A1BG response element negative results
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] |
| C/EBP boxes | 5'-TTAGGACAT-3',[18] 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 |
| Circadian control elements | 5'-CAACTTTA-3' | ⌘F | CCE |
| 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′[19] |
| 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.
- ↑ 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 and 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, and 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, and 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 and 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, and 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, and 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.
- ↑ Ravi P. Misra, Azad Bonni, Cindy K. Miranti, Victor M. Rivera, Morgan Sheng, and 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.
- ↑ Hideharu Hashimoto, Dongxue Wang, John R. Horton, Xing Zhang, Victor G. Corces and 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.
- ↑ 20.0 20.1 Yan-Hui Li and 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 and 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.