Adenylate–uridylate rich element gene transcriptions: Difference between revisions

Revision as of 15:15, 24 March 2021

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

"Functionally defined and derived adenylate–uridylate rich element (ARE) consensus sequences have been shown to exist in the 3′UTR of selected mRNAs belonging to interferons, cytokines and proto-oncogenes ( 1 ). A 13-bp ARE motif was computationally derived from a list of functionally labile ARE-mRNAs and was the basis of the ARE-mRNA database (ARED) which contains GenBank entries where the 3′UTR matches the motif ( 2 )."^[1]

Human genes

The ARE-mRNA database (ARED) "demonstrated that ARE-mRNAs represent as much as 5–8% of human genes and encode functionally diverse proteins that are important in many transient biological processes including cell growth and differentiation, signal transduction, transcriptional and translational control, hematopoiesis, apoptosis, nutrient transport, and metabolism ( 2 )."^[1]

"The 3′UTRs were searched for the 13-bp pattern WWWUAUUUAUWW with mismatch=−1 which was computationally derived as previously described ( 2 ). The pattern was further statistically validated against larger sets of mRNA data (10 872 mRNA with 3′UTR; GenBank 119) showing occurrence of the motif in 6.8% of human mRNA."^[1]

"The ARED website ( http://rc.kfshrc.edu.sa/ared ) offers a query search engine that allows searches for ARE-genes using multiple identifier numbers or descriptions such as UniGene IDs, UniGene definition, RefSeq IDs, accession numbers, alternative names, official Gene symbols and mouse homologs (MGD) ( 10 )."^[1]

Gene expressions

"3′ untranslated regions play an important role in regulating mRNA fate by complexing with RNA binding proteins that help control mRNA localization, translation, and stability [1, 2, 3]. Identification of a consensus UUAUUUAU sequence in the 3′ UTRs of human and mouse mRNAs encoding tumor necrosis factor (TNF-α) and a variety of other inflammatory mediators led to the suggestion that these AU-rich elements AREs) could be important for regulating gene expression [4]."^[2]

Interactions

Consensus sequences

WWWUAUUUAUWW=(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T).^[1]

Binding site for

Adenylate–uridylate rich element (Bakheet) samplings

Copying a responsive elements consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) 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 (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) (starting with SuccessablesAAA.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 (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 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 (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 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 (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
inverse complement, positive strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 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 (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 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.

Adenylate–uridylate rich element (Bakheet) UTRs

Adenylate–uridylate rich element (Bakheet) core promoters

Adenylate–uridylate rich element (Bakheet) proximal promoters

Adenylate–uridylate rich element (Bakheet) distal promoters

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar (1 January 2003). "ARED 2.0: an update of AU-rich element mRNA database". Nucleic Acids Research. 31 (1): 421–423. doi:10.1093/nar/gkg023. Retrieved 23 March 2021.
↑ David A. Siegel, Olivier Le Tonqueze, Anne Biton, Noah Zaitlen, and David J. Erle (12 February 2020). "Massively Parallel Analysis of Human 3′ UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization" (PDF). bioRxiv. doi:10.1101/2020.02.12.945063. Retrieved 23 March 2021.

External links

[Bakheet-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar (1 January 2003). "ARED 2.0: an update of AU-rich element mRNA database". Nucleic Acids Research. 31 (1): 421–423. doi:10.1093/nar/gkg023. Retrieved 23 March 2021.

[Siegel-2] David A. Siegel, Olivier Le Tonqueze, Anne Biton, Noah Zaitlen, and David J. Erle (12 February 2020). "Massively Parallel Analysis of Human 3′ UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization" (PDF). bioRxiv. doi:10.1101/2020.02.12.945063. Retrieved 23 March 2021.

[1]

[2]

@@ Line 46: / Line 46: @@
 ==Consensus sequences==
 {{main|Consensus sequence gene transcriptions}}
+WWWUAUUUAUWW=(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T).<ref name=Bakheet/>
 ==Binding site for==
-==Samplings==
+==Adenylate–uridylate rich element (Bakheet) samplings==
 {{main|Model samplings}}
-Copying a responsive elements consensus sequence AAAAAAAA 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.
+Copying a responsive elements consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) 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 AAAAAAAA (starting with SuccessablesAAA.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:
+For the Basic programs testing consensus sequence (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T) (starting with SuccessablesAAA.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 AAAAAAAA, 0.
+# negative strand, negative direction, looking for (A/T)(A/T)(A/T)TATTTAT(A/T)(A/T), 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, negative direction, looking for (A/T)(A/T)(A/T)ATAAATA(A/T)(A/T), 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, negative strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 0.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for (A/T)(A/T)ATAAATA(A/T)(A/T)(A/T), 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 negative strand, negative direction, looking for (A/T)(A/T)TATTTAT(A/T)(A/T)(A/T), 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.
-===AAA UTRs===
+===Adenylate–uridylate rich element (Bakheet) UTRs===
 {{main|UTR promoter gene transcriptions}}
-===AAA core promoters===
+===Adenylate–uridylate rich element (Bakheet) core promoters===
 {{main|Core promoter gene transcriptions}}
-===AAA proximal promoters===
+===Adenylate–uridylate rich element (Bakheet) proximal promoters===
 {{main|Proximal promoter gene transcriptions}}
-===AAA distal promoters===
+===Adenylate–uridylate rich element (Bakheet) distal promoters===
 {{main|Distal promoter gene transcriptions}}

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gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Factor II B recognition element gene transcriptions F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene 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 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 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 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 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 gene transcriptions 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 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