Calcium-response element gene transcriptions

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

Human genes

Gene ID: 106736470 is LOC106736470 PTH negative calcium response element (nCARE) region on chromosome 11: "This region contains two negative calcium response elements (nCAREs) that regulate expression of the downstream PTH (parathyroid hormone) gene. nCARE motifs are present upstream of multiple calcium-regulated genes and are comprised of a palindromic motif that derives from Alu retroelement sequence. This sequence is bound by a protein complex containing AP endonuclease (Ape1) and Ku antigen (X-ray repair complementing defective repair in Chinese hamster cells). Increased calcium results in acetylation of Ape1 by p300 and recruitment of histone deacetylases to this complex, leading to repression of gene expression."^[1]

Gene ID: 627 is BDNF brain derived neurotrophic factor on 11p14.1: "This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders."^[2]

Consensus sequences

The calcium-response element (CaRE1) has the consensus sequence: 5'-CTATTTCGAG-3'^[3]

Promoter occurrences

"The Bdnf gene contains nine alternative promoters, each of which is activity inducible in neurons and most of which are regulated by multiple activity‐dependent transcription factors (West et al. 2014). Bdnf exon IV‐containing transcripts (Bdnf IV) are the most highly expressed and activity regulated of the Bdnf splice variants in developing neurons, and the transcription factors that regulate Bdnf promoter IV have been well described. We first identified calcium response factor (CaRF) as a transcription factor based on its ability to bind the L‐VGCC‐responsive calcium‐response element 1 (CaRE1) in Bdnf promoter IV (Tao et al. 2002). Basal expression of Bdnf IV is reduced in the cortex of adult CaRF knockout mice, consistent with CaRF functioning as an activator of Bdnf promoter IV (McDowell et al. 2010). However, L‐VGCC‐induced transcription of Bdnf IV is unaffected by the loss of CaRF and instead the transcription factor MEF2C mediates the actions of CaRE1 in response to this stimulus (Lyons et al. 2012)."^[4]

Hypotheses

A1BG has no Calcium-response elements in either promoter.
A1BG is not transcribed by a Calcium-response element.
A calcium-response element does not participate in the transcription of A1BG.

Samplings

Copying a responsive elements consensus sequence 5'-CTATTTCGAG-3' 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 5'-CTATTTCGAG-3' (starting with SuccessablesCalR.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'-CTATTTCGAG-3', 0.
negative strand, positive direction, looking for 5'-CTATTTCGAG-3', 0.
positive strand, negative direction, looking for 5'-CTATTTCGAG-3', 0.
positive strand, positive direction, looking for 5'-CTATTTCGAG-3', 0.
complement, negative strand, negative direction, looking for 5'-GATAAAGCTC-3', 0.
complement, negative strand, positive direction, looking for 5'-GATAAAGCTC-3', 0.
complement, positive strand, negative direction, looking for 5'-GATAAAGCTC-3', 0.
complement, positive strand, positive direction, looking for 5'-GATAAAGCTC-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-CTCGAAATAG-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-CTCGAAATAG-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-CTCGAAATAG-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-CTCGAAATAG-3', 0.
inverse negative strand, negative direction, looking for 5'-GAGCTTTATC-3', 0.
inverse negative strand, positive direction, looking for 5'-GAGCTTTATC-3', 0.
inverse positive strand, negative direction, looking for 5'-GAGCTTTATC-3', 0.
inverse positive strand, positive direction, looking for 5'-GAGCTTTATC-3', 0.

CalR core promoters

CalR proximal promoters

CalR distal promoters

Acknowledgements

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

References

↑ RefSeq (November 2015). "LOC106736470 PTH negative calcium response element [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 6 November 2020.
↑ RefSeq (November 2015). "BDNF brain derived neurotrophic factor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 7 November 2020.
↑ Xu Tao, Anne E. West, Wen G. Chen, Gabriel Corfas, Michael E. Greenberg (2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33: 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226. Retrieved 2 September 2020.
↑ Michelle R. Lyons, Liang‐Fu Chen, Jie V. Deng, Caitlin Finn, Andreas R. Pfenning, Aditi Sabhlok, Kelli M. Wilson, Anne E. West (April 2016). "The transcription factor calcium‐response factor limits NMDA receptor‐dependent transcription in the developing brain". Journal of Neurochemistry. 137 (2): 164–176. doi:10.1111/jnc.13556. Retrieved 7 November 2020.

External links

[RefSeq106736470-1] RefSeq (November 2015). "LOC106736470 PTH negative calcium response element [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 6 November 2020.

[RefSeq2015-2] RefSeq (November 2015). "BDNF brain derived neurotrophic factor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 7 November 2020.

[Tao-3] Xu Tao, Anne E. West, Wen G. Chen, Gabriel Corfas, Michael E. Greenberg (2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33: 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226. Retrieved 2 September 2020.

[Lyons-4] Michelle R. Lyons, Liang‐Fu Chen, Jie V. Deng, Caitlin Finn, Andreas R. Pfenning, Aditi Sabhlok, Kelli M. Wilson, Anne E. West (April 2016). "The transcription factor calcium‐response factor limits NMDA receptor‐dependent transcription in the developing brain". Journal of Neurochemistry. 137 (2): 164–176. doi:10.1111/jnc.13556. Retrieved 7 November 2020.

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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 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