Polycomb response element gene transcriptions

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

"Recruitment of Drosophila melanogaster [Polycomb-group] PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs)."^[1]

Only "Pleiohomeotic (Pho) is present at all strong PREs."^[1]

"The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2."^[1]

"PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites".^[1]

Human genes

Consensus sequences

"Two predicted [Pleiohomeotic] Pho-Phol binding sites, CGCCATTT, that closely resemble the extended Pho-Phol consensus sequence, CGCCAT(T/A)TT (Kahn et al. 2014), are located within PRE1.1 [...]."^[1]

"Only one additional site resembling the Pho-Phol core consensus sequence (GCCAT) is near region 4, 137-bp downstream from the TSS. The nearest upstream GCCAT sequences are ∼1 kb from the TSS (−968 and −1049)."^[1]

Core samplings

Copying the apparent consensus sequence for the PRE (GCCAT) and putting it in "⌘F" finds none located between ZSCAN22 or between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GCCAT (starting with SuccessablesPRE1.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 GCCAT, 0.
positive strand, negative direction, looking for GCCAT, 3, GCCAT at 3685, GCCAT at 3283, GCCAT at 38.
positive strand, positive direction, looking for GCCAT, 0.
negative strand, positive direction, looking for GCCAT, 0.
complement, negative strand, negative direction, looking for CGGTA, 3, CGGTA at 3685, CGGTA at 3283, CGGTA at 38.
complement, positive strand, negative direction, looking for CGGTA, 0.
complement, positive strand, positive direction, looking for CGGTA, 0.
complement, negative strand, positive direction, looking for CGGTA, 0.
inverse complement, negative strand, negative direction, looking for ATGGC, 0.
inverse complement, positive strand, negative direction, looking for ATGGC, 7, ATGGC at 3629, ATGGC at 3005, ATGGC at 2907, ATGGC at 2153, ATGGC at 1949, ATGGC at 1743, ATGGC at 954.
inverse complement, positive strand, positive direction, looking for ATGGC, 0.
inverse complement, negative strand, positive direction, looking for ATGGC, 1, ATGGC at 2160.
inverse negative strand, negative direction, looking for TACCG, 7, TACCG at 3629, TACCG at 3005, TACCG at 2907, TACCG at 2153, TACCG at 1949, TACCG at 1743, TACCG at 954.
inverse positive strand, negative direction, looking for TACCG, 0.
inverse positive strand, positive direction, looking for TACCG, 1, TACCG at 2160.
inverse negative strand, positive direction, looking for TACCG, 0.

PRE1 UTRs

Positive strand, negative direction: GCCAT at 3685, ATGGC at 3629, GCCAT at 3283, ATGGC at 3005, ATGGC at 2907.

PRE1 distal promoters

Positive strand, negative direction: ATGGC at 2153, ATGGC at 1949, ATGGC at 1743, ATGGC at 954, GCCAT at 38.

Positive strand, positive direction: TACCG at 2160.

"Only one additional site resembling the Pho-Phol core consensus sequence (GCCAT) is near region 4, 137-bp downstream from the TSS. The nearest upstream GCCAT sequences are ∼1 kb from the TSS (−968 and −1049)."^[1]

Extended Pho-Phol samplings

Copying a responsive elements consensus sequence CGCCAT(A/T)TT 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 CGCCAT(A/T)TT (starting with SuccessablesPhol.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 CGCCAT(A/T)TT, 0.
positive strand, negative direction, looking for CGCCAT(A/T)TT, 0.
positive strand, positive direction, looking for CGCCAT(A/T)TT, 0.
negative strand, positive direction, looking for CGCCAT(A/T)TT, 0.
complement, negative strand, negative direction, looking for GCGGTA(A/T)AA, 0.
complement, positive strand, negative direction, looking for GCGGTA(A/T)AA, 0.
complement, positive strand, positive direction, looking for GCGGTA(A/T)AA, 0.
complement, negative strand, positive direction, looking for GCGGTA(A/T)AA, 0.
inverse complement, negative strand, negative direction, looking for AA(A/T)ATGGCG, 0.
inverse complement, positive strand, negative direction, looking for AA(A/T)ATGGCG, 0.
inverse complement, positive strand, positive direction, looking for AA(A/T)ATGGCG, 0.
inverse complement, negative strand, positive direction, looking for AA(A/T)ATGGCG, 0.
inverse negative strand, negative direction, looking for TT(A/T)TACCGC, 0.
inverse positive strand, negative direction, looking for TT(A/T)TACCGC, 0.
inverse positive strand, positive direction, looking for TT(A/T)TACCGC, 0.
inverse negative strand, positive direction, looking for TT(A/T)TACCGC, 0.

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 Elnaz Ghotbi, Kristina Lackey, Vicki Wong, Katie T. Thompson, Evan G. Caston, Minna Haddadi, Judith Benes and Richard S. Jones (1 March 2020). "Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene" (PDF). Genetics. 214 (3): 623–634. doi:10.1534/genetics.119.302981. PMID 31919108. Retrieved 7 September 2020.

External links

[Ghotbi-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 Elnaz Ghotbi, Kristina Lackey, Vicki Wong, Katie T. Thompson, Evan G. Caston, Minna Haddadi, Judith Benes and Richard S. Jones (1 March 2020). "Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene" (PDF). Genetics. 214 (3): 623–634. doi:10.1534/genetics.119.302981. PMID 31919108. Retrieved 7 September 2020.

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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