HY box gene transcriptions

Editor-In-Chief: Henry A. Hoff

"Deletion, mutagenesis, and tandem repeat analyses identified the core responsive element as the region between −89 and −60 bp (termed the hypertrophy box [HY box]), which showed specific binding to RUNX‐2."^[1]

The "HY box is the core element responsive to RUNX‐2 in human COL10A1 promoter."^[1]

Boxes

A repeating sequence of nucleotides that forms a transcription or a regulatory signal is a box.

Consensus sequences

"Deletion analysis by a series of 5′-deletion constructs identified the responsive region to RUNX-2 as being between −81 bp and −76 bp, containing a putative RUNX-2 binding sequence (TGAGGG), which is similar to that identified in the promoter region of human interleukin-3 (TGTGGG) (33)."^[1] This suggests a consensus sequence of 3'-TG(A/T)GGG-5' on the template strand in the direction of transcription.

RUNX2

The gene RUNX2 "is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex."^[2]

COL10A1

The gene COL10A1 "encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer."^[3]

Human COL10A1, GeneID: 1300, has an HY box as the core responsive element.^[1]

Hypotheses

A1BG is not transcribed by an HY box.

HY box samplings

For the Basic programs (starting with SuccessablesHY.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 in the negative direction is SuccessablesHY--.bas, looking for TG(A/T)GGG, 1, TGTGGG at 749,
negative strand in the positive direction is SuccessablesHY-+.bas, looking for TG(A/T)GGG, 4, TGAGGG at 258, TGAGGG at 3479, TGAGGG at 3879, TGTGGG at 4395,
positive strand in the negative direction is SuccessablesHY+-.bas, looking for TG(A/T)GGG, 5, TGAGGG at 88, TGAGGG at 2699, TGAGGG at 3652, TGTGGG at 3712, TGAGGG at 4558,
positive strand in the positive direction is SuccessablesHY++.bas, looking for TG(A/T)GGG, 2, TGTGGG at 2965, TGTGGG at 3533,
complement, negative strand, negative direction is SuccessablesHYc--.bas, looking for AC(A/T)CCC, 0,
complement, negative strand, positive direction is SuccessablesHYc-+.bas, looking for AC(A/T)CCC, 2, ACACCC at 2965, ACACCC at 3533,
complement, positive strand, negative direction is SuccessablesHYc+-.bas, looking for AC(A/T)CCC, 1 , ACACCC at 749,
complement, positive strand, positive direction is SuccessablesHYc++.bas, looking for AC(A/T)CCC, 4, ACTCCC at 258, ACTCCC at 3479, ACTCCC at 3879, ACACCC at 4395,
inverse complement, negative strand, negative direction is SuccessablesHYci--.bas, looking for CCC(A/T)CA, 4, CCCTCA at 2702, CCCACA at 3184, CCCTCA at 3889, CCCTCA at 4498,
inverse complement, negative strand, positive direction is SuccessablesHYci-+.bas, looking for CCC(A/T)CA, 3, CCCTCA at 88, CCCTCA at 3207, CCCTCA at 3503,
inverse complement, positive strand, negative direction is SuccessablesHYci+-.bas, looking for CCC(A/T)CA, 0,
inverse complement, positive strand, positive direction is SuccessablesHYci++.bas, looking for CCC(A/T)CA, 5, CCCTCA at 494, CCCTCA at 662, CCCTCA at 1783, CCCACA at 1803, CCCTCA at 3185,
inverse, negative strand, negative direction, is SuccessablesHYi--.bas, looking for GGG(A/T)GT, 0,
inverse, negative strand, positive direction, is SuccessablesHYi-+.bas, looking for GGG(A/T)GT, 5, GGGAGT at 494, GGGAGT at 662, GGGAGT at 1783, GGGTGT at 1803, GGGAGT at 3185,
inverse, positive strand, negative direction, is SuccessablesHYi+-.bas, looking for GGG(A/T)GT, 4, GGGAGT at 2702, GGGTGT at 3184, GGGAGT at 3889, GGGAGT at 4498,
inverse, positive strand, positive direction, is SuccessablesHYi++.bas, looking for GGG(A/T)GT, 3, GGGAGT at 88, GGGAGT at 3207, GGGAGT at 3503.

HY box UTRs

Negative strand, negative direction: CCCTCA at 4498, CCCTCA at 3889, CCCACA at 3184.

Positive strand, negative direction: TGAGGG at 4558, TGTGGG at 3712, TGAGGG at 3652.

HY box core promoters

Negative strand, positive direction: TGTGGG at 4395.

HY box proximal promoters

Negative strand, negative direction: CCCTCA at 2702.

Positive strand, negative direction: TGAGGG at 2699.

HY box distal promoters

Negative strand, negative direction: TGTGGG at 749.

Positive strand, negative direction: TGAGGG at 88.

Negative strand, positive direction: TGAGGG at 3879, CCCTCA at 3503, TGAGGG at 3479, CCCTCA at 3207, TGAGGG at 258, CCCTCA at 88.

Positive strand, positive direction: TGTGGG at 3533, CCCTCA at 3185, TGTGGG at 2965, CCCACA at 1803, CCCTCA at 1783, CCCTCA at 662, CCCTCA at 494.

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

↑ ^1.0 ^1.1 ^1.2 ^1.3 Akiro Higashikawa, Taku Saito, Toshiyuki Ikeda, Satoru Kamekura, Naohiro Kawamura, Akinori Kan, Yasushi Oshima, Shinsuke Ohba, Naoshi Ogata, Katsushi Takeshita, Kozo Nakamura, Ung-Il Chung, Hiroshi Kawaguchi (2009). "Identification of the core element responsive to runt-related transcription factor 2 in the promoter of human type x collagen gene". Arthritis & Rheumatism. 60 (1): 166–78. doi:10.1002/art.24243. PMID 19116917. Retrieved 2013-06-18. Unknown parameter |month= ignored (help)
↑ "RUNX2 runt-related transcription factor 2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. 2013. Retrieved 2013-06-18. Unknown parameter |month= ignored (help)
↑ HGNC (June 9, 2013). "COL10A1 collagen, type X, alpha 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-06-18.

External links

[Higashikawa-1] 1.0 ^1.1 ^1.2 ^1.3 Akiro Higashikawa, Taku Saito, Toshiyuki Ikeda, Satoru Kamekura, Naohiro Kawamura, Akinori Kan, Yasushi Oshima, Shinsuke Ohba, Naoshi Ogata, Katsushi Takeshita, Kozo Nakamura, Ung-Il Chung, Hiroshi Kawaguchi (2009). "Identification of the core element responsive to runt-related transcription factor 2 in the promoter of human type x collagen gene". Arthritis & Rheumatism. 60 (1): 166–78. doi:10.1002/art.24243. PMID 19116917. Retrieved 2013-06-18. Unknown parameter |month= ignored (help)

[RUNX2-2] "RUNX2 runt-related transcription factor 2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. 2013. Retrieved 2013-06-18. Unknown parameter |month= ignored (help)

[HGNC-3] HGNC (June 9, 2013). "COL10A1 collagen, type X, alpha 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-06-18.

[1]

[2]

[3]

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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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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