CARE gene transcriptions: Difference between revisions

Editor-In-Chief: Henry A. Hoff

"Some other cis-acting elements, such as pyrimidine boxes (GGTTTT) and TAT boxes (TATCCAT), are usually present in the vicinity of the GARE sequence of genes regulated by GA in cereal aleurone cells (Gubler and Jacobsen 1992; Cercos et al. 1999; Tsuji et al. 2006). For example, GARE and a novel CARE (CAACTC regulatory elements) elements are present in the promoter of rice RAmy1A (Ueguchi-Tanaka et al. 2000; Sutoh and Yamauchi 2003). Cis-element analyses have shown that the OsGAMYB protein activates RAmy1A expression through interaction with GARE in the promoter (Washio 2003). In addition, GARE and CARE are also present in a cysteine proteinase gene REP-1, which is expressed in rice aleurone and is induced by GAs and repressed by ABA. These two elements have been identified as necessary and sufficient for conferring GA inducibility of the REP-1 promoter. Mutations of CARE in the promoters of RAmy1A and REP-1 result in loss of GA inducibility and GAMYB transactivation, suggesting that CARE is a regulatory element for the GA-inducible expression of hydrolase genes in germinating seeds (Sutoh and Yamauchi 2003)."^[1]

"ATF4 regulates transcription of its target genes through the formation of homodimers or heterooligomers with the transcription factors Jun, AP-1 and C/EBP^38,39 that bind to CARE (C/EBP-ATF) responsive elements having the consensus sequence XTTXCATCA (where X = G, A or T).³⁹ In the region from -625 to -618 bp relative to the SESN2 translation start codon (from -228 to -221 bp relative to the transcription start site) we found a candidate sequence for the ATF4 binding site TTTTCATCA."^[2]

CARE sampling of A1BG promoters

For the Basic programs (starting with SuccessablesCARE.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

Negative strand, negative direction: 1, CAACTC at 86.
Negative strand, positive direction: 1, CAACTC at 3292.
Positive strand, negative direction: 0.
Positive strand, positive direction: 0.
inverse complement, negative strand, negative direction: 1, GAGTTG at 1406.
inverse complement, negative strand, positive direction: 0.
inverse complement, positive strand, negative direction: 4, GAGTTG at 4096, GAGTTG at 3115, GAGTTG at 2704, GAGTTG at 2592.
inverse complement, positive strand, positive direction: 2, GAGTTG at 3290, GAGTTG at 1621.

UTR promoters

Positive strand, negative direction: GAGTTG at 4096, GAGTTG at 3115.

Core promoters

Proximal promoters

Positive strand, negative direction: GAGTTG at 2704.

CARE distal promoters

Negative strand, negative direction: GAGTTG at 1406, CAACTC at 86.
Positive strand, negative direction: GAGTTG at 2592.

Negative strand, positive direction: CAACTC at 3292.
Positive strand, positive direction: GAGTTG at 3290, GAGTTG at 1621.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

References

↑ Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng (2007). "Gibberellin Signal Transduction in Rice". Journal of Integrative Plant Biology. 49 (6): 731−741. doi:10.1111/j.1744-7909.2007.00511.x. Retrieved 16 October 2018.
↑ 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.

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Transcription resources	A1BG gene transcription core promoters A1BG gene transcriptions A1BG regulatory elements and regions A1BG response element gene transcriptions A1BG response element negative results A1BG response element positive results ABA-response element gene transcriptions Abf1 regulatory factor gene transcriptions A box gene transcriptions ACGT-containing element gene transcriptions Activating protein gene transcriptions Activating transcription factor gene transcriptions Adenylate–uridylate rich element gene transcriptions Adr1p gene transcriptions Aft1p gene transcriptions AGC box gene transcriptions AGCE gene transcriptions Alpha-amylase conserved element gene transcriptions Amino acid response element gene transcriptions AARE-like Androgen response element gene transcriptions Angiotensinogen core promoter element gene transcriptions Antioxidant-electrophile responsive element gene transcriptions ATA box gene transcriptions Auxin response factor gene transcriptions B 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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

Template:Sisterlinks

@@ Line 34: / Line 34: @@
 {{main|Gene transcriptions/CAREs|CAREs}}
 For the Basic programs (starting with SuccessablesCARE.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
-# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCARE--.bas, looking for 3'-CAACTC-5', 1, 3'-CAACTC-5', 86,
+# Negative strand, negative direction: 1, CAACTC at 86.
-# negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCARE-+.bas, looking for 3'-CAACTC-5', 1, 3'-CAACTC-5', 3292,
+# Negative strand, positive direction: 1, CAACTC at 3292.
-# positive strand in the negative direction is SuccessablesCARE+-.bas, looking for 3'-CAACTC-5', 0,
+# Positive strand, negative direction: 0.
-# positive strand in the positive direction is SuccessablesCARE++.bas, looking for 3'-CAACTC-5', 0,
+# Positive strand, positive direction: 0.
-# complement, negative strand, negative direction is SuccessablesCAREc--.bas, looking for 3'-GTTGAG-5', 0,
+# inverse complement, negative strand, negative direction: 1, GAGTTG at 1406.
-# complement, negative strand, positive direction is SuccessablesCAREc-+.bas, looking for 3'-GTTGAG-5', 0,
+# inverse complement, negative strand, positive direction: 0.
-# complement, positive strand, negative direction is SuccessablesCAREc+-.bas, looking for 3'-GTTGAG-5', 1, 3'-GTTGAG-5', 86,
+# inverse complement, positive strand, negative direction: 4, GAGTTG at 4096, GAGTTG at 3115, GAGTTG at 2704, GAGTTG at 2592.
-# complement, positive strand, positive direction is SuccessablesCAREc++.bas, looking for 3'-GTTGAG-5', 1, 3'-GTTGAG-5', 3292,
+# inverse complement, positive strand, positive direction: 2, GAGTTG at 3290, GAGTTG at 1621.
-# inverse complement, negative strand, negative direction is SuccessablesCAREci--.bas, looking for 3'-GAGTTG-5', 1, 3'-GAGTTG-5', 1406,
-# inverse complement, negative strand, positive direction is SuccessablesCAREci-+.bas, looking for 3'-GAGTTG-5', 0,
+===UTR promoters===
-# inverse complement, positive strand, negative direction is SuccessablesCAREci+-.bas, looking for 3'-GAGTTG-5', 4, 3'-GAGTTG-5', 2592, 3'-GAGTTG-5', 2704, 3'-GAGTTG-5', 3115, 3'-GAGTTG-5', 4096,
+# Positive strand, negative direction: GAGTTG at 4096, GAGTTG at 3115.
-# inverse complement, positive strand, positive direction is SuccessablesCAREci++.bas, looking for 3'-GAGTTG-5', 2, 3'-GAGTTG-5', 1621, 3'-GAGTTG-5', 3290,
-# inverse, negative strand, negative direction, is SuccessablesCAREi--.bas, looking for 3'-CTCAAC-5', 4, 3'-CTCAAC-5', 2592, 3'-CTCAAC-5', 2704, 3'-CTCAAC-5', 3115, 3'-CTCAAC-5', 4096,
+===Core promoters===
-# inverse, negative strand, positive direction, is SuccessablesCAREi-+.bas, looking for 3'-CTCAAC-5', 2, 3'-CTCAAC-5', 1621, 3'-CTCAAC-5', 3290,
-# inverse, positive strand, negative direction, is SuccessablesCAREi+-.bas, looking for 3'-CTCAAC-5', 1, 3'-CTCAAC-5', 1406,
+===Proximal promoters===
-# inverse, positive strand, positive direction, is SuccessablesCAREi++.bas, looking for 3'-CTCAAC-5', 0.
+# Positive strand, negative direction: GAGTTG at 2704.
 ===CARE distal promoters===
 {{main|Distal promoter gene transcriptions}}
-Negative strand, negative direction: 5'-GAGTTG-3' at 1406, 5'-CAACTC-3' at 86, and complements.
+# Negative strand, negative direction: GAGTTG at 1406, CAACTC at 86.
+# Positive strand, negative direction: GAGTTG at 2592.
-Positive strand, negative direction: 5'-GAGTTG-3' at 4096, 5'-GAGTTG-3' at 3115, 5'-GAGTTG-3' at 2704, 5'-GAGTTG-3' at 2592, and complements.
-Negative strand, positive direction: 5'-CAACTC-3' at 3292, and complement.
-Positive strand, positive direction: 5'-GAGTTG-3' at 3290, 5'-GAGTTG-3' at 1621, and complements.
+# Negative strand, positive direction: CAACTC at 3292.
+# Positive strand, positive direction: GAGTTG at 3290, GAGTTG at 1621.
 ==Acknowledgements==

CARE gene transcriptions: Difference between revisions

Revision as of 04:16, 3 January 2022

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