Curation Information

Publication
Global analysis of the regulon of the transcriptional repressor LexA, a key component of SOS response in Mycobacterium tuberculosis.;Smollett KL, Smith KM, Kahramanoglou C, Arnvig KB, Buxton RS, Davis EO;The Journal of biological chemistry 2012 Jun 22; 287(26):22004-14 [22528497]
TF
LexA [I6Y1J7, view regulon]
Reported TF sp.
Mycobacterium tuberculosis H37Rv
Reported site sp.
Mycobacterium tuberculosis H37Rv
Created by
Erill Lab
Curation notes
finalized

Experimental Process

ChIP seq some expression data by RT-PCR and northern blot and beta-gal

ChIP assay conditions
MtuLexA: The mycobacterial strains used were wild-type M. tuberculosis strains H37Rv and 1424 and M. tuberculosis
ChIP notes
Chromatin Immunoprecipitation (ChIP)—ChIP was performed using a method adapted from Sala et al.(16). Mycobacterial cultures were grown to mid-log phase (A600

Transcription Factor Binding Sites


TCGAACACATGTTCGATT
TCGAACACATGTTCGAGA
TCGAACAATTGTTCGATA
TCGAACACATGTTTGATT
TCGAATACATGTTCGAAT
TCGAAAATATATTCGATA
CCGAACACCTGTTCGATT
TCGATCACTTGTTCGAAT
TCGAAAATATGTTCGAAG
TCGCACACATGTTCGAGA
TCGAACGTATGTTCGAGA
TCGAACTCATATTCGAAT
TCGAACGAATGTGCGATA
CCGAACAATCGTTCGATA
TCGAACAACCGTTCTATA
TCGCTCAAATATTCGAAT
CCGAACATTTGATCGAAG
TCGAACACATGAGTGACT
TCGAACACGCGAGCGATT
GAGAACACCCGTTCGATA
ACGAAAGTCTGTTCGAAG
TCGCTAACATGTTCGAAT
TCGCTAACATGTTCGAAT
TCGAACACATGTTCGATT
TCGAACACATGTTCGAGA
TCGAACAATTGTTCGATA
TCGAACACATGTTTGATT
TCGAATACATGTTCGAAT
TCGAAAATATATTCGATA
CCGAACACCTGTTCGATT
TCGATCACTTGTTCGAAT
TCGAAAATATGTTCGAAG
TCGCACACATGTTCGAGA
TCGAACGTATGTTCGAGA
TCGAACTCATATTCGAAT
TCGAACGAATGTGCGATA
CCGAACAATCGTTCGATA
TCGAACAACCGTTCTATA
TCGCTCAAATATTCGAAT
CCGAACATTTGATCGAAG
TCGAACACATGAGTGACT
TCGAACACGCGAGCGATT
GAGAACACCCGTTCGATA
ACGAAAGTCTGTTCGAAG
TCGCTAACATGTTCGAAT
TCGCTAACATGTTCGAAT

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
TCGAACACATGTTCGATT RVBD_1378c,
... ... RVBD_1378c RVBD_1377c RVBD_1376 RVBD_1375 RVBD_1379 RVBD_1380 RVBD_1381 RVBD_1382 RVBD_1383 RVBD_1384 RVBD_1385
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACACATGTTCGAGA RVBD_3074,
... ... RVBD_3074 RVBD_3073c RVBD_3072c RVBD_3075c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACAATTGTTCGATA RVBD_3370c,
... ... RVBD_3370c RVBD_3371 RVBD_3372
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACACATGTTTGATT RVBD_2719c,
... ... RVBD_2719c RVBD_2720 RVBD_2721c RVBD_2722 RVBD_2723 RVBD_2724c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAATACATGTTCGAAT
... ... RVBD_1702c RVBD_1701 RVBD_1700 RVBD_1699 RVBD_1702Ac
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAAAATATATTCGATA RVBD_1057,
... ... RVBD_1057 RVBD_1056
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
CCGAACACCTGTTCGATT RVBD_2737c,
... ... RVBD_2737c RVBD_2736c RVBD_2735c RVBD_2734 RVBD_2737A RVBD_2738c RVBD_2739c RVBD_2740
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGATCACTTGTTCGAAT RVBD_3260c,
... ... RVBD_3260c RVBD_3259 RVBD_3261 RVBD_3262 RVBD_3262A
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAAAATATGTTCGAAG RVBD_3395c,
... ... RVBD_3395c RVBD_3394c RVBD_3395A
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGCACACATGTTCGAGA RVBD_2100,
... ... RVBD_2100 RVBD_2099c RVBD_2098c RVBD_2101
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACGTATGTTCGAGA
... ... RVBD_3775 RVBD_3774 RVBD_3773c RVBD_3772 RVBD_6095 RVBD_3777 RVBD_3778c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACTCATATTCGAAT RVBD_0071,
... ... RVBD_0071 RVBD_0070c RVBD_0069c RVBD_0068 RVBD_0072 RVBD_0073
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACGAATGTGCGATA RVBD_1000c,
... ... RVBD_1000c RVBD_0999 RVBD_0998 RVBD_0997 RVBD_1001 RVBD_1002c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
CCGAACAATCGTTCGATA RVBD_2594c,
... ... RVBD_2594c RVBD_2593c RVBD_2592c RVBD_2591 RVBD_2595 RVBD_2596
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACAACCGTTCTATA RVBD_2578c, RVBD_2579,
... ... RVBD_2578c RVBD_2579 RVBD_2577
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGCTCAAATATTCGAAT
... ... RVBD_2517c RVBD_2516c RVBD_2518c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
CCGAACATTTGATCGAAG RVBD_2719c,
... ... RVBD_2719c RVBD_2720 RVBD_2721c RVBD_2722 RVBD_2723 RVBD_2724c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACACATGAGTGACT RVBD_2719c,
... ... RVBD_2719c RVBD_2720 RVBD_2721c RVBD_2722 RVBD_2723 RVBD_2724c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGAACACGCGAGCGATT RVBD_2719c,
... ... RVBD_2719c RVBD_2720 RVBD_2721c RVBD_2722 RVBD_2723 RVBD_2724c
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
GAGAACACCCGTTCGATA RVBD_2594c,
... ... RVBD_2594c RVBD_2593c RVBD_2592c RVBD_2591 RVBD_2595 RVBD_2596
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
ACGAAAGTCTGTTCGAAG
... ... RVBD_1374c RVBD_1373 RVBD_1372 RVBD_1371 RVBD_1375 RVBD_1376 RVBD_1377c RVBD_1378c RVBD_1379 RVBD_1380 RVBD_1381 RVBD_1382 RVBD_1383 RVBD_1384 RVBD_1385
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGCTAACATGTTCGAAT RVBD_0095c,
... ... RVBD_0095c RVBD_0094c RVBD_0093c RVBD_0092 RVBD_0096 RVBD_0097 RVBD_0098 RVBD_0099 RVBD_0100 RVBD_0101
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TCGCTAACATGTTCGAAT
... ... RVBD_1588c RVBD_1587c RVBD_1586c RVBD_1585c RVBD_1589 RVBD_1590 RVBD_1591
Experimental technique details Beta-gal reporter assay - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer