Downstream promoter element gene transcriptions

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Editor-In-Chief: Henry A. Hoff

File:Core promoter elements.svg
The diagram is an overview of four core promoter elements. Credit: Jennifer E.F. Butler & James T. Kadonaga.

The figure on the right is an overview of four core promoter elements: the B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.[1]

The downstream promoter element (DPE) is a core promoter element present in other species including humans and excluding Saccharomyces cerevisiae.[2]

Gene transcriptions

Main article: Gene transcriptions

"Transcription by RNA polymerase II is directed by cis-acting [close-acting] DNA sequences that typically consist of a core promoter along with regulatory elements, such as enhancers [trans-acting, or distant-acting, protein factors], that contain binding sites for sequence-specific transcriptional activator and/or repressor proteins."[3]

Core promoters

Main articles: Core promoter gene transcriptions and Core promoters

"[T]he core promoter [consists of] the DNA sequences, which encompass the transcription start site (within about -40 and +40 [nucleotides] relative to the +1 start site"[3].

"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A+1 nucleotide in the Inr"[4]. It is located about 28–33 nucleotides downstream of the transcription start site.[2]

DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements.[5][3][6]

Initiator elements

Main articles: Initiator element gene transcriptions and Initiator elements

"There is a strict requirement for spacing between the [Initiator element] Inr and DPE motifs, as an increase or decrease of 3 nucleotides in the distance between the Inr and DPE causes a seven- to eightfold reduction in transcription as well as a significant reduction in the binding of purified TFIID."[3]

Consensus sequences

Main articles: Consensus sequence gene transcriptions and Consensus sequences

The early DPE consensus sequence was RGWCGTG.[5][7]

The DPE consensus sequence is the more general sequence RGWYVT, or (A/G)G(A/T)(C/T)(A/C/G)T.[2]

The DPE in "the ATP‐binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" is 5'-AGTCTC-3'.[8]

DPE-containing promoters

"The ... Drosophila Antennapedia P2 (Antp P2) [promoter contains] a 7-nucleotide sequence that conforms to the DPE consensus"[3]. GeneID: 40835 Antp Antennapedia [Drosophila melanogaster] is also known as Antp P2.[9] GeneID: 3204 HOXA7 homeobox A7 [ Homo sapiens ] is also known as ANTP and "[t]his gene is highly similar to the antennapedia (Antp) gene of Drosophila."[10] As GeneID: 3204 is " highly similar to the antennapedia (Antp) gene of Drosophila"[10], it may have a DPE like the Drosophila gene core promoter does.

"[T]he TATA-less Drosophila Abdominal-B (Abd-B) promoter [has a] partial DPE sequence"[3]. GeneID: 3205 HOXA9 homeobox A9 [ Homo sapiens] is also known as ABD-B and "[t]his gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila."[11] GeneID: 3205 may also be TATA-less and have a DPE.

General transcription factor II Ds

Main articles: General transcription factor II D gene transcriptions and General transcription factor II Ds

The DPE "is required for the binding of purified [general transcription factor II D] TFIID to a subset of TATA-less promoters"[4].

"Photo-cross-linking analysis of purified TFIID with a TATA-less DPE-containing promoter revealed specific cross-linking of dTAFII60 [TAF6 GeneID: 6878] and dTAFII40 [TAF11 GeneID: 6882] to the DPE, with a higher efficiency of cross-linking to dTAFII60 than to dTAFII40. These data, combined with the previously well-characterized interactions between the two TAFs and their homology to histones H4 and H3, suggest that a dTAFII60–dTAFII40 heterotetramer binds to the DPE."[3]

Hypotheses

Main article: Hypotheses
  1. The DPE is not used to transcribe A1BG.

DPE (Juven-Gershon) samplings

Main article: A1BG gene transcription core promoters

For the Basic programs (starting with SuccessablesDPE.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 expanded in the positive direction from 958 to 4445, are looking for, and found:

  1. Negative strand, negative direction: 63, AGTCCT at 4437, AGATGT at 4213, AGTTCT at 4179, GGTCCT at 4171, AGTCCT at 4139, GGACAT at 4122, AGATGT at 4063, AGTTCT at 4028, GGTTCT at 4020, GGTTGT at 3980, GGACAT at 3971, GGACCT at 3907, AGACCT at 3836, GGACCT at 3745, GGTCGT at 3732, GGTTCT at 3274, GGTCCT at 3250, AGTCCT at 3218, GGTTGT at 3138, AGTCCT at 3111, GGTCGT at 3071, GGACAT at 3062, AGATGT at 2989, GGTTAT at 2849, GGACAT at 2673, GGTTGT at 2611, AGTCCT at 2588, GGTTGT at 2548, GGACAT at 2539, AGTTAT at 2497, GGACAT at 2338, GGACCT at 2269, AGTCCT at 2251, GGTCAT at 2212, GGTTGT at 2149, AGTCCT at 2135, GGACAT at 1912, GGTCGT at 1786, AGACAT at 1777, GGTCGT at 1612, AGATAT at 1526, AGTCCT at 1276, GGACAT at 1259, AGATGT at 1225, GGTTGT at 1204, GGTCGT at 1141, GGACAT at 1132, AGTCCT at 985, GGACAT at 968, GGTTCT at 875, GGTCCT at 851, GGACAT at 802, AGTCCT at 715, GGTCGT at 677, GGACAT at 668, AGTCCT at 579, GGTTCT at 557, GGTCGT at 541, AGATGT at 482, AGTCCT at 442, GGTTCT at 420, GGTCGT at 404, GGACAT at 395.
  2. Negative strand, positive direction: 18, GGTTCT at 4074, AGTCCT at 3864, GGATGT at 3575, AGACCT at 3551, AGTTAT at 3382, GGTTGT at 3051, GGTTAT at 3025, AGTCCT at 2999, AGTTCT at 2955, GGTTCT at 2923, AGACCT at 2862, GGATGT at 2715, GGATAT at 2660, AGTTCT at 1988, GGACAT at 1870, AGTCCT at 758, GGTCCT at 219, GGACCT at 38.
  3. Positive strand, negative direction: 16, AGACAT at 4508, AGTTCT at 4418, AGACGT at 4236, AGATGT at 3621, AGATAT at 3466, AGACAT at 3434, AGATAT at 2982, AGACAT at 2949, AGACAT at 2881, AGATAT at 1596, AGACAT at 1570, GGATGT at 785, AGATGT at 245, AGACAT at 171, GGATAT at 109, GGATAT at 75.
  4. Positive strand, positive direction: 31, AGATCT at 4065, AGTCGT at 4024, AGTCCT at 3869, GGTCGT at 3721, GGTTGT at 3634, AGTTAT at 3425, GGACCT at 3363, AGACGT at 3279, AGACGT at 3268, AGTCGT at 3156, AGACGT at 3061, AGTCGT at 3042, AGACGT at 2857, AGTCCT at 2621, AGTCGT at 2199, AGTCGT at 2103, GGACGT at 1470, GGTCGT at 1458, GGACGT at 1370, GGTCGT at 1358, GGACGT at 1119, GGTCCT at 708, GGTCGT at 618, GGACCT at 599, GGACGT at 436, GGTCCT at 425, AGACCT at 271, AGACGT at 224, GGACGT at 192, GGTTCT at 178, GGACCT at 41.
  5. complement, negative strand, negative direction is SuccessablesDPEJc--.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 16, 5'-CCTATA-3' at 75, 5'-CCTATA-3' at 109, 5'-TCTGTA-3' at 171, 5'-TCTACA-3' at 245, 5'-CCTACA-3' at 785, 5'-TCTGTA-3' at 1570, 5'-TCTATA-3' at 1596, 5'-TCTGTA-3' at 2881, 5'-TCTGTA-3' at 2949, 5'-TCTATA-3' at 2982, 5'-TCTGTA-3' at 3434, 5'-TCTATA-3' at 3466, 5'-TCTACA-3' at 3621, 5'-TCTGCA-3' at 4236, 5'-TCAAGA-3' at 4418, 5'-TCTGTA-3' at 4508.
  6. complement, negative strand, positive direction is SuccessablesDPEJc-+.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 31, 5'-CCTGGA-3' at 41, 5'-CCAAGA-3' at 178, 5'-CCTGCA-3' at 192, 5'-TCTGCA-3' at 224, 5'-TCTGGA-3' at 271, 5'-CCAGGA-3' at 425, 5'-CCTGCA-3' at 436, 5'-CCTGGA-3' at 599, 5'-CCAGCA-3' at 618, 5'-CCAGGA-3' at 708, 5'-CCTGCA-3' at 1119, 5'-CCAGCA-3' at 1358, 5'-CCTGCA-3' at 1370, 5'-CCAGCA-3' at 1458, 5'-CCTGCA-3' at 1470, 5'-TCAGCA-3' at 2103, 5'-TCAGCA-3' at 2199, 5'-TCAGGA-3' at 2621, 5'-TCTGCA-3' at 2857, 5'-TCAGCA-3' at 3042, 5'-TCTGCA-3' at 3061, 5'-TCAGCA-3' at 3156, 5'-TCTGCA-3' at 3268, 5'-TCTGCA-3' at 3279, 5'-CCTGGA-3' at 3363, 5'-TCAATA-3' at 3425, 5'-CCAACA-3' at 3634, 5'-CCAGCA-3' at 3721, 5'-TCAGGA-3' at 3869, 5'-TCAGCA-3' at 4024, 5'-TCTAGA-3' at 4065.
  7. complement, positive strand, negative direction is SuccessablesDPEJc+-.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 63, 5'-CCTGTA-3' at 395, 5'-CCAGCA-3' at 404, 5'-CCAAGA-3' at 420, 5'-TCAGGA-3' at 442, 5'-TCTACA-3' at 482, 5'-CCAGCA-3' at 541, 5'-CCAAGA-3' at 557, 5'-TCAGGA-3' at 579, 5'-CCTGTA-3' at 668, 5'-CCAGCA-3' at 677, 5'-TCAGGA-3' at 715, 5'-CCTGTA-3' at 802, 5'-CCAGGA-3' at 851, 5'-CCAAGA-3' at 875, 5'-CCTGTA-3' at 968, 5'-TCAGGA-3' at 985, 5'-CCTGTA-3' at 1132, 5'-CCAGCA-3' at 1141, 5'-CCAACA-3' at 1204, 5'-TCTACA-3' at 1225, 5'-CCTGTA-3' at 1259, 5'-TCAGGA-3' at 1276, 5'-TCTATA-3' at 1526, 5'-CCAGCA-3' at 1612, 5'-TCTGTA-3' at 1777, 5'-CCAGCA-3' at 1786, 5'-CCTGTA-3' at 1912, 5'-TCAGGA-3' at 2135, 5'-CCAACA-3' at 2149, 5'-CCAGTA-3' at 2212, 5'-TCAGGA-3' at 2251, 5'-CCTGGA-3' at 2269, 5'-CCTGTA-3' at 2338, 5'-TCAATA-3' at 2497, 5'-CCTGTA-3' at 2539, 5'-CCAACA-3' at 2548, 5'-TCAGGA-3' at 2588, 5'-CCAACA-3' at 2611, 5'-CCTGTA-3' at 2673, 5'-CCAATA-3' at 2849, 5'-TCTACA-3' at 2989, 5'-CCTGTA-3' at 3062, 5'-CCAGCA-3' at 3071, 5'-TCAGGA-3' at 3111, 5'-CCAACA-3' at 3138, 5'-TCAGGA-3' at 3218, 5'-CCAGGA-3' at 3250, 5'-CCAAGA-3' at 3274, 5'-CCAGCA-3' at 3732, 5'-CCTGGA-3' at 3745, 5'-TCTGGA-3' at 3836, 5'-CCTGGA-3' at 3907, 5'-CCTGTA-3' at 3971, 5'-CCAACA-3' at 3980, 5'-CCAAGA-3' at 4020, 5'-TCAAGA-3' at 4028, 5'-TCTACA-3' at 4063, 5'-CCTGTA-3' at 4122, 5'-TCAGGA-3' at 4139, 5'-CCAGGA-3' at 4171, 5'-TCAAGA-3' at 4179, 5'-TCTACA-3' at 4213, 5'-TCAGGA-3' at 4437.
  8. complement, positive strand, positive direction is SuccessablesDPEJc++.bas, looking for 5'-(C/T)C(A/T)(A/G)(C/G/T)A-3', 18, 5'-CCTGGA-3' at 38, 5'-CCAGGA-3' at 219, 5'-TCAGGA-3' at 758, 5'-CCTGTA-3' at 1870, 5'-TCAAGA-3' at 1988, 5'-CCTATA-3' at 2660, 5'-CCTACA-3' at 2715, 5'-TCTGGA-3' at 2862, 5'-CCAAGA-3' at 2923, 5'-TCAAGA-3' at 2955, 5'-TCAGGA-3' at 2999, 5'-CCAATA-3' at 3025, 5'-CCAACA-3' at 3051, 5'-TCAATA-3' at 3382, 5'-TCTGGA-3' at 3551, 5'-CCTACA-3' at 3575, 5'-TCAGGA-3' at 3864, 5'-CCAAGA-3' at 4074.
  9. inverse complement, negative strand, negative direction: 18, AGGACC at 4546, ACAACC at 3942, AGGACC at 3906, ACGACC at 3864, AGAACC at 3793, AGGTCC at 3585, ATGACT at 3542, ATAACC at 3529, ACGTCT at 3431, ATATCT at 2903, ACGACC at 2326, ACAACT at 1853, AGGACC at 1841, AGAACC at 1649, ATGTCT at 1567, ACATCT at 970, AGGACC at 596, ACATCT at 284.
  10. inverse complement, negative strand, positive direction: 16, ATGTCC at 4367, AGAACT at 4048, ATGACC at 3784, AGGTCT at 3771, ATGTCC at 3577, ACGTCT at 3256, ATGACT at 3029, AGGTCT at 3019, AGAACC at 2776, AGGTCT at 2258, AGAACC at 2225, AGAACT at 1951, AGAACC at 1811, AGATCC at 965, AGATCC at 865, AGGTCC at 218.
  11. inverse complement, positive strand, negative direction: 12, AGATCC at 4476, AGAACC at 4451, ATGTCT at 3833, AGGACT at 3640, ATGTCT at 2986, ACAACC at 2844, ATGACT at 2786, ATGACC at 2189, ACGTCT at 1774, ACATCC at 1572, ATATCC at 1529, AGATCC at 973.
  12. inverse complement, positive strand, positive direction: 39, AGGACC at 4409, ACGTCT at 4317, AGGACT at 4186, ACGACC at 4177, ATAACT at 4161, AGAACT at 4131, AGATCC at 4077, AGATCT at 4065, AGGTCC at 4032, AGGTCT at 3891, ACGTCT at 3831, AGGTCT at 3806, AGGTCC at 3687, ACGTCC at 3466, AGGACC at 3296, ATGACC at 3117, AGGTCC at 3111, ACGTCT at 2859, ACAACC at 2816, ACGTCC at 2745, ACGTCT at 2721, ACGTCC at 2683, ATATCC at 2550, AGGACC at 2501, ACATCC at 2255, AGGACT at 2211, ACAACC at 2185, ACGTCT at 1937, ACATCC at 1875, ACGTCC at 1788, ACGACC at 1779, ACGACC at 1736, ATGACT at 1286, ACGTCC at 658, ACGTCT at 438, ACGTCC at 194, AGGTCC at 33, AGGTCT at 15, AGGTCC at 8.
  13. inverse, negative strand, negative direction, is SuccessablesDPEJi--.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 12, 5'-TCTAGG-3' at 973, 5'-TATAGG-3' at 1529, 5'-TGTAGG-3' at 1572, 5'-TGCAGA-3' at 1774, 5'-TACTGG-3' at 2189, 5'-TACTGA-3' at 2786, 5'-TGTTGG-3' at 2844, 5'-TACAGA-3' at 2986, 5'-TCCTGA-3' at 3640, 5'-TACAGA-3' at 3833, 5'-TCTTGG-3' at 4451, 5'-TCTAGG-3' at 4476.
  14. inverse, negative strand, positive direction, is SuccessablesDPEJi-+.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 39, 5'-TCCAGG-3' at 8, 5'-TCCAGA-3' at 15, 5'-TCCAGG-3' at 33, 5'-TGCAGG-3' at 194, 5'-TGCAGA-3' at 438, 5'-TGCAGG-3' at 658, 5'-TACTGA-3' at 1286, 5'-TGCTGG-3' at 1736, 5'-TGCTGG-3' at 1779, 5'-TGCAGG-3' at 1788, 5'-TGTAGG-3' at 1875, 5'-TGCAGA-3' at 1937, 5'-TGTTGG-3' at 2185, 5'-TCCTGA-3' at 2211, 5'-TGTAGG-3' at 2255, 5'-TCCTGG-3' at 2501, 5'-TATAGG-3' at 2550, 5'-TGCAGG-3' at 2683, 5'-TGCAGA-3' at 2721, 5'-TGCAGG-3' at 2745, 5'-TGTTGG-3' at 2816, 5'-TGCAGA-3' at 2859, 5'-TCCAGG-3' at 3111, 5'-TACTGG-3' at 3117, 5'-TCCTGG-3' at 3296, 5'-TGCAGG-3' at 3466, 5'-TCCAGG-3' at 3687, 5'-TCCAGA-3' at 3806, 5'-TGCAGA-3' at 3831, 5'-TCCAGA-3' at 3891, 5'-TCCAGG-3' at 4032, 5'-TCTAGA-3' at 4065, 5'-TCTAGG-3' at 4077, 5'-TCTTGA-3' at 4131, 5'-TATTGA-3' at 4161, 5'-TGCTGG-3' at 4177, 5'-TCCTGA-3' at 4186, 5'-TGCAGA-3' at 4317, 5'-TCCTGG-3' at 4409.
  15. inverse, positive strand, negative direction, is SuccessablesDPEJi+-.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 18, 5'-TGTAGA-3' at 284, 5'-TCCTGG-3' at 596, 5'-TGTAGA-3' at 970, 5'-TACAGA-3' at 1567, 5'-TCTTGG-3' at 1649, 5'-TCCTGG-3' at 1841, 5'-TGTTGA-3' at 1853, 5'-TGCTGG-3' at 2326, 5'-TATAGA-3' at 2903, 5'-TGCAGA-3' at 3431, 5'-TATTGG-3' at 3529, 5'-TACTGA-3' at 3542, 5'-TCCAGG-3' at 3585, 5'-TCTTGG-3' at 3793, 5'-TGCTGG-3' at 3864, 5'-TCCTGG-3' at 3906, 5'-TGTTGG-3' at 3942, 5'-TCCTGG-3' at 4546.
  16. inverse, positive strand, positive direction, is SuccessablesDPEJi++.bas, looking for 5'-T(A/C/G)(C/T)(A/T)G(A/G)-3', 16, 5'-TCCAGG-3' at 218, 5'-TCTAGG-3' at 865, 5'-TCTAGG-3' at 965, 5'-TCTTGG-3' at 1811, 5'-TCTTGA-3' at 1951, 5'-TCTTGG-3' at 2225, 5'-TCCAGA-3' at 2258, 5'-TCTTGG-3' at 2776, 5'-TCCAGA-3' at 3019, 5'-TACTGA-3' at 3029, 5'-TGCAGA-3' at 3256, 5'-TACAGG-3' at 3577, 5'-TCCAGA-3' at 3771, 5'-TACTGG-3' at 3784, 5'-TCTTGA-3' at 4048, 5'-TACAGG-3' at 4367.

DPE (Juven-Gershon) UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: AGGACC at 4546, AGTCCT at 4437, AGATGT at 4213, AGTTCT at 4179, GGTCCT at 4171, AGTCCT at 4139, GGACAT at 4122, AGATGT at 4063, AGTTCT at 4028, GGTTCT at 4020, GGTTGT at 3980, GGACAT at 3971, ACAACC at 3942, GGACCT at 3907, AGGACC at 3906, ACGACC at 3864, AGACCT at 3836, AGAACC at 3793, GGACCT at 3745, GGTCGT at 3732, AGGTCC at 3585, ATGACT at 3542, ATAACC at 3529, ACGTCT at 3431, GGTTCT at 3274, GGTCCT at 3250, AGTCCT at 3218, GGTTGT at 3138, AGTCCT at 3111, GGTCGT at 3071, GGACAT at 3062, AGATGT at 2989, ATATCT at 2903, GGTTAT at 2849.

Positive strand, negative direction: AGACAT at 4508, AGATCC at 4476, AGAACC at 4451, AGTTCT at 4418, AGACGT at 4236, AGATGT at 3621, AGATAT at 3466, AGACAT at 3434, ATGTCT at 3833, AGGACT at 3640, ATGTCT at 2986, AGATAT at 2982, AGACAT at 2949, AGACAT at 2881.

DPE (Juven-Gershon) core promoters

Main article: Core promoter gene transcriptions

Positive strand, negative direction: ACAACC at 2844.

Negative strand, positive direction: ATGTCC at 4367.

Positive strand, positive direction: AGGACC at 4409, ACGTCT at 4317.

DPE (Juven-Gershon) proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: GGACAT at 2673, GGTTGT at 2611.

Positive strand, negative direction: ATGACT at 2786.

Negative strand, positive direction: GGTTCT at 4074.

Positive strand, positive direction: AGGACT at 4186, ACGACC at 4177, ATAACT at 4161, AGAACT at 4131, AGATCC at 4077, AGATCT at 4065.

DPE (Juven-Gershon) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: AGTCCT at 2588, GGTTGT at 2548, GGACAT at 2539, AGTTAT at 2497, GGACAT at 2338, ACGACC at 2326, GGACCT at 2269, AGTCCT at 2251, GGTCAT at 2212, GGTTGT at 2149, AGTCCT at 2135, GGACAT at 1912, ACAACT at 1853, AGGACC at 1841, GGTCGT at 1786, AGACAT at 1777, AGAACC at 1649, GGTCGT at 1612, ATGTCT at 1567, AGATAT at 1526, AGTCCT at 1276, GGACAT at 1259, AGATGT at 1225, GGTTGT at 1204, GGTCGT at 1141, GGACAT at 1132, AGTCCT at 985, ACATCT at 970, GGACAT at 968, GGTTCT at 875, GGTCCT at 851, GGACAT at 802, AGTCCT at 715, GGTCGT at 677, GGACAT at 668, AGGACC at 596, AGTCCT at 579, GGTTCT at 557, GGTCGT at 541, AGATGT at 482, AGTCCT at 442, GGTTCT at 420, GGTCGT at 404, GGACAT at 395, ACATCT at 284.

Positive strand, negative direction: ATGACC at 2189, ACGTCT at 1774, AGATAT at 1596, ACATCC at 1572, AGACAT at 1570, ATATCC at 1529, AGATCC at 973, GGATGT at 785, AGATGT at 245, AGACAT at 171, GGATAT at 109, GGATAT at 75.

Negative strand, positive direction: AGAACT at 4048, AGTCCT at 3864, ATGACC at 3784, AGGTCT at 3771, ATGTCC at 3577, GGATGT at 3575, AGACCT at 3551, AGTTAT at 3382, ACGTCT at 3256, GGTTGT at 3051, ATGACT at 3029, GGTTAT at 3025, AGGTCT at 3019, AGTCCT at 2999, AGTTCT at 2955, GGTTCT at 2923, AGACCT at 2862, AGAACC at 2776, GGATGT at 2715, GGATAT at 2660, AGGTCT at 2258, AGAACC at 2225, AGTTCT at 1988, AGAACT at 1951, GGACAT at 1870, AGAACC at 1811, AGATCC at 965, AGATCC at 865, AGTCCT at 758, GGTCCT at 219, AGGTCC at 218, GGACCT at 38.

Positive strand, positive direction: AGGTCC at 4032, AGTCGT at 4024, AGGTCT at 3891, AGTCCT at 3869, ACGTCT at 3831, AGGTCT at 3806, GGTCGT at 3721, GGTTGT at 3634, AGGTCC at 3687, ACGTCC at 3466, AGTTAT at 3425, GGACCT at 3363, AGGACC at 3296, AGACGT at 3279, AGACGT at 3268, AGTCGT at 3156, ATGACC at 3117, AGGTCC at 3111, AGACGT at 3061, AGTCGT at 3042, ACGTCT at 2859, AGACGT at 2857, ACAACC at 2816, ACGTCC at 2745, ACGTCT at 2721, ACGTCC at 2683, AGTCCT at 2621, ATATCC at 2550, AGGACC at 2501, ACATCC at 2255, AGGACT at 2211, AGTCGT at 2199, ACAACC at 2185, AGTCGT at 2103, ACGTCT at 1937, ACATCC at 1875, ACGTCC at 1788, ACGACC at 1779, ACGACC at 1736, GGACGT at 1470, GGTCGT at 1458, GGACGT at 1370, GGTCGT at 1358, ATGACT at 1286, GGACGT at 1119, GGTCCT at 708, ACGTCC at 658, GGTCGT at 618, GGACCT at 599, ACGTCT at 438, GGACGT at 436, GGTCCT at 425, AGACCT at 271, AGACGT at 224, ACGTCC at 194, GGACGT at 192, GGTTCT at 178, GGACCT at 41, AGGTCC at 33, AGGTCT at 15, AGGTCC at 8.

DPE (Kadonaga) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)G(A/T)CGTG and putting the sequence in "⌘F" finds two between ZNF497 and A1BG or seven between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)G(A/T)CGTG (starting with SuccessablesDPEK.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:

  1. negative strand, negative direction, looking for (A/G)G(A/T)CGTG, 7, GGTCGTG at 3733, GGTCGTG at 3072, GGTCGTG at 1787, GGTCGTG at 1142, GGTCGTG at 678, GGTCGTG at 542, GGTCGTG at 405.
  2. positive strand, negative direction, looking for (A/G)G(A/T)CGTG, 1, AGACGTG at 4237.
  3. positive strand, positive direction, looking for (A/G)G(A/T)CGTG, 8, AGTCGTG at 3043, AGTCGTG at 2200, AGTCGTG at 2104, GGACGTG at 1471, GGTCGTG at 1459, GGACGTG at 1371, GGTCGTG at 1359, GGTCGTG at 619.
  4. negative strand, positive direction, looking for (A/G)G(A/T)CGTG, 0.
  5. complement, negative strand, negative direction, looking for (C/T)C(A/T)GCAC, 1, TCTGCAC at 4237.
  6. complement, positive strand, negative direction, looking for (C/T)C(A/T)GCAC, 7, CCAGCAC at 3733, CCAGCAC at 3072, CCAGCAC at 1787, CCAGCAC at 1142, CCAGCAC at 678, CCAGCAC at 542, CCAGCAC at 405.
  7. complement, positive strand, positive direction, looking for (C/T)C(A/T)GCAC, 0.
  8. complement, negative strand, positive direction, looking for (C/T)C(A/T)GCAC, 8, TCAGCAC at 3043, TCAGCAC at 2200, TCAGCAC at 2104, CCAGCAC at 1471, CCAGCAC at 1459, CCAGCAC at 1371, CCAGCAC at 1359, CCAGCAC at 619.
  9. inverse complement, negative strand, negative direction, looking for CACG(A/T)C(C/T), 1, CACGTCT at 3431.
  10. inverse complement, positive strand, negative direction, looking for CACG(A/T)C(C/T), 1, CACGTCT at 1774.
  11. inverse complement, positive strand, positive direction, looking for CACG(A/T)C(C/T), 3, CACGTCC at 3466, CACGTCC at 2683, CACGTCC at 1788.
  12. inverse complement, negative strand, positive direction, looking for CACG(A/T)C(C/T), 1, CACGTCT at 3256.
  13. inverse negative strand, negative direction, looking for GTGC(A/T)G(A/G), 1, GTGCAGA at 1774.
  14. inverse positive strand, negative direction, looking for GTGC(A/T)G(A/G), 1, GTGCAGA at 3431.
  15. inverse positive strand, positive direction, looking for GTGC(A/T)G(A/G), 1, GTGCAGA at 3256.
  16. inverse negative strand, positive direction, looking for GTGC(A/T)G(A/G), 3, GTGCAGG at 3466, GTGCAGG at 2683, GTGCAGG at 1788.

DPE (Kadonaga) UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: GGTCGTG at 3733, CACGTCT at 3431, GGTCGTG at 3072.

Positive strand, negative direction: AGACGTG at 4237.

DPE (Kadonaga) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: GGTCGTG at 1787, GGTCGTG at 1142, GGTCGTG at 678, GGTCGTG at 542, GGTCGTG at 405.

Positive strand, negative direction: CACGTCC at 3466, CACGTCC at 2683, CACGTCC at 1788, CACGTCT at 1774.

Positive strand, positive direction: AGTCGTG at 3043, AGTCGTG at 2200, AGTCGTG at 2104, GGACGTG at 1471, GGTCGTG at 1459, GGACGTG at 1371, GGTCGTG at 1359, GGTCGTG at 619.

Negative strand, positive direction: CACGTCT at 3256.

DPE (Matsumoto) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence AGTCTC and putting the sequence in "⌘F" finds four between ZNF497 and A1BG or two between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGTCTC (starting with SuccessablesDPEM.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:

  1. negative strand, negative direction, looking for AGTCTC, 1, AGTCTC at 3645.
  2. positive strand, negative direction, looking for AGTCTC, 1, AGTCTC at 1445.
  3. positive strand, positive direction, looking for AGTCTC, 3, AGTCTC at 2730, AGTCTC at 2700, AGTCTC at 2610.
  4. negative strand, positive direction, looking for AGTCTC, 1, AGTCTC at 3188.
  5. complement, negative strand, negative direction, looking for TCAGAG, 1, TCAGAG at 1445.
  6. complement, positive strand, negative direction, looking for TCAGAG, 1, TCAGAG at 3645.
  7. complement, positive strand, positive direction, looking for TCAGAG, 1, TCAGAG at 3188.
  8. complement, negative strand, positive direction, looking for TCAGAG, 3, TCAGAG at 2730, TCAGAG at 2700, TCAGAG at 2610.
  9. inverse complement, negative strand, negative direction, looking for GAGACT, 0.
  10. inverse complement, positive strand, negative direction, looking for GAGACT, 4, GAGACT at 4053, GAGACT at 1933, GAGACT at 1081, GAGACT at 915.
  11. inverse complement, positive strand, positive direction, looking for GAGACT, 2, GAGACT at 3123, GAGACT at 255.
  12. inverse complement, negative strand, positive direction, looking for GAGACT, 0.
  13. inverse negative strand, negative direction, looking for CTCTGA, 4, CTCTGA at 4053, CTCTGA at 1933, CTCTGA at 1081, CTCTGA at 915.
  14. inverse positive strand, negative direction, looking for CTCTGA, 0.
  15. inverse positive strand, positive direction, looking for CTCTGA, 0.
  16. inverse negative strand, positive direction, looking for CTCTGA, 2, CTCTGA at 3123, CTCTGA at 255.

DPE (Matsumoto) UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: AGTCTC at 3645.

Positive strand, negative direction: GAGACT at 4053.

DPE (Matsumoto) distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: GAGACT at 1933, AGTCTC at 1445, GAGACT at 1081, GAGACT at 915.

Negative strand, positive direction: AGTCTC at 3188.

Positive strand, positive direction: GAGACT at 3123, AGTCTC at 2730, AGTCTC at 2700, AGTCTC at 2610, GAGACT at 255.

Acknowledgements

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

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

See also

References

  1. ↑ Jennifer E.F. Butler, James T. Kadonaga (October 15, 2002). "The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development. 16 (20): 2583–92. doi:10.1101/gad.1026202. PMID 12381658.
  2. ↑ 2.0 2.1 2.2 Tamar Juven-Gershon, James T. Kadonaga (March 15, 2010). "Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery". Developmental Biology. 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. PMC 2830304. PMID 19682982.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Thomas W. Burke and James T. Kadonaga (November 15, 1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila". Genes & Development. 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMC 316699. PMID 9367984.
  4. ↑ 4.0 4.1 Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  5. ↑ 5.0 5.1 T.W. Burke and James T. Kadonaga (15 March 1996). "Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters" (PDF). Genes & Development. 10 (6): 711–724. doi:10.1101/gad.10.6.711. PMID 8598298.
  6. ↑ Kutach, Alan K.; Kadonaga, James T. (July 2000). "The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters". Molecular and Cellular Biology. 20 (13): 4754–4764. doi:10.1128/MCB.20.13.4754-4764.2000. PMC 85905. PMID 10848601.
  7. ↑ James T. Kadonaga (September 2002). "The DPE, a core promoter element for transcription by RNA polymerase II" (PDF). Experimental & Molecular Medicine. 34 (4): 259–264. PMID 12515390.
  8. ↑ 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.
  9. ↑ FlyBase (February 3, 2013). "Antp Antennapedia [ Drosophila melanogaster ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  10. ↑ 10.0 10.1 HGNC (February 5, 2013). "HOXA7 homeobox A7 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  11. ↑ HGNC (February 5, 2013). "HOXA9 homeobox A9 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.

Further reading

External links

{{Phosphate biochemistry}}

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