CAT box gene transcriptions

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

Human genes

The "four cystatin genes [GeneID: 1469 CST1, GeneID: 1470 CST2, GeneID: 1471 CST3, and GeneID: 1472 CST4] contain the ATA-box sequence (ATAAA) in their 5'-flanking regions; however, the CAT-box sequence (CAT), a binding site of the transcription factor, CTF, is found only in the 5'-flanking region of the S-type cystatin genes."^[1]

Gene expressions

The "5‘ flanking region of the rat acetylcholine receptor (AChR) β subunit gene [with] regulatory elements that confer muscle specificity [includes] a minimal TATA-box-less promoter region containing an initiator motif. An 85-bp fragment [promotes] high muscle-specific expression of a chloramphenicol acetyltransferase (CAT) reporter construct upon transfection in primary muscle cells. This sequence can be functionally dissected in a basal muscle-specific promoter element carrying a M-CAT box that is flanked at the 5’ end by an enhancer element with two binding sites for myogenic factors. Point mutations in the M-CAT box cause the loss of transcriptional activity of the basal promoter fragment. The enhancer activity depends on the presence of both E boxes that cooperate in a synergistic fashion. [The] control of muscle-specific and developmental expression of the rat AChR β subunit gene requires both regulatory elements, the M-CAT box and two adjacent E boxes, located in close proximity to each other."^[2]

Interactions

The "minimal regulatory region of the 5’ flanking sequence contains E box elements that are defined by the nucleotides CANNTG [26, 271. E boxes are shown to provide binding sites for helix-loop-helix proteins of the MyoDl family including MyoDl [28], myogenin [29, 301, MRF4/ herculin [31] and myf5 [32]."^[2]

Enhancer activity

"Partial sequence of the 5' flanking region of the rat AChR β subunit gene [contains] putative E box element [CAGGTG], putative Sp1 element [GGGGCGGGT at -85 nts], putative Shue box element [CCCTGGCCTGG at -15 nts], M-CAT box element [GCGGCCTC at -8 nts]."^[2]

"Within the first 140bp of the 5’ flanking region the position and sequence of three other putative regulatory elements, the Spl [43, 44], M-CAT [34] and Shue box [45], are conserved between mouse and rat".^[2]

Consensus sequences

"The M-CAT consensus sequence [is] CATTCCT".^[2]

Promoter occurrences

"A CAT-box-like element, GCCATT [34], adjacent to the GC-box, is conserved in the three promoters."^[2]

Hypotheses

A1BG has no CAT boxes in either promoter.
A1BG is not transcribed by a CAT box.
CAT box does not participate in the transcription of A1BG.

CAT box samplings

Copying a CAT box consensus sequence 5'-CATTCCT-3' and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-CATTCCT-3' (starting with SuccessablesCAT.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 5'-CATTCCT-3', 0.
negative strand, positive direction, looking for 5'-CATTCCT-3', 1, 5'-CATTCCT-3' at 2209, and complement.
positive strand, negative direction, looking for 5'-CATTCCT-3', 0.
positive strand, positive direction, looking for 5'-CATTCCT-3', 1, 5'-CATTCCT-3' at 2458, and complement.
complement, negative strand, negative direction, looking for 5'-GTAAGGA-3', 0.
complement, negative strand, positive direction, looking for 5'-GTAAGGA-3', 1, 5'-GTAAGGA-3' at 2458.
complement, positive strand, negative direction, looking for 5'-GTAAGGA-3', 0.
complement, positive strand, positive direction, looking for 5'-GTAAGGA-3', 1, 5'-GTAAGGA-3' at 2209.
inverse complement, negative strand, negative direction, looking for 5'-AGGAATG-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-AGGAATG-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-AGGAATG-3', 1, 5'-AGGAATG-3' at 4554.
inverse complement, positive strand, positive direction, looking for 5'-AGGAATG-3', 0.
inverse negative strand, negative direction, looking for 5'-TCCTTAC-3', 1, 5'-TCCTTAC-3' at 4554.
inverse negative strand, positive direction, looking for 5'-TCCTTAC-3', 0.
inverse positive strand, negative direction, looking for 5'-TCCTTAC-3', 0.
inverse positive strand, positive direction, looking for 5'-TCCTTAC-3', 0.

CAT box UTR promoters

Negative strand, negative direction: TCCTTAC at 4554.

CAT box distal promoters

Negative strand, positive direction: CATTCCT at 2209.
Positive strand, positive direction: CATTCCT at 2458.

CAT box random dataset samplings

CATr0: 0.
CATr1: 0.
CATr2: 0.
CATr3: 1, CATTCCT at 3089.
CATr4: 1, CATTCCT at 1553.
CATr5: 1, CATTCCT at 985.
CATr6: 0.
CATr7: 0.
CATr8: 0.
CATr9: 0.
CATr0ci: 0.
CATr1ci: 0.
CAT2ci: 1, AGGAATG at 4356.
CATr3ci: 0.
CATr4ci: 1, AGGAATG at 2701.
CATr5ci: 0.
CATr6ci: 0.
CATr7ci: 0.
CATr8ci: 1, AGGAATG at 157.
CATr9ci: 1, AGGAATG at 3677.

CATr UTRs

CAT2ci: AGGAATG at 4356.

CATr proximal promoters

CATr4ci: AGGAATG at 2701.

CATr distal promoters

CATr4: CATTCCT at 1553.
CATr8ci: AGGAATG at 157.

CATr3: CATTCCT at 3089.
CATr5: CATTCCT at 985.
CATr9ci: AGGAATG at 3677.

CAT box analysis and results

The real promoters have one consensus sequence in the ZSCAN22-side UTR to A1BG (occurrence 0.5), none in the core promoter or proximal promoter and two in the positive direction only in the distal promoter (occurrence 1).

The random datasets had one consensus sequence in the ZSCAN22-side UTR of A1BG (occurrence 0.1), no core promoter sequences, one in the promoter in the negative direction (occurrence 0.1) and five in the distal promoters (occurrence 0.2 in the negative direction) and (occurrence 0.3 in the positive direction).

Based on the mismatching occurrences the real CAT boxes are likely active or activable.

CAT-box-like element samplings

Copying a responsive elements consensus sequence AAAAAAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AAAAAAAA (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 AAAAAAAA, 0.
positive strand, negative direction, looking for AAAAAAAA, 0.
positive strand, positive direction, looking for AAAAAAAA, 0.
negative strand, positive direction, looking for AAAAAAAA, 0.
complement, negative strand, negative direction, looking for TTTTTTTT, 0.
complement, positive strand, negative direction, looking for TTTTTTTT, 0.
complement, positive strand, positive direction, looking for TTTTTTTT, 0.
complement, negative strand, positive direction, looking for TTTTTTTT, 0.
inverse complement, negative strand, negative 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 complement, negative strand, positive direction, looking for TTTTTTTT, 0.
inverse negative strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, positive direction, looking for AAAAAAAA, 0.
inverse negative strand, positive direction, looking for AAAAAAAA, 0.

AAA UTRs

AAA core promoters

AAA proximal promoters

AAA distal promoters

CAT-box-like element random dataset samplings

RDr0: 0.
RDr1: 0.
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.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Response element analysis and results

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

References

↑ Eiichi Saitoh and Satoko Isemura (January 1, 1993). "Molecular Biology of Human Salivary Cysteine Proteinase Inhibitors" (PDF). Critical Reviews in Oral Biology and Medicine. 4 (3/4): 487–93. doi:10.1177/10454411930040033301. Retrieved 2013-06-28.
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 Christof Berberich, Ingolf Dürr, Michael Koenen and Veit Witzemann (September 1993). "Two adjacent E box elements and a M‐CAT box are involved in the muscle‐specific regulation of the rat acetylcholine receptor β subunit gene". European Journal of Biochemistry. 216 (2): 395–404. doi:10.1111/j.1432-1033.1993.tb18157.x. Retrieved 27 December 2019.

External links

[Saitoh-1] Eiichi Saitoh and Satoko Isemura (January 1, 1993). "Molecular Biology of Human Salivary Cysteine Proteinase Inhibitors" (PDF). Critical Reviews in Oral Biology and Medicine. 4 (3/4): 487–93. doi:10.1177/10454411930040033301. Retrieved 2013-06-28.

[Berberich-2] 2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 Christof Berberich, Ingolf Dürr, Michael Koenen and Veit Witzemann (September 1993). "Two adjacent E box elements and a M‐CAT box are involved in the muscle‐specific regulation of the rat acetylcholine receptor β subunit gene". European Journal of Biochemistry. 216 (2): 395–404. doi:10.1111/j.1432-1033.1993.tb18157.x. Retrieved 27 December 2019.

[1]

[2]

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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 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