Proximal promoter gene transcriptions

Editor-In-Chief: Henry A. Hoff

The proximal sequence upstream of the gene that tends to contain primary regulatory elements is a proximal promoter.

It is approximately 250 base pairs or nucleotides, nts upstream of the transcription start site.

Genetics

Def. "[a] unit of heredity; a segment of DNA or RNA that is transmitted from one generation to the next, and that carries genetic information such as the sequence of amino acids for a protein"^[1] is called a gene.

The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame.

Promoters

Def. a "section of DNA that controls the initiation of RNA transcription as a product of a gene"^[2] is called a promoter.

Proximus

Def. "neighbour, nearest person or thing"^[3] is called proximus.

Theoretical proximal promoters

Def. a "promoter region [juxtaposed to the core promoter that] binds transcription factors that modify the affinity of the core promoter for RNA polymerase.^[12][13]"^[4] is called a proximal promoter.

Distal promoters

A distal promoter is a distant (in numbers of nucleotides) portion of the promoter for a particular gene.

This distal sequence is upstream of the gene.

It is a region of DNA that may contain additional regulatory elements, often with a weaker influence than the proximal promoter.

Dispersed promoters

A dispersed promoter is a region of DNA that facilitates the transcription of a particular gene, where this promoter region contains several transcription start sites over 50-100 nucleotides.

Dispersed promoters are more recent and less widespread throughout nature than focused promoters.^[5]

Focused promoters

A focused promoter contains either a single transcription start site or a distinct cluster of start sites over several nucleotides.^[5] Focused promoters are sometimes referred to as narrow peak (NP) promoters.^[6]

Intermediate promoters

"The intermediate transcription factor genes have early promoters, late transcription factor genes have intermediate promoters, and early transcription factor genes have late promoters, providing a cascade mechanism of regulation (4, 9, 10, 15, 22)."^[7]

Minimal promoters

File:Minimal promoter.png

Diagram is of the βH-2K-DCR microlocus cassette and the β-globinpromoter. Credit: Michael Antoniou and Frank Grosveld.{{fairuse}}

There is "interaction between the dominant control region (DCR) and the promoter of the human β-globin gene. Expression analysis in [murine erythroleukemia] MEL cells has revealed that the DCR contains a number of elements capable of replacing the upstream (- 250 to - 100) erythroid-specific region of the promoter. The DCR strongly stimulates expression from a promoter possessing only a TATA box. However, this basic level of transcription is not induced upon erythroid differentiation of the cells. Mutational analysis of the minimal (- 100, noninducible) promoter shows that only the combination of the DCR and the CAC/CCAAT elements provides erythroid-specific transcription. These regions act synergistically to produce full regulated expression during erythroid differentiation."^[8]

The "murine NF-E1 alone is incapable of inducing regulated expression on the minimal β-globin promoter (see [above diagram]) but needs to interact with at least one ubiquitous DNA-binding protein at a neighboring site ([above diagram], CP-1 at -160; deBoer et al. 1988)."^[8]

"Only the minimal promoter is essential in the presence of the DCR."^[8]

"The upstream part of the β-globin promoter confers inducible expression on the gene, mediated by the presence of at least one of the two NF-E1 and the (-150) CP-l-binding sites ([above diagram]; deBoer et al. 1988)".^[8]

"Deletion analysis revealed that only the minimal part of the promoter is, in fact, sufficient for full regulated expression ([...], - 103). Thus, the upstream region of the promoter that contains the binding sites for the erythroid-specific transcription factor NF-E1 (see [above diagram]), like the enhancers, is also made completely redundant by the DCR."^[8]

Hypotheses

At least one promoter occurs within the proximal promoter of A1BG.

References

↑ "gene". San Francisco, California: Wikimedia Foundation, Inc. December 13, 2012. Retrieved 2012-12-13.
↑ promoter. San Francisco, California: Wikimedia Foundation, Inc. 28 May 2014. Retrieved 2014-06-08.
↑ "proximus". San Francisco, California: Wikimedia Foundation, Inc. 17 April 2014. Retrieved 2014-06-08.
↑ Thomas Shafee and Rohan Lowe (2017). "Eukaryotic and prokaryotic gene structure" (PDF). WikiJournal of Medicine. 4 (1): 2. doi:10.15347/wjm/2017.002. Retrieved 2017-04-06. Unknown parameter |month= ignored (help)
↑ ^5.0 ^5.1 T Juven-Gershon, JY Hsu, JWM Theisen, JT Kadonaga (2008). "The RNA polymerase II core promoter - the gateway to transcription". Current Opinion in Cell Biology. 20 (3): 253–9. doi:10.1016/j.ceb.2008.03.003. PMID 18436437. Unknown parameter |month= ignored (help); |access-date= requires |url= (help)
↑ Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U (2011). "Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level". PLoS Genetics. 7 (1): e1001274. doi:10.1371/journal.pgen.1001274. PMID 21249180. Unknown parameter |month= ignored (help); |access-date= requires |url= (help)
↑ Zhilong Yang, Sara E. Reynolds, Craig A. Martens, Daniel P. Bruno, Stephen F. Porcella and Bernard Moss (2011). "Expression profiling of the intermediate and late stages of poxvirus replication". Journal of Virology. 85 (19): 9899–908. doi:10.1128/JVI.05446-11. Retrieved 2017-04-06. Unknown parameter |month= ignored (help)
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 Michael Antoniou and Frank Grosveld (1990). "β-Globin dominant control region interacts differently with distal and proximal promoter elements" (PDF). Genes & Development. 4 (6): 1007–1013. doi:10.1101/gad.4.6.1007. Retrieved 2018-2-23. Check date values in: |accessdate= (help)

External links

Template:Sisterlinks

[GeneWikt-1] "gene". San Francisco, California: Wikimedia Foundation, Inc. December 13, 2012. Retrieved 2012-12-13.

[PromoterWikt-2] promoter. San Francisco, California: Wikimedia Foundation, Inc. 28 May 2014. Retrieved 2014-06-08.

[ProximusWikt-3] "proximus". San Francisco, California: Wikimedia Foundation, Inc. 17 April 2014. Retrieved 2014-06-08.

[Shafee-4] Thomas Shafee and Rohan Lowe (2017). "Eukaryotic and prokaryotic gene structure" (PDF). WikiJournal of Medicine. 4 (1): 2. doi:10.15347/wjm/2017.002. Retrieved 2017-04-06. Unknown parameter |month= ignored (help)

[Gershon-5] 5.0 ^5.1 T Juven-Gershon, JY Hsu, JWM Theisen, JT Kadonaga (2008). "The RNA polymerase II core promoter - the gateway to transcription". Current Opinion in Cell Biology. 20 (3): 253–9. doi:10.1016/j.ceb.2008.03.003. PMID 18436437. Unknown parameter |month= ignored (help); |access-date= requires |url= (help)

[Rach-6] Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U (2011). "Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level". PLoS Genetics. 7 (1): e1001274. doi:10.1371/journal.pgen.1001274. PMID 21249180. Unknown parameter |month= ignored (help); |access-date= requires |url= (help)

[Yang2011-7] Zhilong Yang, Sara E. Reynolds, Craig A. Martens, Daniel P. Bruno, Stephen F. Porcella and Bernard Moss (2011). "Expression profiling of the intermediate and late stages of poxvirus replication". Journal of Virology. 85 (19): 9899–908. doi:10.1128/JVI.05446-11. Retrieved 2017-04-06. Unknown parameter |month= ignored (help)

[Antoniou-8] 8.0 ^8.1 ^8.2 ^8.3 ^8.4 Michael Antoniou and Frank Grosveld (1990). "β-Globin dominant control region interacts differently with distal and proximal promoter elements" (PDF). Genes & Development. 4 (6): 1007–1013. doi:10.1101/gad.4.6.1007. Retrieved 2018-2-23. Check date values in: |accessdate= (help)

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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 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 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 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