Vitamin D response element gene transcriptions: Difference between revisions
m (→Samplings) |
|||
| Line 53: | Line 53: | ||
|pmid=9265628 | |pmid=9265628 | ||
|accessdate=4 September 2020 }}</ref> | |accessdate=4 September 2020 }}</ref> | ||
"Using the Jasper and Consite algorithms, the A/GGG/TTCAnnnA/GGG/TTCA and GA/GGTTCATnnnGTTCA sequences were considered as human and mouse VDRE consensus sequences, respectively, as previously shown.17, 18 Previous studies have suggested that regulatory VDREs could locate distally, i.e. > 1 Mb, to the transcription starting site.19 We analysed the entire genomic sequence of the human and murine HOTAIR and ANRIL genes as well as 5 kb upstream the transcription starting sites to include proximal promoter regions. Our analysis revealed two and three potential VDREs in the human HOTAIR and ANRIL genes, respectively, all of them were located within the intron 1 [...]."<ref name=Kakhki>{{ cite journal | |||
|author=Majid Pahlevan Kakhki, Abbas Nikravesh, Zeinab Shirvani Farsani, Mohammad Ali Sahraian, Mehrdad Behmanesh | |||
|title=''HOTAIR'' but not ''ANRIL'' long non‐coding RNA contributes to the pathogenesis of multiple sclerosis | |||
|journal=Immunology | |||
|date=April 2018 | |||
|volume=153 | |||
|issue=4 | |||
|pages=479-487 | |||
|url=https://onlinelibrary.wiley.com/doi/full/10.1111/imm.12850 | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1111/imm.12850 | |||
|pmid= | |||
|accessdate=8 March 2021 }}</ref> | |||
==VDRE samplings== | ==VDRE samplings== | ||
Revision as of 03:51, 9 March 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
Vitamin D response elements (VDRE) typically consist of two conserved hexameric half-sites separated by a three nucleotide spacer, referred to as a DR3 type element.[1] Although it is known that the sequence of a VDRE can have a strong influence on the degree of protein binding, particularly at the fifth position in the half-site,[2] previous studies have focused on synthetic variations of response elements and not naturally occurring sequences.[3]
The VDR is widely distributed in tissues, and is not restricted to those tissues considered the classic targets of vitamin D. The VDR upon binding to 1,25(OH)2D heterodimerizes with other nuclear hormone receptors, in particular the family of retinoid X receptors. This complex then binds to special DNA sequences called vitamin D response elements (VDRE) in the promoters of genes which it regulates. A variety of additional proteins called coactivators complex with the activated VDR/RXR heterodimers either to form a bridge from the VDR/RXR complex binding to the VDRE to the proteins responsible for transcription such as RNA polymerase II binding to the transcription start site or to help unravel the chromatin at the site of the gene via recruitment of histone acetyl transferases (HAT), allowing transcription to proceed.[4]
Human genes
Consensus sequences
"The following VDRE oligonucleotides were used: mouse osteopontin, 5′-GCTCGGGTAGGGTTCACGAGGTTCACTCGACTCG-3′; DR3, 5′-GCTCGGGTAGAGGTCAAGGAGGTCACTCGACTCG-3′; DR3′, 5′-GCTCGGGTAGAGTTCAAGGAGTTCACTCGACTCG-3′; human osteocalcin, 5′-GCTCGGGTAGGGGTGACTCACCGGGTGAACGGGGGCATCTCGACTCG-3′; and Random, 5′-GCTCGGGTAGCTAATCCGTTTCGAGCTCGACTCG-3′."[5] Likely general consensus sequence for the VDRE: (A/G)G(G/T)(G/T)CA.[5]
"Using the Jasper and Consite algorithms, the A/GGG/TTCAnnnA/GGG/TTCA and GA/GGTTCATnnnGTTCA sequences were considered as human and mouse VDRE consensus sequences, respectively, as previously shown.17, 18 Previous studies have suggested that regulatory VDREs could locate distally, i.e. > 1 Mb, to the transcription starting site.19 We analysed the entire genomic sequence of the human and murine HOTAIR and ANRIL genes as well as 5 kb upstream the transcription starting sites to include proximal promoter regions. Our analysis revealed two and three potential VDREs in the human HOTAIR and ANRIL genes, respectively, all of them were located within the intron 1 [...]."[6]
VDRE samplings
Copying the consensus of the VDRE: AGGTCA and putting the sequence in "⌘F" finds no locations for this sequence between ZSCAN22 and A1BG but there three between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesVDRE.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 AGGTCA, 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.
VDRE UTRs
VDRE core promoters
VDRE proximal promoters
VDRE distal promoters
See also
References
- ↑ Roff A, Wilson RT (March 2009). "A Novel SNP in a Vitamin D Response Element of the CYP24A1 Promoter Reduces Protein Binding, Transactivation, and Gene Expression". Journal of Steroid Biochem Mol Biol. 112 (1–3): 47–54. doi:10.1016/j.jsbmb.2008.08.009. PMC 2749287. PMID 18824104.
- ↑ Jin CH, Pike JW (1996). "Human vitamin D receptor-dependent transactivation in Saccharomyces cerevisiae requires retinoid X receptor". Mol. Endocrinol. 10 (2): 196–205. doi:10.1210/mend.10.2.8825559. PMID 8825559.
- ↑ Umesono K, Murakami KK, Thompson CC, Evans RM (28 June 1991). "HDirect repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors". Cell. 65 (7): 1255–66. doi:10.1016/0092-8674(91)90020-Y. PMC 6159884. PMID 1648450.
- ↑ Daniel Bikle (2014). Kenneth R Feingold, Bradley Anawalt, Alison Boyce, George Chrousos, Wouter W de Herder, Kathleen Dungan, Ashley Grossman, Jerome M Hershman, Hans J Hofland, Gregory Kaltsas, Christian Koch, Peter Kopp, Márta Korbonits, Robert McLachlan, John E Morley, Maria New, Jonathan Purnell, Frederick Singer, Constantine A Stratakis, Dace L Trence, Don P Wilson, ed. Vitamin D: Production, Metabolism, and Mechanisms of Action, In: Endotext. South Dartmouth (MA): MDText.com, Inc. PMID 25905172.
- ↑ 5.0 5.1 Theodore A. Craig, Timothy D. Veenstra, Stephen Naylor, Andy J. Tomlinson, Kenneth L. Johnson, Slobodan Macura, Nenad Juranić, and Rajiv Kumar (26 August 1997). "Zinc Binding Properties of the DNA Binding Domain of the 1,25-Dihydroxyvitamin D3 Receptor". Biochemistry. 36 (34): 10482–10491. doi:10.1021/bi970561b. PMID 9265628. Retrieved 4 September 2020.
- ↑ Majid Pahlevan Kakhki, Abbas Nikravesh, Zeinab Shirvani Farsani, Mohammad Ali Sahraian, Mehrdad Behmanesh (April 2018). "HOTAIR but not ANRIL long non‐coding RNA contributes to the pathogenesis of multiple sclerosis". Immunology. 153 (4): 479–487. doi:10.1111/imm.12850. Retrieved 8 March 2021.