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Table 1 Locations of BarR genomic binding regions as determined by ChIP-seq

From: The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

Peak summit coordinate Growth conditiona Fold enrich-mentb Nearest ORF Annotation Peak summit locationc In vitro bindingd Predicted binding motif Gene regulatione
19904 w/o N.A./5.3 Saci_0028 Hypothetical protein intra-5’ N.A. - N.A.
46668 both 4.9/8.7 Saci_0061 Lysine arginine ornithine transport system kinase intra-3’ ++ + -
554848 w/o N.A./4.4 Saci_0695 Translation initiation factor IF-2 intra N.A. + N.A.
577211 both 4.8/12.7 Saci_0720 Nicotinamide-nucleotide adenylyltransferase intra-5’ (operon) + + N.A.
674867 both 11.1/13.8 Saci_0839 Reverse gyrase intra ++ + -
676039 w/o N.A./4.3 Saci_0839 Reverse gyrase intra N.A. + N.A.
850922 w 4.2/N.A. Saci_1050 ParA, chromosome partitioning ATPase intra-5’ + + -
918486 both 3.6/5.4 Saci_1115 Alcohol dehydrogenase intra + + N.A.
999186 both 4.0/11.9 Saci_1182 Major facilitator superfamily permease intra N.A. + N.A.
1421788 both 3.0/7.3 Saci_1664 Protein kinase intra N.A. + N.A.
1431591 w/o N.A./5.5 Saci_1674 Gluconolactonase intra-5’ ++ + -
1563444 w/o N.A./3.7 Saci_1796 Hypothetical protein intra-3’ N.A. + N.A.
1563826 w/o N.A./9.2 Saci_1796 Hypothetical protein inter-3’ ++ + -
1598826 w 3.9/N.A. Saci_1833 Hypothetical protein intra-3’ N.A. + N.A.
1773917 w/o N.A./5.8 Saci_1964 Hypothetical protein intra-5’ N.A. + N.A.
1840150 w/o N.A./4.4 Saci_2025 ATPase inter-3’ N.A. + N.A.
1889870 w/o N.A./6.4 Saci_2073 Major facilitator superfamily permease inter-3’ N.A. + N.A.
1964012 w/o N.A./3.6 Saci_2136 BarR intra-3’ +* + +*
1964490 both 4.3/6.6 Saci_2137 Aminotransferase inter-5’ +* + +*
2000304 w/o N.A./3.7 Saci_2166 Uroporphyrin-III methyltransferase intra-5’ N.A. + N.A.
2166455 both 2.2/7.2 Saci_2319 Hypothetical protein inter ++ + +**
  1. aGrowth condition in which the binding region was detected above the significance level: both = detected in absence and presence of exogenously added β-alanine, w = detected only in the presence of β-alanine, w/o = detected only in the absence of β-alanine, bfold-enrichment value in the presence of β-alanine/in the absence of β-alanine against input sample, clocation of the peak summit with respect to the nearest gene: intra = intragenic, inter = intergenic, 5’ = within 150 bp (intragenic) or 300 bp (intergenic) of the 5’ end of the gene, 3’ = within 150 bp (intragenic) or 300 bp (intergenic) of the 3’ end of the gene. “Operon” means that the gene for which the peak summit is located within 150 bp of the 5’ end, is a second or next gene that is part of an operon, dEMSA results, with “+” indicating the observation of binding and “++” indicating the observation of high-affinity binding, eqRT-PCR results. N.A. = not analyzed; an asterisk indicates that this result was previously published [17]; a double asterisk indicates that it is not the nearest ORF that is regulated. All gene annotations were manually curated
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BMC Genomics

ISSN: 1471-2164

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