V box gene transcriptions

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Editor-In-Chief: Henry A. Hoff

File:Platypus.jpg
Ornithorhynchus anatinus is the platypus. Credit: Stefan Kraft.{{free media}}

"The V boxes encompass a leader exon and first intron of the mature transcript."[1]

"REV-ERBα and RORa are nuclear receptors rather than bZIP transcription factors like VRI [target gene: vrille (VRI)] and PDP1ϵ, and they regulate transcription by binding RORE elements rather than V/P-boxes (Bell-Pedersen et al., 2005)."[2]

"A delayed accumulation of PDP1 leads to a replacement of VRI from P/V (PDP1 and VRI) boxes and restimulates clk transcription."[3]

"For VRI to be a direct repressor of Clk, the 8.0 kb Clk genomic fragment should contain binding sites for VRI. The consensus binding site for VRI has not been determined; however, the basic (DNA binding) domain shares >85% homology with that of mammalian E4BP4, and hence, VRI should bind similar DNA sequences as E4BP4 (George and Terracol, 1997). The optimal binding site for E4BP4 has been determined as 5′-(A/G): (A/G)T(A/C)A(A/T/C)-3′ (Cowell et al., 1992)."[4]

"EMSA confirms that the W and V boxes each binds proteins that also recognize the X box."[5]

Consensus sequences

"As VRI accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[2]

Human genes

Gene ID: 3119 is HLA-DQB1 major histocompatibility complex, class II, DQ beta 1. "HLA-DQB1 belongs to the HLA class II beta chain paralogs. This class II molecule is a heterodimer consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and it contains six exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. Within the DQ molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to four different molecules. Typing for these polymorphisms is routinely done for bone marrow transplantation. Alternative splicing results in multiple transcript variants."[6]

  1. NP_002114.3 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor (variant 1).
  2. NP_001230890.1 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 2 precursor (variant 2).
  3. NP_001230891.1 HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1 precursor (variant 3).

Gene ID: 3120 is HLA-DQB2 major histocompatibility complex, class II, DQ beta 2. "HLA-DQB2 belongs to the family of HLA class II beta chain paralogs. Class II molecules are heterodimers consisting of an alpha (DQA) and a beta chain (DQB), both anchored in the membrane. They play a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). Polymorphisms in the alpha and beta chains specify the peptide binding specificity, and typing for these polymorphisms is routinely done for bone marrow transplantation. However this gene, HLA-DQB2, is not routinely typed, as it is not thought to have an effect on transplantation. There is conflicting evidence in the literature and public sequence databases for the protein-coding capacity of HLA-DQB2. Because there is evidence of transcription and an intact ORF, HLA-DQB2 is represented in Entrez Gene and in RefSeq as a protein-coding locus."[7]

  1. NP_001287719.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform 1 precursor (variant 1).
  2. NP_001185787.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform 2 precursor (variant 2).
  3. XP_005249108.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X1.
  4. XP_011512862.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X2.
  5. XP_011512863.1 HLA class II histocompatibility antigen, DQ beta 2 chain isoform X3.

Gene ID: 3121 is HLA-DQB3 major histocompatibility complex, class II, DQ beta 3.

"Structural and functional studies indicate that a proximal promoter region exists, extending up to approx. -250 bp upstream of the transcription start site involving a set of conserved cis-acting elements defined as Y, X1/X2, S, W, J and V boxes in addition to the TATA and CAAT box sequences. However, locus-specific differences with respect to the presence and sequence of these elements exist. Although allelic polymorphism is a key feature of HLA class II genes, it was somewhat surprising to learn that the upstream regulatory regions of these genes also harbor allelic variability. This variability affects the array of highly conserved regulatory sequences consisting of the X, Y and W/Z box elements. For the DQB1 proximal promoter, termed QBP1, 10 different alleles have been identified in previous analyses of approx. 600bp immediately upstream of the first exon of the DQB1 gene.6–8 Functional studies indicated that this allelic polymorphism is associated with differences in both transcriptional activity and affinity for DNA-binding proteins.6,9"[8]

"HLA class II expression requires coordinate binding of transcription factors to the W-X-Y box region of the proximal promoter."[8]

Gene ID: 4783 is NFIL3 nuclear factor, interleukin 3 regulated (aka E4BP4; IL3BP1; NFIL3A; NF-IL3A). "The protein encoded by this gene is a transcriptional regulator that binds as a homodimer to activating transcription factor (ATF) sites in many cellular and viral promoters. The encoded protein represses PER1 and PER2 expression and therefore plays a role in the regulation of circadian rhythm. Three transcript variants encoding the same protein have been found for this gene."[9]

  1. NP_001276928.1 nuclear factor interleukin-3-regulated protein (variant 1).
  2. NP_001276929.1 nuclear factor interleukin-3-regulated protein (variant 2).
  3. NP_005375.2 nuclear factor interleukin-3-regulated protein (variant 3).
  4. XP_016870232.1 nuclear factor interleukin-3-regulated protein isoform X1.
  5. XP_016870233.1 nuclear factor interleukin-3-regulated protein isoform X1.

Hypotheses

  1. A1BG has no V boxes in either promoter.

Samplings

Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in A1BG gene transcriptions revealed two occurrences (GTTTT) and (ATTTT) on the ZSCAN22 side.

For the Basic programs testing consensus sequence (A/G)TT(A/T)(C/T) (starting with SuccessablesVbox.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: 60, GTTTC at 4504, GTTTT at 4376, GTTTT at 4310, ATTAT at 4223, GTTTT at 4216, ATTAT at 4077, GTTTT at 4066, GTTTT at 3767, ATTAC at 3658, ATTAT at 3538, ATTTT at 3439, ATTTT at 3353, GTTTT at 3326, GTTTT at 3313, ATTTT at 3171, ATTTT at 3163, ATTTT at 3024, ATTTT at 3010, GTTTC at 2891, GTTTT at 2866, ATTTC at 2857, GTTAT at 2849, GTTTT at 2795, GTTTT at 2644, GTTAT at 2497, GTTTT at 2490, GTTTT at 2476, GTTTT at 2307, ATTTT at 2299, GTTTT at 2182, ATTTC at 2174, GTTTT at 2036, GTTTT at 1880, ATTTT at 1872, ATTTT at 1737, ATTAT at 1708, GTTTC at 1638, GTTTT at 1561, ATTTC at 1548, GTTTT at 1394, GTTTT at 1384, GTTTT at 1371, GTTAT at 1362, GTTTT at 1228, GTTTT at 1092, GTTTT at 926, GTTTT at 771, ATTTT at 763, GTTTT at 637, ATTTT at 629, ATTAT at 602, GTTTT at 485, ATTAT at 271, GTTTT at 257, ATTAT at 249, ATTTT at 222, ATTTT at 183, GTTTT at 164, GTTTC at 93, ATTTT at 66.
  2. Negative strand, positive direction: 15, ATTAT at 4165, ATTAT at 4158, ATTTT at 4120, GTTTT at 4109, GTTAT at 3382, GTTAT at 3025, GTTTT at 2687, ATTTC at 2645, ATTAT at 2547, ATTTT at 2449, ATTTT at 2441, GTTTC at 2301, GTTTC at 2263, ATTTC at 1978, GTTTT at 147.
  3. Positive strand, negative direction: 14, ATTTT at 4511, ATTTC at 3688, ATTAC at 3469, GTTTT at 3349, ATTTC at 2884, ATTTT at 2853, ATTTT at 1727, ATTAT at 1724, ATTTC at 1603, ATTTC at 1380, ATTAC at 1296, GTTTT at 215, ATTTT at 190, ATTTC at 22.
  4. Positive strand, positive direction: 11, GTTAT at 3425, GTTAT at 3159, GTTTC at 3064, GTTAC at 2909, GTTTC at 2827, GTTTT at 2707, GTTTC at 2535, GTTTT at 2494, ATTTT at 2445, GTTTT at 2003, GTTAC at 227.
  5. complement, negative strand, negative direction is SuccessablesVboxc--.bas, looking for (C/T)AA(A/T)(A/G), 14: TAAAG at 22, TAAAA at 190, CAAAA at 215, TAATG at 1296, TAAAG at 1380, TAAAG at 1603, TAATA at 1724, TAAAA at 1727, TAAAA at 2853, TAAAG at 2884, CAAAA at 3349, TAATG at 3469, TAAAG at 3688, TAAAA at 4511.
  6. complement, negative strand, positive direction is SuccessablesVboxc-+.bas, looking for (C/T)AA(A/T)(A/G), 11: CAATG at 227, CAAAA at 2003, TAAAA at 2445, CAAAA at 2494, CAAAG at 2535, CAAAA at 2707, CAAAG at 2827, CAATG at 2909, CAAAG at 3064, CAATA at 3159, CAATA at 3425.
  7. complement, positive strand, negative direction is SuccessablesVboxc+-.bas, looking for (C/T)AA(A/T)(A/G), 60: TAAAA at 66, CAAAG at 93, CAAAA at 164, TAAAA at 183, TAAAA at 222, TAATA at 249, CAAAA at 257, TAATA at 271, CAAAA at 485, TAATA at 602, TAAAA at 629, CAAAA at 637, TAAAA at 763, CAAAA at 771, CAAAA at 926, CAAAA at 1092, CAAAA at 1228, CAATA at 1362, CAAAA at 1371, CAAAA at 1384, CAAAA at 1394, TAAAG at 1548, CAAAA at 1561, CAAAG at 1638, TAATA at 1708, TAAAA at 1737, TAAAA at 1872, CAAAA at 1880, CAAAA at 2036, TAAAG at 2174, CAAAA at 2182, TAAAA at 2299, CAAAA at 2307, CAAAA at 2476, CAAAA at 2490, CAATA at 2497, CAAAA at 2644, CAAAA at 2795, CAATA at 2849, TAAAG at 2857, CAAAA at 2866, CAAAG at 2891, TAAAA at 3010, TAAAA at 3024, TAAAA at 3163, TAAAA at 3171, CAAAA at 3313, CAAAA at 3326, TAAAA at 3353, TAAAA at 3439, TAATA at 3538, TAATG at 3658, CAAAA at 3767, CAAAA at 4066, TAATA at 4077, CAAAA at 4216, TAATA at 4223, CAAAA at 4310, CAAAA at 4376, CAAAG at 4504.
  8. complement, positive strand, positive direction is SuccessablesVboxc++.bas, looking for (C/T)AA(A/T)(A/G), 15: CAAAA at 147, TAAAG at 1978, CAAAG at 2263, CAAAG at 2301, TAAAA at 2441, TAAAA at 2449, TAATA at 2547, TAAAG at 2645, CAAAA at 2687, CAATA at 3025, CAATA at 3382, CAAAA at 4109, TAAAA at 4120, TAATA at 4158, TAATA at 4165.
  9. inverse complement, negative strand, negative direction: 38, ATAAT at 4538, AAAAT at 4512, GAAAC at 4462, GAAAC at 3985, ATAAC at 3528, ATAAT at 3468, ATAAT at 3454, GTAAT at 3436, AAAAT at 3350, GTAAC at 3285, GAAAC at 3076, AAAAT at 3021, ATAAT at 2998, ATAAT at 2977, GTAAT at 2951, AAAAT at 2854, GAAAC at 2553, GAAAC at 2217, GAAAC at 2100, GAAAC at 1791, GAAAT at 1734, AAAAT at 1728, GAAAC at 1688, AAAAC at 1433, GTAAC at 1343, GAAAC at 1146, GTAAC at 886, GAAAC at 682, GAAAC at 546, GAAAC at 409, GAAAT at 348, ATAAT at 236, AAAAT at 217, AAAAT at 191, GTAAT at 173, GTAAT at 153, GAAAT at 48, AAAAC at 28.
  10. inverse complement, negative strand, positive direction is SuccessablesVboxci-+.bas, looking for (A/G)(A/T)AA(C/T), 12: AAAAC at 292, GAAAC at 2147, AAAAT at 2446, AAAAC at 2495, GAAAT at 2624, GAAAC at 2630, GAAAC at 2832, GAAAT at 3166, GTAAC at 3732, GAAAT at 3795, GAAAT at 4092, ATAAT at 4168.
  11. inverse complement, positive strand, negative direction is SuccessablesVboxci+-.bas, looking for (A/G)(A/T)AA(C/T), 81: AAAAC at 67, GAAAC at 127, AAAAC at 165, GAAAC at 227, GTAAT at 248, AAAAC at 258, ATAAT at 270, GAAAC at 304, GAAAC at 313, AAAAC at 359, GTAAT at 397, GAAAC at 474, AAAAT at 488, AAAAT at 496, GTAAT at 534, GTAAC at 613, AAAAT at 631, AAAAT at 640, GTAAT at 670, AAAAT at 765, AAAAT at 774, GTAAT at 804, GTAAT at 1134, GAAAC at 1213, AAAAT at 1231, GTAAT at 1261, AAAAC at 1372, AAAAC at 1386, AAAAT at 1562, GAAAC at 1583, GAAAT at 1631, GAAAC at 1643, GAAAT at 1661, GTAAT at 1707, AAAAT at 1738, GTAAT at 1779, GAAAC at 1856, AAAAT at 1874, AAAAT at 1884, GTAAT at 1914, AAAAT at 2061, GTAAT at 2088, GAAAT at 2158, AAAAT at 2185, GAAAC at 2283, AAAAT at 2301, AAAAC at 2310, AAAAC at 2491, AAAAC at 2507, GAAAC at 2620, AAAAT at 2646, GTAAT at 2675, GAAAT at 2747, AAAAC at 2840, AAAAT at 2867, AAAAT at 2930, GAAAC at 2958, AAAAC at 2969, AAAAT at 3011, AAAAC at 3027, GTAAT at 3064, GAAAC at 3147, AAAAC at 3165, AAAAT at 3173, AAAAT at 3314, AAAAC at 3328, AAAAT at 3355, AAAAC at 3510, ATAAT at 3537, GAAAC at 3592, ATAAT at 3657, AAAAT at 3768, GTAAT at 3973, AAAAT at 4069, ATAAT at 4076, AAAAT at 4088, AAAAT at 4219, ATAAT at 4222, ATAAT at 4225, AAAAC at 4311, AAAAC at 4396.
  12. inverse complement, positive strand, positive direction is SuccessablesVboxci++.bas, looking for (A/G)(A/T)AA(C/T), 15: CAAAA at 147, TAAAG at 1978, CAAAG at 2263, CAAAG at 2301, TAAAA at 2441, TAAAA at 2449, TAATA at 2547, TAAAG at 2645, CAAAA at 2687, CAATA at 3025, CAATA at 3382, CAAAA at 4109, TAAAA at 4120, TAATA at 4158, TAATA at 4165.
  13. inverse negative strand, negative direction is SuccessablesVboxi--.bas, looking for (C/T)(A/T)TT(A/G), 81: TTTTG at 67, CTTTG at 127, TTTTG at 165, CTTTG at 227, CATTA at 248, TTTTG at 258, TATTA at 270, CTTTG at 304, CTTTG at 313, TTTTG at 359, CATTA at 397, CTTTG at 474, TTTTA at 488, TTTTA at 496, CATTA at 534, CATTG at 613, TTTTA at 631, TTTTA at 640, CATTA at 670, TTTTA at 765, TTTTA at 774, CATTA at 804, CATTA at 1134, CTTTG at 1213, TTTTA at 1231, CATTA at 1261, TTTTG at 1372, TTTTG at 1386, TTTTA at 1562, CTTTG at 1583, CTTTA at 1631, CTTTG at 1643, CTTTA at 1661, CATTA at 1707, TTTTA at 1738, CATTA at 1779, CTTTG at 1856, TTTTA at 1874, TTTTA at 1884, CATTA at 1914, TTTTA at 2061, CATTA at 2088, CTTTA at 2158, TTTTA at 2185, CTTTG at 2283, TTTTA at 2301, TTTTG at 2310, TTTTG at 2491, TTTTG at 2507, CTTTG at 2620, TTTTA at 2646, CATTA at 2675, CTTTA at 2747, TTTTG at 2840, TTTTA at 2867, TTTTA at 2930, CTTTG at 2958, TTTTG at 2969, TTTTA at 3011, TTTTG at 3027, CATTA at 3064, CTTTG at 3147, TTTTG at 3165, TTTTA at 3173, TTTTA at 3314, TTTTG at 3328, TTTTA at 3355, TTTTG at 3510, TATTA at 3537, CTTTG at 3592, TATTA at 3657, TTTTA at 3768, CATTA at 3973, TTTTA at 4069, TATTA at 4076, TTTTA at 4088, TTTTA at 4219, TATTA at 4222, TATTA at 4225, TTTTG at 4311, TTTTG at 4396.
  14. inverse negative strand, positive direction is SuccessablesVboxi-+.bas, looking for (C/T)(A/T)TT(A/G), 21: CATTG at 23, CTTTG at 111, TTTTA at 148, CATTG at 1703, CTTTG at 1831, CTTTG at 1982, TTTTG at 2282, TATTG at 2348, TTTTA at 2442, TTTTG at 2452, CTTTA at 2586, TTTTG at 2688, CATTG at 2903, CTTTG at 3398, CTTTG at 3946, TTTTA at 4110, TTTTA at 4121, TATTA at 4143, TATTG at 4160, CTTTG at 4208, CATTG at 4310.
  15. inverse positive strand, negative direction is SuccessablesVboxi+-.bas, looking for (C/T)(A/T)TT(A/G), 38: TTTTG at 28, CTTTA at 48, CATTA at 153, CATTA at 173, TTTTA at 191, TTTTA at 217, TATTA at 236, CTTTA at 348, CTTTG at 409, CTTTG at 546, CTTTG at 682, CATTG at 886, CTTTG at 1146, CATTG at 1343, TTTTG at 1433, CTTTG at 1688, TTTTA at 1728, CTTTA at 1734, CTTTG at 1791, CTTTG at 2100, CTTTG at 2217, CTTTG at 2553, TTTTA at 2854, CATTA at 2951, TATTA at 2977, TATTA at 2998, TTTTA at 3021, CTTTG at 3076, CATTG at 3285, TTTTA at 3350, CATTA at 3436, TATTA at 3454, TATTA at 3468, TATTG at 3528, CTTTG at 3985, CTTTG at 4462, TTTTA at 4512, TATTA at 4538.
  16. inverse positive strand, positive direction is SuccessablesVboxi++.bas, looking for (C/T)(A/T)TT(A/G), 12: TTTTG at 292, CTTTG at 2147, TTTTA at 2446, TTTTG at 2495, CTTTA at 2624, CTTTG at 2630, CTTTG at 2832, CTTTA at 3166, CATTG at 3732, CTTTA at 3795, CTTTA at 4092, TATTA at 4168.

V box core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: ATAAT at 4538, AAAAT at 4512, GTTTC at 4504, GAAAC at 4462, and complements

Positive strand, negative direction: ATTTT at 4511, and complement

V box proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: GTTTT at 4376, GTTTT at 4310, ATTAT at 4223, GTTTT at 4216, and complements

Positive strand, negative direction: AAAAC at 4396, AAAAC at 4311, ATAAT at 4225, ATAAT at 4222, AAAAT at 4219, and complements

Negative strand, positive direction: ATAAT at 4168, ATTAT at 4165, ATTAT at 4158, ATTTT at 4120, GTTTT at 4109, GAAAT at 4092, and complements

Positive strand, positive direction: TAATA at 4165, TAATA at 4158, TAAAA at 4120, CAAAA at 4109, and complements.

V box distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 90 between 28 and 4077, and complements

Positive strand, negative direction: 89 between 22 and 4088, and complements

Negative strand, positive direction: 21 between 147 and 3795, and complements

Positive strand, positive direction: 22 between 147 and 3425, and complements

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. ↑ Louis M Staudt and Michael J Lenardo (April 1991). "Immunoglobulin gene transcription". Annual Review of Immunology. 9: 373–98. doi:10.1146/annurev.iy.09.040191.002105. Retrieved 20 November 2018.
  2. ↑ 2.0 2.1 Wangjie Yu and Paul E. Hardin (2006). "Circadian oscillators of Drosophila and mammals". Journal of Cell Science. 119: 4793–5. doi:10.1242/jcs.03174. Retrieved 2017-02-19.
  3. ↑ Alexandra Schoenle (August 7, 2015). Time to (dia)pause - Clock gene expression patterns in the calanoid copepod Calanus finmarchicus during early and late diapause (PDF). Leobener Str., 28358 Bremen: University Bremen. p. 49. Retrieved 28 November 2018.
  4. ↑ Nicholas R. J. Glossop, Jerry H. Houl, Hao Zheng, Fanny S. Ng, Scott M. Dudek, Paul E. Hardin (23 January 2003). "VRILLE Feeds Back to Control Circadian Transcription of Clock in the Drosophila Circadian Oscillator". Neuron. 37 (2): 249–261. Retrieved 28 November 2018.
  5. ↑ Y. Koide and T. O. Yoshida (May 1995). "Dissection of positive regulatory elements in the upstream region of the HLA–DBP1 gene". Tissue Antigens. 45 (5): 309–316. doi:10.1111/j.1399-0039.1995.tb02459.x. Retrieved 20 November 2018.
  6. ↑ RefSeq (September 2011). HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 20 November 2018.
  7. ↑ RefSeq (October 2010). HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 20 November 2018.
  8. ↑ 8.0 8.1 B. Ferstl, T. Zacher, B. Lauer, N. Blagitko-Dorfs, A. Carl and R. Wassmuth (2004). "Allele-specific quantification of HLA-DQB1 gene expression by real-time reverse transcriptase-polymerase chain reaction" (PDF). Genes and Immunity. 5: 405–416. doi:10.1038/sj.gene.6364108. Retrieved 20 November 2018.
  9. ↑ RefSeq (February 2014). NFIL3 nuclear factor, interleukin 3 regulated [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 29 November 2018.

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