A1BG response element negative results: Difference between revisions
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Revision as of 02:33, 1 December 2020
Associate Editor(s)-in-Chief: Henry A. Hoff
Def. nucleotide "sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents", [that] "may be found in both promoter and enhancer regions"[1] are called response elements.
Hypotheses
- A1BG has no response elements in either promoter.
- A1BG is not transcribed by a response element.
- Each response element does not participate in the transcription of A1BG.
Response element negative results
| Name of elements | Consensus sequences | Testing | Notes |
|---|---|---|---|
| ABA-response elements | 5'-GATCGATC-3', 5'-CGATCGAT-3', 5'-ACGTGTCC-3', 5'-GATCGAT-3' | 16 | ABREN, CGATCGAT motif, ABRE, and core of ABREN and CGATCGAT motif.[2] |
| Abf1 regulatory factors | 5'-CGTCCTCTACG-3' | 16 | 5'-CGTNNNNNACGAT-3'[3] |
| Activating proteins | 5'-GCCCACGGG-3' | 16 | Activating protein 2 (AP-2)[4] |
| Activating proteins | 5'-GGCCAA-3' | 16 | Activating protein 2 (AP-2)[5] |
| Alpha-amylase conserved elements | 5'-TATCCA-3' | 16 | 5'-TATCCATCCATCC-3'[6] |
| Amino acid response elements | 5'-ATTGCATCA-3' | 16 | AARE1 (5'-ATTGCATCA-3')[7] |
| Amino acid response elements | 5'-TTTGCATCA-3' | 16 | 5'-TTTGCATCA-3'.[8][9] |
| AARE-like | 5'-TGGTGAAAG-3' | 16 | AARE-like sequence (5′- TGGTGAAAG-3′, named AARE3)[7] |
| Androgen response elements | 5'-GGTACANNNTGTTCT-3'[10] | 16 | 5′-GGTACACGGTGTTCT-3′[10] |
| Androgen response elements | 5'-TGATTCGTGAG-3' | 16 | 5'-AGAACANNNTGTTCT-3'[11] |
| Antioxidant-electrophile responsive elements | 5'-GTGAGGTCGC-3' | 16 | 5'-GTGAGGTCGC-3'[12] or 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3'[13], an antioxidant response element (ARE) |
| CAAT boxes | 5'-(C/T)(A/G)(A/G)CCAATC(A/G)-3' | 16 | consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT |
| Calcium-response elements | 5'-CTATTTCGAG-3' | 16 | CaRE1 5'-CTATTTCGAG-3'[14] |
| Carbohydrate response elements | 5'-CACGTGACCGGATCTTG-3', 5'-TCCGCCCCCATCACGTG-3' | 16 | ChoRE1, ChoRE2[15] |
| Cbf1 regulatory factors | 5'-TCACGTGA-3' | 8 | strongly bound Cbf1 motifs enriched at both ends with a "T" on the 5′ and "A" on the 3′ end |
| C-boxes | 5'-GAGGCCATCT-3' | 16 | 5'-GAGGCCATCT-3'[16] |
| C/A hybrid boxes | 5'-TGACGTAT-3' | 16 | 5'-TGACGTAT-3'[17] |
| C/T hybrid boxes | 5'-TGACGTTA-3' | 16 | 5'-TGACGTTA-3'[17] |
| CCCTC-binding factors (CTCF) | 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3' | 16 | 5′-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3′[18] |
| C/EBP boxes | 5'-TTAGGACAT-3',[19] or 5'-TAGCATT-3'[5] | 16 | CCAAT-enhancer-binding site (C/EBP) is TAGCATT |
| Cell cycle regulation | 5'-CCCAACGGT-3'[6] | 16 | tomato genome-wide analysis |
| CENP-B boxes | 5'-TTTCGTTGGAAGCGGGA-3' | 16 | specifically localized at the centromere |
| Coupling elements | 5'-TGCCACCGG-3'[2] | 16 | CE1 (Watanabe) |
| DAF-16-associated elements | 5'-TGATAAG-3' | ⌘F | DAF-16-associated element (DAE)[20] |
| DAF-16 binding elements | 5'-GTAAACA-3' | ⌘F | DAF-16 binding element (DBE)[20] |
| D boxes | 5'-GTTGTATAAC-3' | ⌘F | 5′-CTTATGTAAA-3′[21] |
| D-boxes | 5'-TCTCACA-3' | ⌘F | TCTCACATT(A/C)AATAAGTCA is a D-box.[16] |
| Defense and stress-responsive elements | 5'-ATTTTCTTCA-3' | ⌘F | Defense and stress-responsive elements (DREs) |
| DNA damage response elements (DREs) | 5'-TAGCCGCCG-3' or 5'-TTTCAAT-3' | ⌘F | in the upstream repression sequence (URS) |
| DNA replication-related elements | 5'-TATCGATA-3' | ⌘F | DNA replication-related element (DRE)[22] |
| DREB boxes | 5'-TACCGACAT-3' | 16 | CRT/DREB box |
| EIF4E basal elements | 5'-TTACCCCCCCTT-3' | 16 | poly(C) motif |
| Endoplasmic reticulum stress response elements | 5'-CCAAT-3' | ⌘F | 5'-CCAATGGGCTGAAAC-3' between ZNF497 and A1BG |
| Estrogen response elements | 5'-AGGTTA-3' or 5'-GGTCAGGAT-3' | ⌘F | 5'-AGGTTATTGCCTCCT-3' or 5'-GGTCAGGATGAC-3' |
| Forkhead boxes | 5'-(A/G)(C/T)AAA(C/T)A-3' | ⌘F | 5'-GTAAACAA-3' FOXO1 |
| Gal4ps | 5'-CGGACCGC-3' | ⌘F | 5'-CGG(A/G)NN(A/G)C(C/T)N(C/T)NCNCCG-3' |
| G boxes | 5'-(G/T)CCACGTG(G/T)C-3' | ⌘F | no "perfect palindrome" G boxes in either promoter |
| GCN4 motifs | 5'-TGACTCA-3', 5'-TGAGTCA-3' | ⌘F | ACGT motif |
| Gcn4ps | 5'-ATGACTCTT-3' | ⌘F | GCN4 motifs |
| GLM boxes | 5′-(G/A)TGA(G/C)TCA(T/C)-3′ | 16 | GCN4-like motif |
| γ-interferon activated sequences (GAS) | 5'-TTCCTAGAA-3' | ⌘F | ALS-GAS1 between nt −633 and nt −625 |
| Grainy head transcription factor binding sites | 5'-AACCGGTT-3' | ⌘F | also 5'-GACTGGTT-3' |
| GT boxes | 5'-GGGGTGGGG-3' | ⌘F | (-78 to -69) |
| Hac1ps | 5'-CAGCGTG-3' | ⌘F | Regulates the unfolded protein response |
| Heat-responsive elements | 5'-AAAAAATTTC-3' | ⌘F | four nGAAn motifs |
| Hex sequences | 5'-TGACGTGGC-3' | ⌘F | the Hex sequence (TGACGTGGC)[17] |
| HMG boxes | 5'-(A/T)(A/T)CAAAG-3' | ⌘F | two or more HMG boxes |
| Hybrid C, A boxes | 5'-TGACGTAT-3' | ⌘F | A at the 12 position |
| Hybrid C, G boxes | 5'-TGACGTGT-3' | ⌘F | G at the 12 position |
| Hybrid C, T boxes | 5'-TGACGTTA-3' | ⌘F | T at the 12 position |
| Hypoxia-inducible factors | 5'-GCCCTACGT-3' | ⌘F | composed of HIF-1α and HIF-1β |
| I boxes | 5'-GATAAG-3' | ⌘F | 5'-GGATGAGATAAGA-3' |
| Inositol, choline-responsive element | 5'-TYTTCACATGY-3' | ⌘F | 5'-TCTTCAC, TCTTCACAT-3' |
| Kozak sequences | 5'-(GCC)GCC(A/G)CCATGG-3' | ⌘F | 5'-GAAAATGG-3'[23] |
| L boxes | 5'-TAAATG(A/C/G)A-3' | ⌘F | L1 box |
| MAREs | 5'-TGCTGA(G/C)TCAGCA-3' | ⌘F | and 5'-TGCTGA(GC/CG)TCAGCA-3' |
| M boxes | 5'-GTCATGTGCT-3' | ⌘F | upstream of the TATA box |
| Mcm1 regulatory factors | 5'-(A/C/T)(A/C/T)NC(C/T)(A/C/T)(A/C/T)(A/T)(A/C/T)(A/C/T)N(A/G)(C/G/T)(A/C/T)-3' | ⌘F | Genome-wide determinant search |
| Met31ps | 5'-AAACTGTGG-3' | ⌘F | Sulfur amino acid metabolism [72] |
| Middle sporulation elements | 5'-C(A/G)CAAA(A/T)-3' | ⌘F | 5'-ACACAAA-3' (2017) |
| Motif ten elements | 5'-C-C/G-A-A/G-C-C/G-C/G-A-A-C-G-C/G-3' | 16 | Gene ID: 6309 |
| Ndt80ps | 5'-TCCGCA-3' | ⌘F | 5'-DNCRCAAAW-3' |
| Nuclear factor Y | 5'-TACCGACAT-3' | ⌘F | NF-Y is a trimeric complex |
| Nutrient-sensing response element 1 | 5'-GTTTCATCA-3' | ⌘F | only one nucleotide difference between the SESN2 CARE and the ASNS |
| Oaf1ps | 5'-(A/C/G/T)(A/C/G/T)(A/C/G/T)T(A/C/G/T)A(A/C/G/T)-3' | ⌘F | 5'-CGG(A/C/G/T)3T(A/C/G/T)A(A/C/G/T)9-12CCG-3' |
| Pdr1p/Pdr3ps | 5'-TCCGCGGA-3' | ⌘F | Pdr1p/Pdr3p response element (PDRE) |
| Polycomb response elements | 5'-CGCCATTT-3' | ⌘F | closely resembles the extended Pho-Phol consensus sequence |
| Rap1 regulatory factors | 5'-C(A/C/G)(A/C/G)(A/G)(C/G/T)C(A/C/T)(A/G/T)(C/G/T)(A/G/T)(A/C/G)(A/C)(A/C/T)(A/C/T)-3' | ⌘F | Rap1 (CCCACCAACAAAA) none |
| Rgt1ps | 5'-CGGACCA-3' | ⌘F | Glucose-responsive transcription factor |
| Rlm1ps | 5'-CTATATATAG-3' | ⌘F | CTA(T/A)4TAG |
| Rox1ps | 5'-GGGTAA-3' | ⌘F | Heme-dependent repressor of hypoxic genes [78] |
| Rpn4ps | 5'-GGTGGCAAA-3' | ⌘F | proteasome genes |
| Seed-specific elements | 5'-CATGCATG-3' | ⌘F | SRE consensus: 5'-CAGCAGATTGCG-3' is none |
| Shoot specific elements | 5'-GATAATGATG-3' | ⌘F | SRE consensus: 5'-CAGCAGATTGCG-3' is none |
| Sip4ps | 5'-CCGTCCGT-3' | ⌘F | 5'-CC(C/G)T(C/T)C(C/G)TCCG-3' |
| Smp1ps | 5'-ACTACTA-3' | ⌘F | 5-ACTACTA(T/A)4TAG-3' |
| Sterol response elements | 5'-TCGTATA-3' | ⌘F | perhaps plant specific |
| TATCCAC boxes | 5'-TATCCAC-3' | 16 | GA responsive complex component |
| TCCACCATA elements | 5'-TCCACCATA-3' | ⌘F | adjacent co-dependent regulatory element of POLLEN1 |
| Tec1ps | 5'-GAATGT-3' | ⌘F | Ste12p cofactor |
| Tetradecanoylphorbol-13-acetate response elements (TREs) | 5'-TGA(G/C)TCA-3' | 16 | cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40 |
| TGF-β control elements (TCEs) | 5'-GAGTGGGGCG-3' | ⌘F | in mouse and rat, 5'-GCGTGGGGGA-3' in humans |
| TGF-β inhibitory elements (TIEs) | 5'-GAGTGGTGA-3' | 16 | in the rat transin/stromelysin promoter |
| Thyroid hormone response elements (TREs) | 5'-AGGTCA-3' | ⌘F | See VDREs, X boxes |
| TCCACCATA elements | 5'-TCCACCATA-3' | ⌘F | adjacent co-dependent regulatory element of POLLEN1 |
| Tec1ps | 5'-GAATGT-3' | ⌘F | Ste12p cofactor |
| Tetradecanoylphorbol-13-acetate response elements (TREs) | 5'-TGA(G/C)TCA-3' | 16 | cis-regulatory element of the human metallothionein IIa (hMTIIa) promoter and SV40 |
| TGF-β control elements (TCEs) | 5'-GAGTGGGGCG-3' | ⌘F | in mouse and rat, 5'-GCGTGGGGGA-3' in humans |
| TGF-β inhibitory elements (TIEs) | 5'-GAGTGGTGA-3' | 16 | in the rat transin/stromelysin promoter |
| Thyroid hormone response elements (TREs) | 5'-AGGTCA-3' | ⌘F | See VDREs, X boxes |
| Unfolded protein response elements (UPREs) | 5'-TGACGTG(G/A)-3' | ⌘F | XBP1 binds to UPRE |
| Vhr1ps | 5'-AATCA-N8-TGA(C/T)T-3' | ⌘F | Response to low biotin [71] concentrations |
| Vitamin D response elements (VDREs) | 5'-(A/G)G(G/T)(G/T)CA-3' | ⌘F | 5'-AGGTCA-3' not ⌘F |
| X boxes | 5'-GTTGGCATGGCAAC-3' | 16 | X2 box is 5'-AGGTCCA-3' not ⌘F |
| Xbp1ps | 5'-GcCTCGA(G/A)G(C/A)g(a/g)-3' | ⌘F | Transcriptional repressor |
| Xenobiotic response elements (XREs) | 5'-(T/G)NGCGTG(A/C)(G/C)A-3' | ⌘F | contains the core sequence 5'-GCGTG-3' |
| Yap1p,2ps | 5'-TTACTAA-3' | ⌘F | Yap1p binding sites |
| Y boxes | 5'-(A/G)CTAACC(A/G)(A/G)(C/T)-3' | 16 | inverted CAAT box |
| Zap1ps | 5'-ACCCTCA-3' | ⌘F | 5'-ACC(C/T)(C/T)(A/C/G/T)AAGGT-3' |
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ MeSH (8 July 2008). "Response Elements". U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894: National Institutes of Health, Health & Human Services. Retrieved 2 September 2020.
- ↑ 2.0 2.1 Kenneth A. Watanabe; Arielle Homayouni; Lingkun Gu; Kuan‐Ying Huang; Tuan‐Hua David Ho; Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.
- ↑ Matthew J. Rossi; William K.M. Lai; B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.
- ↑ Takayuki Murata; Chieko Noda; Yohei Narita1; Takahiro Watanabe; Masahiro Yoshida; Keiji Ashio; Yoshitaka Sato; Fumi Goshima; Teru Kanda; Hironori Yoshiyama; Tatsuya Tsurumi; Hiroshi Kimura (27 January 2016). "Induction of Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (LMP1) by Transcription Factors Activating Protein 2 (AP-2) and Early B Cell Factor (EBF)" (PDF). Journal of Virology. doi:10.1128/JVI.03227-15. Retrieved 4 October 2020.
- ↑ 5.0 5.1 Yao EF; Denison MS (June 1992). "DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer". Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.
- ↑ 6.0 6.1 Bhaskar Sharma; Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check
|pmid=value (help). Retrieved 27 August 2020. - ↑ 7.0 7.1 Ryuto Maruyama; Makoto Shimizu; Juan Li, Jun Inoue; Ryuichiro Sato (24 March 2016). "Fibroblast growth factor 21 induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region". Bioscience, Biotechnology, and Biochemistry. 80 (5): 929–934. doi:10.1080/09168451.2015.1135045. Retrieved 4 October 2020.
- ↑ Angelika Bröer; Gregory Gauthier-Coles; Farid Rahimi; Michelle van Geldermalsen; Dieter Dorsch; Ansgar Wegener; Jeff Holst; Stefan Bröer (March 15, 2019). "Ablation of the ASCT2 (SLC1A5) gene encoding a neutral amino acid transporter reveals transporter plasticity and redundancy in cancer cells" (PDF). Journal of Biological Chemistry. 294 (11): 4012–4026. doi:10.1074/jbc.RA118.006378. Retrieved 4 October 2020.
- ↑ Alisa A. Garaeva; Irina E. Kovaleva; Peter M. Chumakov; Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.
- ↑ 10.0 10.1 S Kouhpayeh; AR Einizadeh; Z Hejazi; M Boshtam; L Shariati; M Mirian; L Darzi; M Sojoudi; H Khanahmad; A Rezaei (1 July 2016). "Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line" (PDF). Cancer Gene Therapy. 23: 254–257. doi:10.1038/cgt.2016.26. Retrieved 3 October 2020.
- ↑ Stephen Wilson; Jianfei Qi; Fabian V. Filipp (14 September 2016). "Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines". Scientific Reports. 6: 32611. doi:10.1038/srep32611. Retrieved 3 October 2020.
- ↑ Akihito Otsuki; Mikiko Suzuki; Fumiki Katsuoka; Kouhei Tsuchida; Hiromi Suda; Masanobu Morita; Ritsuko Shimizu; Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.
- ↑ Sarah E. Lacher; Daniel C. Levings; Samuel Freeman; Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 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.
- ↑ Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.
- ↑ 16.0 16.1 PA Johnson; D Bunick; NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. doi:10.1095/biolreprod44.1.127. PMID 2015343. Retrieved 6 April 2019.
- ↑ 17.0 17.1 17.2 Young Hun Song; Cheol Min Yoo; An Pio Hong; Seong Hee Kim; Hee Jeong Jeong; Su Young Shin; Hye Jin Kim; Dae-Jin Yun; Chae Oh Lim; Jeong Dong Bahk; Sang Yeol Lee; Ron T. Nagao; Joe L. Key; Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.
- ↑ Hideharu Hashimoto; Dongxue Wang; John R. Horton; Xing Zhang; Victor G. Corces; Xiaodong Cheng (1 June 2017). "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA". Molecular Cell. 66 (5): 711–720.e3. doi:10.1016/j.molcel.2017.05.004. PMID 28529057. Retrieved 28 August 2020.
- ↑ Ravi P. Misra; Azad Bonni; Cindy K. Miranti; Victor M. Rivera; Morgan Sheng; Michael E.Greenberg (14 October 1994). "L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway" (PDF). The Journal of Biological Chemistry. 269 (41): 25483–25493. PMID 7929249. Retrieved 7 December 2019.
- ↑ 20.0 20.1 Yan-Hui Li; Gai-Gai Zhang (12 April 2016). "Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans". Oncotarget. 7 (15): 19185–19192. doi:10.18632/oncotarget.8313. PMID 2702736. Retrieved 27 August 2020.
- ↑ Philipp Mracek; Cristina Santoriello; M. Laura Idda; Cristina Pagano; Zohar Ben-Moshe; Yoav Gothilf; Daniela Vallone; Nicholas S. Foulkes (December 6, 2012). "Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression". PLoS ONE. 7 (12): e51278. doi:10.1371/journal.pone.0051278. Retrieved 10 February 2019.
- ↑ Fumiko Hirose; Masamitsu Yamaguchi; Akio Matsukage (September 1999). "Targeted Expression of the DNA Binding Domain of DRE-Binding Factor, a Drosophila Transcription Factor, Attenuates DNA Replication of the Salivary Gland and Eye Imaginal Disc". Molecular and Cellular Biology. 19 (9): 6020–6028. doi:10.1128/MCB.19.9.6020. PMID 10454549. Retrieved 4 September 2020.
- ↑ Takuya Matsumoto; Saemi Kitajima; Chisato Yamamoto; Mitsuru Aoyagi; Yoshiharu Mitoma; Hiroyuki Harada; Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.