA(UGC)A tA(UGC)E tA(UGC)G tA(UGC)L tA(UGC)O tC(GCA)B
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Topics Genes linked to topics (#61 - 70 )
tC(GCA)G tC(GCA)P1 tC(GCA)P2 tD(GUC)B tD(GUC)D tD(GUC)G1 tD(GUC)G2 tD(GUC)I1 tD(GUC)I2 tD(GUC)J1
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Topics Genes linked to topics (#71 - 80 )
tD(GUC)J2 tD(GUC)J3 tD(GUC)J4 tD(GUC)K tD(GUC)L1 tD(GUC)L2 tD(GUC)M tD(GUC)N tD(GUC)O tE(CUC)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 (#81 - 90 )
tE(CUC)I tE(UUC)B tE(UUC)C tE(UUC)E1 tE(UUC)E2 tE(UUC)E3 tE(UUC)G2 tE(UUC)G3 tE(UUC)I tE(UUC)J
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Topics Genes linked to topics (#91 - 100 )
tE(UUC)K tE(UUC)L tE(UUC)M tE(UUC)P tF(GAA)B tF(GAA)D tF(GAA)F tF(GAA)G tF(GAA)H1 tF(GAA)H2
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Topics Genes linked to topics (#101 - 110 )
tF(GAA)M tF(GAA)N tF(GAA)P1 tF(GAA)P2 tG(GCC)B tG(GCC)D1 tG(GCC)D2 tG(GCC)E tG(GCC)F2 tG(GCC)G1
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Topics Genes linked to topics (#111 - 120 )
tG(GCC)G2 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
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 (#121 - 130 )
tH(GUG)G2 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
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
Non-Fungal Related Genes/Proteins 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 (#131 - 140 )
tI(AAU)I2 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
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
Non-Fungal Related Genes/Proteins 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 )
tK(CUU)D1 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
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
Non-Fungal Related Genes/Proteins 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)K 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
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
Non-Fungal Related Genes/Proteins 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 (#161 - 170 )
tL(CAA)D 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
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 (#171 - 180 )
tL(UAA)D 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
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 )
tN(GUU)G 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
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
Non-Fungal Related Genes/Proteins 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 )
tP(UGG)N2 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
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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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Transcription 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 (#201 - 210 )
tQ(UUG)H 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
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 )
tR(UCU)E 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
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 (#221 - 230 )
TRR4 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
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 (#231 - 240 )
tS(AGA)J 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
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
Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription 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 )
tT(AGU)I2 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
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
Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription 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 )
tV(AAC)E1 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
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 (#261 - 270 )
tV(AAC)M1 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
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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Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Regulation of blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Transcription 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 - 276 )
tW(CCA)J 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 blue ball
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball blue ball blue ball
Non-Fungal Related Genes/Proteins blue ball blue ball blue ball blue ball blue ball blue ball
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Transcription blue ball blue ball blue ball blue ball blue ball blue ball

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