Glucocorticoid response element gene transcriptions

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

"DNA-binding by the GR-DBD has been well-characterized; it is highly sequence-specific, directly recognizing invariant guanine nucleotides of two AGAACA [TGTTCT] half sites called the glucocorticoid response element (GRE), and binds as a dimer in head-to-head orientation with mid-nanomolar affinity (4,12–18). [...] The consensus DNA glucocorticoid response element (GRE) is comprised of two half-sites (AGAACA) separated by a three base-pair spacer (13,15,60,61)."^[1]

Human genes

Interactions

Consensus sequences

Hypotheses

A1BG has no GREs in either promoter.
A1BG is not transcribed by a GRE.
A GRE does not participate in the transcription of A1BG.

Glu samplings

Copying an apparent consensus sequence of AGAACA and putting it in "⌘F" finds one located between ZSCAN22 and A1BG and two between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGAACA (starting with SuccessablesGlu.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 AGAACA, 1, AGAACA at 281.
positive strand, negative direction, looking for AGAACA, 2, AGAACA at 3668, AGAACA at 287.
negative strand, positive direction, looking for AGAACA, 2, AGAACA at 4068, AGAACA at 3094.
positive strand, positive direction, looking for AGAACA, 0.
inverse complement, negative strand, negative direction, looking for TGTTCT, 4, TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
inverse complement, positive strand, negative direction, looking for TGTTCT, 1, TGTTCT at 45.
inverse complement, negative strand, positive direction, looking for TGTTCT, 1, TGTTCT at 108.
inverse complement, positive strand, positive direction, looking for TGTTCT, 0.

Glu (4560-2846) UTRs

Negative strand, negative direction: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
Positive strand, negative direction: AGAACA at 3668.

Glu positive direction (4265-4050) proximal promoters

Negative strand, positive direction: AGAACA at 4068.

Glu negative direction (2596-1) distal promoters

Negative strand, negative direction: AGAACA at 281.
Positive strand, negative direction: AGAACA at 287, TGTTCT at 45.

Glu positive direction (4050-1) distal promoters

Negative strand, positive direction: AGAACA at 3094, TGTTCT at 108.

Glu random dataset samplings

Glur0: 0.
Glur1: 2, AGAACA at 4240, AGAACA at 2607.
Glur2: 1, AGAACA at 908.
Glur3: 0.
Glur4: 0.
Glur5: 1, AGAACA at 1196.
Glur6: 1, AGAACA at 646.
Glur7: 0.
Glur8: 1 AGAACA at 4495.
Glur9: 0.
Glur0ci: 1, TGTTCT at 1979.
Glur1ci: 1, TGTTCT at 1218.
Glur2ci: 0.
Glur3ci: 0.
Glur4ci: 0.
Glur5ci: 2, TGTTCT at 2442, TGTTCT at 958.
Glur6ci: 1, TGTTCT at 827.
Glur7ci: 1, TGTTCT at 1886.
Glur8ci: 1, TGTTCT at 217.
Glur9ci: 1, TGTTCT at 1534.

Glur arbitrary (evens) (4560-2846) UTRs

Glur8: AGAACA at 4495.

Glur alternate (odds) (4560-2846) UTRs

Glur1: AGAACA at 4240.

Glur alternate negative direction (odds) (2811-2596) proximal promoters

Glur1: AGAACA at 2607.

Glur arbitrary positive direction (odds) (4265-4050) proximal promoters

Glur1: AGAACA at 4240.

Glur arbitrary negative direction (evens) (2596-1) distal promoters

Glur2: AGAACA at 908.
Glur6: AGAACA at 646.
Glur0ci: TGTTCT at 1979.
Glur6ci: TGTTCT at 827.
Glur8ci: TGTTCT at 217.

Glur alternate negative direction (odds) (2596-1) distal promoters

Glur5: AGAACA at 1196.
Glur1ci: TGTTCT at 1218.
Glur5ci: TGTTCT at 2442, TGTTCT at 958.
Glur7ci: TGTTCT at 1886.
Glur9ci: TGTTCT at 1534.

Glur arbitrary positive direction (odds) (4050-1) distal promoters

Glur1: AGAACA at 2607.
Glur5: AGAACA at 1196.
Glur1ci: TGTTCT at 1218.
Glur5ci: TGTTCT at 2442, TGTTCT at 958.
Glur7ci: TGTTCT at 1886.
Glur9ci: TGTTCT at 1534.

Glur alternate positive direction (evens) (4050-1) distal promoters

Glur2: AGAACA at 908.
Glur6: AGAACA at 646.
Glur0ci: TGTTCT at 1979.
Glur6ci: TGTTCT at 827.
Glur8ci: TGTTCT at 217.

Glu response element analysis and results

"DNA-binding by the GR-DBD has been well-characterized; it is highly sequence-specific, directly recognizing invariant guanine nucleotides of two AGAACA [TGTTCT] half sites called the glucocorticoid response element (GRE), and binds as a dimer in head-to-head orientation with mid-nanomolar affinity (4,12–18). [...] The consensus DNA glucocorticoid response element (GRE) is comprised of two half-sites (AGAACA) separated by a three base-pair spacer (13,15,60,61)."^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	5	2	2.5	2.5 ± 1.5 (--4,+-1)
Randoms	UTR	arbitrary negative	1	10	0.1	0.1
Randoms	UTR	alternate negative	1	10	0.1	0.1
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	0	10	0	0
Randoms	Core	alternate negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	arbitrary negative	0	10	0	0.05
Randoms	Proximal	alternate negative	1	10	0.1	0.05
Reals	Proximal	positive	1	2	0.5	0.5 ± 0.5 (-+1,++0)
Randoms	Proximal	arbitrary positive	1	10	0.1	0.05
Randoms	Proximal	alternate positive	0	10	0	0.05
Reals	Distal	negative	3	2	1.5	1.5 ± 1.5 (--1,+-2)
Randoms	Distal	arbitrary negative	5	10	0.5	0.55
Randoms	Distal	alternate negative	6	10	0.6	0.55
Reals	Distal	positive	2	2	1	1 ± 1 (-+2,++0)
Randoms	Distal	arbitrary positive	7	10	0.7	0.6
Randoms	Distal	alternate positive	5	10	0.5	0.6

Comparison:

The occurrences of real Glucocorticoid UTRs, proximals and distals are greater than the randoms. This suggests that the real Glucocorticoid response elements are likely active or activable.

Pathways

Stimulation of the pathway gluconeogenesis, in particular, in the liver results in the synthesis of glucose from non-hexose substrates, such as amino acids and glycerol from triglyceride breakdown, and is particularly important in carnivores and certain herbivores.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

References

↑ ^1.0 ^1.1 Nicholas V Parsonnet, Nickolaus C Lammer, Zachariah E Holmes, Robert T Batey, Deborah S Wuttke (5 September 2019). "The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity". Nucleic Acids Research. 47 (15): 8180–8192. doi:10.1093/nar/gkz486. PMID 31147715. Retrieved 28 August 2020.

External links

[Parsonnet-1] 1.0 ^1.1 Nicholas V Parsonnet, Nickolaus C Lammer, Zachariah E Holmes, Robert T Batey, Deborah S Wuttke (5 September 2019). "The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity". Nucleic Acids Research. 47 (15): 8180–8192. doi:10.1093/nar/gkz486. PMID 31147715. Retrieved 28 August 2020.

[1]

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Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Heat shock elements Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family 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 M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 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 Nanos/Pumilio response element 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 Shue boxes Sip4p gene transcriptions Smp1p gene transcriptions Sp1 (Berberich) elements 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 actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family 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 Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream repressor site 1 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

Glucocorticoid response element gene transcriptions

Contents

Human genes

Interactions

Consensus sequences

Hypotheses

Glu samplings

Glu (4560-2846) UTRs

Glu positive direction (4265-4050) proximal promoters

Glu negative direction (2596-1) distal promoters

Glu positive direction (4050-1) distal promoters

Glu random dataset samplings

Glur arbitrary (evens) (4560-2846) UTRs

Glur alternate (odds) (4560-2846) UTRs

Glur alternate negative direction (odds) (2811-2596) proximal promoters

Glur arbitrary positive direction (odds) (4265-4050) proximal promoters

Glur arbitrary negative direction (evens) (2596-1) distal promoters

Glur alternate negative direction (odds) (2596-1) distal promoters

Glur arbitrary positive direction (odds) (4050-1) distal promoters

Glur alternate positive direction (evens) (4050-1) distal promoters

Glu response element analysis and results

Pathways

Acknowledgements

See also

References

External links