Gcr1p gene transcriptions: Difference between revisions

Revision as of 06:20, 23 April 2022

Associate Editor(s)-in-Chief: Henry A. Hoff

"The transcription regulators (Gcr1 and Gcr2) are responsible for inducing the expression of the glycolytic genes in S. cerevisiae [14, 15], Gcr1p binds to CT boxes (5′-CTTCC-3′) upstream of the glycolytic genes and Gcr2p acts as a co-activator by forming a complex with Gcr1p [16]."^[1]

Human genes

Consensus sequences

The upstream activating sequence (UAS) for Gcr1p is 5'-CTTCC-3' for the transcriptional activator involved in the regulation of glycolysis [77].^[2]

GCR1 samplings

Copying the apparent consensus sequence for Gcr1p CTTCC and putting it in "⌘F" finds four located between ZSCAN22 and six between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs (starting with SuccessablesE.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 looking for, and found:

negative strand, negative direction, looking for CTTCC, 4, CTTCC at 3611, CTTCC at 2558, CTTCC at 1656, CTTCC at 1556.
negative strand, positive direction, looking for CTTCC, 6, CTTCC at 4242, CTTCC at 1433, CTTCC at 1333, CTTCC at 1070, CTTCC at 734, CTTCC at 677.
positive strand, negative direction, looking for CTTCC, 1, CTTCC at 3777.
positive strand, positive direction, looking for CTTCC, 3, CTTCC at 4249, CTTCC at 3852, CTTCC at 210.
complement, negative strand, negative direction, looking for GAAGG, 1, GAAGG at 3777.
complement, negative strand, positive direction, looking for GAAGG, 3, GAAGG at 4249, GAAGG at 3852, GAAGG at 210.
complement, positive strand, negative direction, looking for GAAGG, 4, GAAGG at 3611, GAAGG at 2558, GAAGG at 1656, GAAGG at 1556.
complement, positive strand, positive direction, looking for GAAGG, 6, GAAGG at 4242, GAAGG at 1433, GAAGG at 1333, GAAGG at 1070, GAAGG at 734, GAAGG at 677.
inverse complement, negative strand, negative direction, looking for GGAAG, 1, GGAAG at 619, and complement.
inverse complement, negative strand, positive direction, looking for GGAAG, 9, GGAAG at 4263, GGAAG at 4248, GGAAG at 3871, GGAAG at 3762, GGAAG at 3667, GGAAG at 2784, GGAAG at 2748, GGAAG at 1594, GGAAG at 209, and complements.
inverse complement, positive strand, negative direction, looking for GGAAG, 7, GGAAG at 3909, GGAAG at 3610, GGAAG at 2730, GGAAG at 2557, GGAAG at 331, GGAAG at 241, GGAAG at 81, and complements.
inverse complement, positive strand, positive direction, looking for GGAAG, 20, GGAAG at 4241, GGAAG at 4061, GGAAG at 3312, GGAAG at 2582, GGAAG at 1516, GGAAG at 1432, GGAAG at 1405, GGAAG at 1332, GGAAG at 1305, GGAAG at 1264, GGAAG at 1153, GGAAG at 1069, GGAAG at 1012, GGAAG at 928, GGAAG at 828, GGAAG at 760, GGAAG at 733, GGAAG at 676, GGAAG at 592, GGAAG at 456, and complements.
inverse negative strand, negative direction, looking for CCTTC, 7, CCTTC at 3909, CCTTC at 3610, CCTTC at 2730, CCTTC at 2557, CCTTC at 331, CCTTC at 241, CCTTC at 81.
inverse negative strand, positive direction, looking for CCTTC, 9, CCTTC at 4263, CCTTC at 4248, CCTTC at 3871, CCTTC at 3762, CCTTC at 3667, CCTTC at 2784, CCTTC at 2748, CCTTC at 1594, CCTTC at 209.
inverse positive strand, negative direction, looking for CCTTC, 1, CCTTC at 619.
inverse positive strand, positive direction, looking for CCTTC, 20, CCTTC at 4241, CCTTC at 4061, CCTTC at 3312, CCTTC at 2582, CCTTC at 1516, CCTTC at 1432, CCTTC at 1405, CCTTC at 1332, CCTTC at 1305, CCTTC at 1264, CCTTC at 1153, CCTTC at 1069, CCTTC at 1012, CCTTC at 928, CCTTC at 828, CCTTC at 760, CCTTC at 733, CCTTC at 676, CCTTC at 592, CCTTC at 456.

Gcr UTRs

Negative strand, negative direction: CTTCC at 3611.
Positive strand, negative direction: GGAAG at 3909, GGAAG at 3610, CTTCC at 3777.

Gcr proximal promoters

Positive strand, negative direction: GGAAG at 2730.

Negative strand, positive direction: GGAAG at 4263, GGAAG at 4248, CTTCC at 4242.
Positive strand, positive direction: CTTCC at 4249, GGAAG at 4241, GGAAG at 4061.

Gcr distal promoters

Negative strand, negative direction: CTTCC at 2558, CTTCC at 1656, CTTCC at 1556, GGAAG at 619.
Positive strand, negative direction: GGAAG at 2557, GGAAG at 331, GGAAG at 241, GGAAG at 81.

Negative strand, positive direction: GGAAG at 3871, GGAAG at 3762, GGAAG at 3667, GGAAG at 2784, GGAAG at 2748, GGAAG at 1594, CTTCC at 1433, CTTCC at 1333, CTTCC at 1070, CTTCC at 734, CTTCC at 677, GGAAG at 209.
Positive strand, positive direction: CTTCC at 3852, GGAAG at 3312, GGAAG at 2582, GGAAG at 1516, GGAAG at 1432, GGAAG at 1405, GGAAG at 1332, GGAAG at 1305, GGAAG at 1264, GGAAG at 1153, GGAAG at 1069, GGAAG at 1012, GGAAG at 928, GGAAG at 828, GGAAG at 760, GGAAG at 733, GGAAG at 676, GGAAG at 592, GGAAG at 456, CTTCC at 210.

GCR random dataset samplings

GCRr0: 4, CTTCC at 3519, CTTCC at 1594, CTTCC at 1119, CTTCC at 122.
GCRr1: 6, CTTCC at 4075, CTTCC at 4067, CTTCC at 2093, CTTCC at 732, CTTCC at 650, CTTCC at 293.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

GCRr UTRs

GCRr0: CTTCC at 3519.

RDr core promoters

GCRr proximal promoters

GCRr1: 6, CTTCC at 4075, CTTCC at 4067.

GCRr distal promoters

GCRr0: CTTCC at 1594, CTTCC at 1119, CTTCC at 122.

GCRr1: CTTCC at 2093, CTTCC at 732, CTTCC at 650, CTTCC at 293.

Response element analysis and results

Gcr1p binds to CT boxes (5′-CTTCC-3′) upstream of the glycolytic genes and Gcr2p acts as a co-activator by forming a complex with Gcr1p [16]."^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	4	2	2.0	2.0
Randoms	UTR	arbitrary negative	0	10	0	0
Randoms	UTR	alternate negative	0	10	0	0
Reals	Core	negative	0	2	0	0
Randoms	Core	negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	positive	0	10	0	0
Reals	Proximal	negative	1	2	0.5	1.75
Randoms	Proximal	negative	0	10	0	0
Reals	Proximal	positive	6	2	3.0	1.75
Randoms	Proximal	positive	0	10	0	0
Reals	Distal	negative	8	2	4.0	10
Randoms	Distal	negative	1	10	0.1	0.05
Reals	Distal	positive	32	2	16	10
Randoms	Distal	positive	0	10	0	0.05

Comparison:

The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

References

↑ ^1.0 ^1.1 Doblin Sandai, Yasser Tabana and Rosline Sandai (5 November 2018). Doblin Sandai, ed. Carbon Sources Attribute to Pathogenicity in Candida albicans, in Candida albicans. IntechOpen. doi:10.5772/intechopen.80211. Retrieved 7 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.

External links

[Sandai-1] 1.0 ^1.1 Doblin Sandai, Yasser Tabana and Rosline Sandai (5 November 2018). Doblin Sandai, ed. Carbon Sources Attribute to Pathogenicity in Candida albicans, in Candida albicans. IntechOpen. doi:10.5772/intechopen.80211. Retrieved 7 January 2021.

[Tang-2] 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.

[1]

[2]

@@ Line 82: / Line 82: @@
 ==GCR random dataset samplings==
-# RDr0: 0.
+# GCRr0: 4, CTTCC at 3519, CTTCC at 1594, CTTCC at 1119, CTTCC at 122.
-# RDr1: 0.
+# GCRr1: 6, CTTCC at 4075, CTTCC at 4067, CTTCC at 2093, CTTCC at 732, CTTCC at 650, CTTCC at 293.
 # RDr2: 0.
 # RDr3: 0.
@@ Line 103: / Line 103: @@
 # RDr9ci: 0.
-===RDr UTRs===
+===GCRr UTRs===
-{{main|UTR promoter gene transcriptions}}
+# GCRr0: CTTCC at 3519.
 ===RDr core promoters===
-{{main|Core promoter gene transcriptions}}
-===RDr proximal promoters===
+===GCRr proximal promoters===
-{{main|Proximal promoter gene transcriptions}}
+# GCRr1: 6, CTTCC at 4075, CTTCC at 4067.
+===GCRr distal promoters===
+# GCRr0: CTTCC at 1594, CTTCC at 1119, CTTCC at 122.
-===RDr distal promoters===
+# GCRr1: CTTCC at 2093, CTTCC at 732, CTTCC at 650, CTTCC at 293.
-{{main|Distal promoter gene transcriptions}}
 ==Response element analysis and results==

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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions