Hsf1p gene transcriptions
Associate Editor(s)-in-Chief: Henry A. Hoff
"In response to elevated temperatures, cells from many organisms rapidly transcribe a number of mRNAs. In Saccharomyces cerevisiae, this protective response involves two regulatory systems: the heat shock transcription factor (Hsf1) and the Msn2 and Msn4 (Msn2/4) transcription factors."[1]
"Yeast Hsf1 is an essential protein that binds to inverted repeats of nGAAn called heat shock elements (HSEs) within the promoters of many HSPs and activates their transcription."[1]
Human genes
"In response to heat shock, mammalian HSF undergoes nuclear localization, trimerizes, and binds to HSEs."[1]
Interactions
Consensus sequences
The upstream activating sequence (UAS) for the Hsf1p is 5'-NGAAN-3' or 5'-(A/C/G/T)GAA(A/C/G/T)-3'.[2]
Complement-inverse copies
Recent "studies on the MDJ1 promoter identified a novel non-consensus HSE that consists of three separated nGAAn motifs, nTTCn-(11-bp)-nGAAn-(5-bp)-nGAAn (58). When we analyzed promoters of the genes induced by HSF for this non-consensus HSE, we found 2.9% of the genes contained this novel HSE."[1]
"Of the 90 heat-induced genes that contain HSEs in their promoters, there is an equal number of HSEs that start with nGAAn and nTTCn, but genes with a -fold change >5-fold have HSEs with the sequences nTTCnnGAAn or nTTCnnNNNnnTTC than any combination starting with nGAAn (66.7%). These findings suggest that the type of Hsf1 binding site is not as important as the topology of the HSE. Previous studies have revealed that all three DNA-binding domains of the trimeric Hsf1 bind to one face of the DNA (59), and our studies confirm that the orientation of the HSE with respect to the transcriptional start site can affect its transcriptional activity."[1]
Complement copies
"To identify Hsf1 binding sites in the promoter sequences, we analyzed 1000 bp upstream of the start codon of the loci that represented verifiable [open reading frame] ORFs. Sequences were retrieved from the [Saccharomyces Genome Database] SGD (36, 37) and analyzed using a simple pattern-identification program. We defined three types of HSEs, each having three nGAAn repeats in Perfect (PFT), GAP (GAP), and STEP (STP) arrangements. The perfect HSE (PFT) consists of three contiguous, inverted repeats of the nGAAn sequence, either nGAAnnTTCnnGAAn or nTTCnnGAAnnTTCn. The GAP HSE consists of an nGAAn repeat, followed by any 5 bp and 2 inverted nGAAn repeats (nGAAn-(5-bp)-nGAAnnTTCn) and its complement (nGAAnnTTCn-(5-bp)-nTTCn), as well as the related sequences nTTCn-(5-bp)-nTTCnnGAAn and nTTC-nnGAAn-(5-bp)-nGAAn. The STP HSE has a 5-bp insert between each of the 3 nGAAn repeats, yielding the sequences nGAAn-(5-bp)-nGAAn-(5-bp)-nGAAn and nTTCn-(5-bp)-nTTCn-(5-bp)-nTTCn (30). As per previous studies (27, 30), we also allowed a single mismatch (nGAR) in one of the three nGAAn repeats for PFT or GAP."[1]
Inverse copies
"HSEs are composed of inverted, alternating repeats of the 5-bp sequence nGAAn, where n is any nucleotide (53, 54, 55, 56). The number of pentameric units in an HSE varies, but three to six units are thought to be required for heat regulation in vivo (30, 57). Deviations from the consensus in both sequence and/or the distance between the modules can be tolerated, but to what extent is unknown. To determine if there is a correlation between the different HSEs and the affinity of Hsf1 for the motif and, thereby, the level of transcription activation, we searched in the promoters of the genes for three types of HSEs. Each type contains three nGAAn core motifs, but the variants are distinguishable from each other by the location of the core motifs within the HSE [...]."[1]
Hypotheses
- A1BG has no Hsf1s in either promoter.
- A1BG is not transcribed by an Hsf1.
- No Hsf1s participates in the transcription of A1BG.
Samplings
Copying 5'-TGAAA-3' in "⌘F" yields twelve between ZSCAN22 and A1BG and 5'-CGAAC-3' one between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence NGAAN (starting with SuccessablesAAA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for NGAAN, 52, AGAAG at 4528, TGAAA at 4461, AGAAT at 4406, CGAAC at 4293, TGAAC at 4267, CGAAC at 4187, TGAAT at 4162, TGAAC at 4011, TGAAA at 3984, AGAAC at 3792, CGAAG at 3776, GGAAC at 3570, AGAAG at 3553, CGAAC at 3400, TGAAC at 3241, TGAAC at 3102, TGAAA at 3075, TGAAA at 3018, CGAAT at 2935, TGAAC at 2920, CGAAC at 2713, TGAAC at 2579, TGAAA at 2552, CGAAC at 2378, TGAAA at 2216, TGAAC at 2126, TGAAA at 2099, CGAAC at 1972, TGAAC at 1926, TGAAA at 1790, AGAAA at 1733, TGAAA at 1687, AGAAC at 1648, TGAAC at 1618, AGAAC at 1606, TGAAT at 1545, AGAAA at 1418, TGAAC at 1299, TGAAA at 1145, TGAAG at 1053, CGAAC at 1008, CGAAC at 842, TGAAA at 681, GGAAG at 619, TGAAA at 545, TGAAA at 408, AGAAA at 347, TGAAC at 327, GGAAT at 317, AGAAC at 280, AGAAA at 47, AGAAA at 25.
- negative strand, positive direction, looking for NGAAN, 62, GGAAC at 4443, GGAAG at 4263, GGAAG at 4248, AGAAG at 4197, TGAAA at 4091, AGAAC at 4067, AGAAC at 4047, TGAAC at 3936, TGAAA at 3926, AGAAA at 3918, GGAAG at 3871, GGAAC at 3855, AGAAG at 3851, TGAAC at 3837, AGAAT at 3833, GGAAA at 3794, TGAAT at 3780, GGAAG at 3762, GGAAG at 3667, TGAAA at 3596, GGAAT at 3565, TGAAT at 3443, GGAAT at 3439, GGAAT at 3365, AGAAG at 3216, GGAAA at 3165, AGAAC at 3093, AGAAT at 3067, TGAAA at 2917, AGAAT at 2839, GGAAA at 2831, GGAAG at 2784, AGAAC at 2775, GGAAG at 2748, AGAAT at 2723, AGAAA at 2629, GGAAA at 2623, GGAAC at 2578, AGAAT at 2241, AGAAC at 2224, AGAAG at 2192, TGAAA at 2146, AGAAC at 1950, AGAAC at 1810, AGAAG at 1633, GGAAG at 1594, AGAAT at 1418, AGAAT at 1318, AGAAG at 1231, GGAAA at 1089, AGAAG at 1063, TGAAG at 961, TGAAG at 861, CGAAG at 768, TGAAG at 727, AGAAG at 643, AGAAG at 559, CGAAC at 362, GGAAA at 290, TGAAG at 232, GGAAG at 209, AGAAG at 48.
- positive strand, negative direction, looking for NGAAN, 93, GGAAT at 4553, AGAAC at 4450, AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAG at 3936, TGAAA at 3922, GGAAG at 3909, TGAAC at 3783, GGAAC at 3723, GGAAT at 3677, AGAAC at 3667, GGAAA at 3663, GGAAG at 3610, AGAAA at 3591, TGAAA at 3507, GGAAC at 3459, AGAAG at 3407, AGAAA at 3376, AGAAA at 3342, TGAAC at 3244, AGAAT at 3235, TGAAA at 3146, AGAAT at 3002, GGAAA at 2967, GGAAA at 2957, GGAAA at 2926, AGAAA at 2838, AGAAA at 2831, AGAAG at 2828, AGAAA at 2821, AGAAA at 2814, AGAAG at 2811, AGAAA at 2804, AGAAA at 2800, TGAAA at 2746, GGAAG at 2730, TGAAC at 2716, TGAAT at 2707, TGAAA at 2619, TGAAG at 2595, GGAAG at 2557, AGAAA at 2505, GGAAA at 2458, TGAAC at 2381, AGAAT at 2372, TGAAA at 2282, CGAAA at 2157, AGAAA at 2055, TGAAC at 1955, AGAAT at 1946, TGAAA at 1855, GGAAT at 1693, GGAAC at 1684, GGAAA at 1676, GGAAA at 1660, AGAAG at 1655, GGAAA at 1642, AGAAA at 1630, TGAAA at 1625, TGAAA at 1582, CGAAG at 1555, AGAAC at 1551, AGAAT at 1520, AGAAT at 1413, TGAAC at 1302, AGAAT at 1293, TGAAA at 1212, TGAAC at 1011, AGAAT at 1002, TGAAC at 845, AGAAT at 836, CGAAA at 494, TGAAA at 473, TGAAG at 367, AGAAA at 357, GGAAG at 331, CGAAA at 312, AGAAA at 303, AGAAT at 291, AGAAC at 286, GGAAG at 241, AGAAA at 226, AGAAT at 196, AGAAA at 135, TGAAG at 132, TGAAA at 126, AGAAA at 102, GGAAG at 81, AGAAA at 52, TGAAT at 19.
- positive strand, positive direction, looking for NGAAN, 64, AGAAC at 4388, AGAAA at 4382, GGAAC at 4299, GGAAG at 4241, GGAAA at 4207, AGAAC at 4130, GGAAG at 4061, TGAAC at 4015, CGAAG at 3994, GGAAA at 3945, AGAAA at 3397, AGAAG at 3394, GGAAC at 3373, GGAAG at 3312, AGAAG at 3247, AGAAG at 3057, TGAAG at 3031, GGAAC at 3001, TGAAG at 2947, GGAAT at 2763, TGAAC at 2741, AGAAA at 2585, GGAAG at 2582, TGAAC at 2418, AGAAT at 2364, TGAAG at 2361, AGAAA at 2278, TGAAA at 2273, CGAAA at 2163, TGAAG at 2107, CGAAG at 2095, AGAAA at 1981, TGAAG at 1914, AGAAT at 1886, GGAAA at 1830, GGAAC at 1798, TGAAA at 1746, GGAAA at 1599, CGAAC at 1578, AGAAT at 1537, GGAAG at 1516, GGAAG at 1432, GGAAG at 1405, GGAAG at 1332, GGAAG at 1305, GGAAG at 1264, CGAAA at 1179, GGAAG at 1153, CGAAA at 1095, GGAAG at 1069, GGAAG at 1012, GGAAG at 928, GGAAG at 828, GGAAG at 760, GGAAG at 733, GGAAG at 676, CGAAC at 654, GGAAG at 592, TGAAC at 526, AGAAT at 522, GGAAG at 456, GGAAA at 134, TGAAC at 129, AGAAA at 110.
- complement, negative strand, negative direction, looking for NCTTN, 93, CCTTA at 4553, TCTTG at 4450, TCTTT at 4394, TCTTT at 4389, TCTTT at 4382, TCTTT at 4085, TCTTT at 4081, TCTTC at 3936, ACTTT at 3922, CCTTC at 3909, ACTTG at 3783, CCTTG at 3723, CCTTA at 3677, TCTTG at 3667, CCTTT at 3663, CCTTC at 3610, TCTTT at 3591, ACTTT at 3507, CCTTG at 3459, TCTTC at 3407, TCTTT at 3376, TCTTT at 3342, ACTTG at 3244, TCTTA at 3235, ACTTT at 3146, TCTTA at 3002, CCTTT at 2967, CCTTT at 2957, CCTTT at 2926, TCTTT at 2838, TCTTT at 2831, TCTTC at 2828, TCTTT at 2821, TCTTT at 2814, TCTTC at 2811, TCTTT at 2804, TCTTT at 2800, ACTTT at 2746, CCTTC at 2730, ACTTG at 2716, ACTTA at 2707, ACTTT at 2619, ACTTC at 2595, CCTTC at 2557, TCTTT at 2505, CCTTT at 2458, ACTTG at 2381, TCTTA at 2372, ACTTT at 2282, GCTTT at 2157, TCTTT at 2055, ACTTG at 1955, TCTTA at 1946, ACTTT at 1855, CCTTA at 1693, CCTTG at 1684, CCTTT at 1676, CCTTT at 1660, TCTTC at 1655, CCTTT at 1642, TCTTT at 1630, ACTTT at 1625, ACTTT at 1582, GCTTC at 1555, TCTTG at 1551, TCTTA at 1520, TCTTA at 1413, ACTTG at 1302, TCTTA at 1293, ACTTT at 1212, ACTTG at 1011, TCTTA at 1002, ACTTG at 845, TCTTA at 836, GCTTT at 494, ACTTT at 473, ACTTC at 367, TCTTT at 357, CCTTC at 331, GCTTT at 312, TCTTT at 303, TCTTA at 291, TCTTG at 286, CCTTC at 241, TCTTT at 226, TCTTA at 196, TCTTT at 135, ACTTC at 132, ACTTT at 126, TCTTT at 102, CCTTC at 81, TCTTT at 52, ACTTA at 19.
- complement, negative strand, positive direction, looking for NCTTN, 0.
- complement, positive strand, negative direction, looking for NCTTN, 0.
- complement, positive strand, positive direction, looking for NCTTN, 0.
- inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
- inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
- inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
- inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
- inverse negative strand, negative direction, looking for AAAAAAAA, 0.
- inverse negative strand, positive direction, looking for AAAAAAAA, 0.
- inverse positive strand, negative direction, looking for AAAAAAAA, 0.
- inverse positive strand, positive direction, looking for AAAAAAAA, 0.
Hsf core promoters
Hsf proximal promoters
Hsf distal promoters
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Dawn L. Eastmond and Hillary C. M. Nelson (October 27, 2006). "Genome-wide Analysis Reveals New Roles for the Activation Domains of the Saccharomyces cerevisiae Heat Shock Transcription Factor (Hsf1) during the Transient Heat Shock Response". Journal of Biological Chemistry. 281 (43): P32909–32921. doi:10.1074/jbc.M602454200. Retrieved 19 January 2021.
- ↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check
|pmid=value (help). Retrieved 18 September 2020.