CENP-B box gene transcriptions: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
Line 138: Line 138:
# Ohr2ci: 5, TTCCAA at 4465, TTCCAA at 2935, TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
# Ohr2ci: 5, TTCCAA at 4465, TTCCAA at 2935, TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
# Ohr3ci: 4, TTCCAA at 3665, TTCCAA at 3592, TTCCAA at 1642, TTCCAA at 263.
# Ohr3ci: 4, TTCCAA at 3665, TTCCAA at 3592, TTCCAA at 1642, TTCCAA at 263.
# RDr4ci: 0.
# Ohr4ci: 2, TTCCAA at 2725, TTCCAA at 551.
# RDr5ci: 0.
# Ohr5ci: 0.
# RDr6ci: 0.
# Ohr6ci: 1, TTCCAA at 3062.
# RDr7ci: 0.
# Ohr7ci: 0.
# RDr8ci: 0.
# Ohr8ci: 3, TTCCAA at 3655, TTCCAA at 615, TTCCAA at 55.
# RDr9ci: 0.
# Ohr9ci: 2, TTCCAA at 2317, TTCCAA at 1694.


===Ohr arbitrary (evens) (4560-2846) UTRs===
===Ohr arbitrary (evens) (4560-2846) UTRs===
Line 150: Line 150:
# Ohr8: TTGGAA at 3165.
# Ohr8: TTGGAA at 3165.
# Ohr2ci: TTCCAA at 4465, TTCCAA at 2935.
# Ohr2ci: TTCCAA at 4465, TTCCAA at 2935.
# Ohr6ci: TTCCAA at 3062.
# Ohr8ci: TTCCAA at 3655.


===Ohr alternate (odds) (4560-2846) UTRs===
===Ohr alternate (odds) (4560-2846) UTRs===
Line 157: Line 159:
# Ohr7: TTGGAA at 2943.
# Ohr7: TTGGAA at 2943.
# Ohr3ci: TTCCAA at 3665, TTCCAA at 3592.
# Ohr3ci: TTCCAA at 3665, TTCCAA at 3592.
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===


===Ohr alternate negative direction (odds) (2846-2811) core promoters===
===Ohr alternate negative direction (odds) (2846-2811) core promoters===
Line 168: Line 168:
# Ohr3: TTGGAA at 4303.
# Ohr3: TTGGAA at 4303.


===RDr alternate positive direction (evens) (4445-4265) core promoters===
===Ohr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
 
===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===


===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
# Ohr4ci: TTCCAA at 2725.


===Ohr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===Ohr arbitrary positive direction (odds) (4265-4050) proximal promoters===


# Ohr3: TTGGAA at 4224.
# Ohr3: TTGGAA at 4224.
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===


===Ohr arbitrary negative direction (evens) (2596-1) distal promoters===
===Ohr arbitrary negative direction (evens) (2596-1) distal promoters===
Line 188: Line 183:
# Ohr0ci: TTCCAA at 1121.
# Ohr0ci: TTCCAA at 1121.
# Ohr2ci: TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
# Ohr2ci: TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
# Ohr4ci: TTCCAA at 551.
# Ohr8ci: TTCCAA at 615, TTCCAA at 55.


===Ohr alternate negative direction (odds) (2596-1) distal promoters===
===Ohr alternate negative direction (odds) (2596-1) distal promoters===
Line 196: Line 193:
# Ohr1ci: TTCCAA at 2095, TTCCAA at 295.
# Ohr1ci: TTCCAA at 2095, TTCCAA at 295.
# Ohr3ci: TTCCAA at 1642, TTCCAA at 263.
# Ohr3ci: TTCCAA at 1642, TTCCAA at 263.
# Ohr9ci: TTCCAA at 2317, TTCCAA at 1694.


===Ohr arbitrary positive direction (odds) (4050-1) distal promoters===
===Ohr arbitrary positive direction (odds) (4050-1) distal promoters===
Line 205: Line 203:
# Ohr1ci: TTCCAA at 2095, TTCCAA at 295.
# Ohr1ci: TTCCAA at 2095, TTCCAA at 295.
# Ohr3ci: TTCCAA at 3665, TTCCAA at 3592, TTCCAA at 1642, TTCCAA at 263.
# Ohr3ci: TTCCAA at 3665, TTCCAA at 3592, TTCCAA at 1642, TTCCAA at 263.
# Ohr9ci: TTCCAA at 2317, TTCCAA at 1694.


===Ohr alternate positive direction (evens) (4050-1) distal promoters===
===Ohr alternate positive direction (evens) (4050-1) distal promoters===
Line 214: Line 213:
# Ohr0ci: TTCCAA at 1121.
# Ohr0ci: TTCCAA at 1121.
# Ohr2ci: TTCCAA at 2935, TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
# Ohr2ci: TTCCAA at 2935, TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
# Ohr4ci: TTCCAA at 2725, TTCCAA at 551.
# Ohr6ci: TTCCAA at 3062.
# Ohr8ci: TTCCAA at 3655, TTCCAA at 615, TTCCAA at 55.


==Ohzeki analysis and results==
==Ohzeki analysis and results==

Revision as of 17:53, 16 September 2023

Editor-In-Chief: Henry A. Hoff

"Centromere protein B (CENP-B) specifically binds to the centromeric 17 base-pair CENP-B box DNA, which contains two CpG dinucleotides."[1]

Methylations

Main articles: Genes/Methylations and Methylations

"In eukaryotes, CpG methylation is an epigenetic DNA modification that is important for heterochromatin formation."[1]

"CENP-B preferentially binds to the unmethylated CENP-B box DNA."[1]

The "CpG methylations of the CENP-B box sequence may function in [RNA interference (RNAi)] RNAi-dependent heterochromatin formation by regulating CENP-B-binding to the CENP-B box sequence in the α-satellite repeats."[1]

Centromeres

Main article: Centromeres

"The centromere of eukaryotic chromosomes plays an essential role in the proper segregation of chromosomes at mitosis and meiosis, and has a special heterochromatin structure, which is composed of α-satellite DNA repeats and their associated proteins. The human centromere proteins A, B and C (CENP-A, CENP-B and CENP-C, respectively) are such centromere-specific DNA-binding proteins [1–7]."[1]

The centromere "has several functions, including sister chromatid adhesion, linking chromosomes to spindle microtubules, and synchronous separation of sister chromatids at anaphase onset (Choo, 1997a). These centromere functions are important for maintaining chromosomal euploidy in eukaryotic organisms."[2]

"CENP-B, a highly conserved protein in humans and mice, is specifically localized at the centromere (Earnshaw and Rothfield, 1985). This protein binds to the 17-bp motif of the CENP-B box sequence in alphoid DNA at its amino-terminal region and forms homodimers at its carboxy-terminal region (Masumoto et al., 1989; Yoda et al., 1992)."[2]

"CENP-B–CENP-B box interaction is involved in the centromere assembly mechanism."[2]

DNA binding

"Neither CENP-A nor CENP-C shows any sequence specificity in DNA binding. In contrast, CENP-B is known to specifically bind a 17 base-pair sequence (the CENP-B box), which appears in every other α-satellite repeat (171 base-pairs) in human centromeres [8–10]."[1]

Minichromosomes

The "CENP-B box is essential for the formation of functional minichromosomes [15,16]."[1]

Functional homologues

"CENP-B-like proteins have been identified in humans, and the functional redundancy of CENP-B homologues has also been found in the fission yeast Schizosaccharomyces pombe [20–22]."[1]

Consensus sequences

File:CENP-B box.png
The 17-bp motif of the CENP-B box repeats in DNA monomers. Credit: Jun-ichirou Ohzeki, Megumi Nakano, Teruaki Okada, Hiroshi Masumoto.

"The human α-satellite consensus sequence contains only three CpG sequences within its 17 base-pair sequence [23]. Interestingly, two of the three CpG sequences in the α-satellite consensus sequence are located within site 1 (5′-pTpTpCpG-3′) and site 3 (5′-pCpGpGpG-3′) of the CENP-B box (Fig. 1A;[9])."[1]

Nucleosomes

"CENP-B has the potential to induce nucleosome assembly in the vicinity of the CENP-B box sequence [14]."[1]

Human alphoid DNAs

"Human alphoid DNA contains a huge repetitive sequence, exists only at the centromeric region, and is found in all human chromosomes (Alexandrov et al., 2001). Alphoid sequences consist of tandem repeats of an AT-rich 171-bp alphoid monomer unit, and some alphoid monomers form chromosome-specific higher-order repeated units (Willard, 1985; for review see Willard and Waye, 1987). The repetitive structure of alphoid DNA can be classified into two types of repeats (Ikeno et al., 1994): units composed of several monomers (type-I alphoid repeat; Fig. 1 a, α21-I) and monomeric organization consisting of diverged alphoid monomer units (type-II alphoid repeat; Fig. 1 a, α21-II). Centromere components are mainly assembled on type-I alphoid sequences (Ikeno et al., 1994; Ando et al., 2002, Politi et al., 2002). Human artificial chromosome formation is associated only with type-I alphoid sequences (Harrington et al., 1997; Ikeno et al., 1998; Masumoto et al., 1998; Schueler et al., 2001). The CENP-B box appears only in type-I alphoid sequences (Masumoto et al., 1989; Muro et al., 1992; Haaf and Ward, 1994) of autosomes and X chromosomes."[2]

Neocentromeres "(a rare phenomenon in which centromeres form on fragmented chromosomes) have no significant centromeric DNA sequences, not even alphoid DNA (du Sart et al., 1997; Lo et al., 2001). Like the Y chromosome, neocentromere-containing chromosomes are stably maintained in cells that undergo mitosis (Tyler-Smith et al., 1999)."[2]

Ohzeki samplings

For the Basic programs (starting with SuccessablesCENPB.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesCENPB--.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesCENPB-+.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  3. positive strand in the negative direction is SuccessablesCENPB+-.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  4. positive strand in the positive direction is SuccessablesCENPB++.bas, looking for 3'-TTTCGTTGGAAGCGGGA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesCENPBc--.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  6. complement, negative strand, positive direction is SuccessablesCENPBc-+.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesCENPBc+-.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  8. complement, positive strand, positive direction is SuccessablesCENPBc++.bas, looking for 3'-AAAGCAACCTTCGCCCT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesCENPBci--.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesCENPBci-+.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesCENPBci+-.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesCENPBci++.bas, looking for 3'-TCCCGCTTCCAACGAAA-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesCENPB--.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesCENPB-+.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesCENPBi+-.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesCENPBi++.bas, looking for 3'-AGGGCGAAGGTTGCTTT-5', 0.

Increasing the number of nts from A1BG to ZNF497 from 958 to 4445 has yielded no CENP-B boxes.

Ohzeki samplings

For the Basic programs testing consensus sequence TTGGAA (starting with SuccessablesTTGGAA.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: 1, TTGGAA at 316.
  2. positive strand, negative direction: 2, TTGGAA at 2556, TTGGAA at 330.
  3. negative strand, positive direction: 0.
  4. positive strand, positive direction: 1, TTGGAA at 2581.
  5. inverse complement, negative strand, negative direction: 1, TTCCAA at 3347.
  6. inverse complement, positive strand, negative direction: 0.
  7. inverse complement, negative strand, positive direction: 0.
  8. inverse complement, positive strand, positive direction: 1, TTCCAA at 2921.

Ohzeki (4560-2846) UTRs

  1. Negative strand, negative direction: TTCCAA at 3347.

Ohzeki negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTGGAA at 316.
  2. Positive strand, negative direction: TTGGAA at 2556, TTGGAA at 330.

Ohzeki positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: TTGGAA at 2581.
  2. Positive strand, positive direction: TTCCAA at 2921.

Ohzeki random dataset samplings

  1. Ohr0: 1, TTGGAA at 3205.
  2. Ohr1: 1, TTGGAA at 2035.
  3. Ohr2: 0.
  4. Ohr3: 3, TTGGAA at 4303, TTGGAA at 4224, TTGGAA at 2844.
  5. Ohr4: 2, TTGGAA at 2262, TTGGAA at 1385.
  6. Ohr5: 3, TTGGAA at 3100, TTGGAA at 1890, TTGGAA at 26.
  7. Ohr6: 1, TTGGAA at 2491.
  8. Ohr7: 2, TTGGAA at 2943, TTGGAA at 101.
  9. Ohr8: 3, TTGGAA at 3165, TTGGAA at 2303, TTGGAA at 1837.
  10. Ohr9: 1, TTGGAA at 3838.
  11. Ohr0ci: 1, TTCCAA at 1121.
  12. Ohr1ci: 2, TTCCAA at 2095, TTCCAA at 295.
  13. Ohr2ci: 5, TTCCAA at 4465, TTCCAA at 2935, TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
  14. Ohr3ci: 4, TTCCAA at 3665, TTCCAA at 3592, TTCCAA at 1642, TTCCAA at 263.
  15. Ohr4ci: 2, TTCCAA at 2725, TTCCAA at 551.
  16. Ohr5ci: 0.
  17. Ohr6ci: 1, TTCCAA at 3062.
  18. Ohr7ci: 0.
  19. Ohr8ci: 3, TTCCAA at 3655, TTCCAA at 615, TTCCAA at 55.
  20. Ohr9ci: 2, TTCCAA at 2317, TTCCAA at 1694.

Ohr arbitrary (evens) (4560-2846) UTRs

  1. Ohr0: TTGGAA at 3205.
  2. Ohr8: TTGGAA at 3165.
  3. Ohr2ci: TTCCAA at 4465, TTCCAA at 2935.
  4. Ohr6ci: TTCCAA at 3062.
  5. Ohr8ci: TTCCAA at 3655.

Ohr alternate (odds) (4560-2846) UTRs

  1. Ohr3: TTGGAA at 4303, TTGGAA at 4224.
  2. Ohr5: TTGGAA at 3100.
  3. Ohr7: TTGGAA at 2943.
  4. Ohr3ci: TTCCAA at 3665, TTCCAA at 3592.

Ohr alternate negative direction (odds) (2846-2811) core promoters

  1. Ohr3: TTGGAA at 2844.

Ohr arbitrary positive direction (odds) (4445-4265) core promoters

  1. Ohr3: TTGGAA at 4303.

Ohr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. Ohr4ci: TTCCAA at 2725.

Ohr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. Ohr3: TTGGAA at 4224.

Ohr arbitrary negative direction (evens) (2596-1) distal promoters

  1. Ohr4: TTGGAA at 2262, TTGGAA at 1385.
  2. Ohr6: TTGGAA at 2491.
  3. Ohr8: TTGGAA at 2303, TTGGAA at 1837.
  4. Ohr0ci: TTCCAA at 1121.
  5. Ohr2ci: TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
  6. Ohr4ci: TTCCAA at 551.
  7. Ohr8ci: TTCCAA at 615, TTCCAA at 55.

Ohr alternate negative direction (odds) (2596-1) distal promoters

  1. Ohr1: TTGGAA at 2035.
  2. Ohr5: TTGGAA at 1890, TTGGAA at 26.
  3. Ohr7: TTGGAA at 101.
  4. Ohr1ci: TTCCAA at 2095, TTCCAA at 295.
  5. Ohr3ci: TTCCAA at 1642, TTCCAA at 263.
  6. Ohr9ci: TTCCAA at 2317, TTCCAA at 1694.

Ohr arbitrary positive direction (odds) (4050-1) distal promoters

  1. Ohr1: TTGGAA at 2035.
  2. Ohr3: TTGGAA at 2844.
  3. Ohr5: TTGGAA at 3100, TTGGAA at 1890, TTGGAA at 26.
  4. Ohr7: TTGGAA at 2943, TTGGAA at 101.
  5. Ohr1ci: TTCCAA at 2095, TTCCAA at 295.
  6. Ohr3ci: TTCCAA at 3665, TTCCAA at 3592, TTCCAA at 1642, TTCCAA at 263.
  7. Ohr9ci: TTCCAA at 2317, TTCCAA at 1694.

Ohr alternate positive direction (evens) (4050-1) distal promoters

  1. Ohr0: TTGGAA at 3205.
  2. Ohr4: TTGGAA at 2262, TTGGAA at 1385.
  3. Ohr6: TTGGAA at 2491.
  4. Ohr8: TTGGAA at 3165, TTGGAA at 2303, TTGGAA at 1837.
  5. Ohr0ci: TTCCAA at 1121.
  6. Ohr2ci: TTCCAA at 2935, TTCCAA at 1518, TTCCAA at 742, TTCCAA at 118.
  7. Ohr4ci: TTCCAA at 2725, TTCCAA at 551.
  8. Ohr6ci: TTCCAA at 3062.
  9. Ohr8ci: TTCCAA at 3655, TTCCAA at 615, TTCCAA at 55.

Ohzeki analysis and results

Main article: Complex locus A1BG and ZNF497 § TTGGAAs

The Centromere protein B (CENP-B) box TTTCGTTGGAAGCGGGA[2] in Table 2 number 91, order 16, is absent.

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 2 10 0.2 0.3 ± 0.1
Randoms UTR alternate negative 4 10 0.4 0.3 ± 0.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.1 ± 0
Randoms Core alternate negative 1 10 0.1 0.1 ± 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.05 ± 0.05
Randoms Core alternate positive 0 10 0 0.05 ± 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.05 ± 0.05
Randoms Proximal alternate positive 0 10 0 0.05 ± 0.05
Reals Distal negative 3 2 1.5 1.5 ± 0.5 (--1,+-2)
Randoms Distal arbitrary negative 6 10 0.6 0.5 ± 0.1
Randoms Distal alternate negative 4 10 0.4 0.5 ± 0.1
Reals Distal positive 2 2 1 1 ± 1 (-+0,++2)
Randoms Distal arbitrary positive 7 10 0.7 0.75 ± 0.05
Randoms Distal alternate positive 8 10 0.8 0.75 ± 0.05

Comparison:

The occurrences of real Ohzeki TTGGAAs are greater than the randoms. This suggests that the real Ohzeki TTGGAAs are likely active or activable.

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Yoshinori Tanaka, Hitoshi Kurumizaka, and Shigeyuki Yokoyama (January 2005). "CpG methylation of the CENP-B box reduces human CENP-B binding". The FEBS Journal. 272 (1): 282–289. doi:10.1111/j.1432-1033.2004.04406.x. PMID 15634350. Retrieved 2017-02-05.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Jun-ichirou Ohzeki, Megumi Nakano, Teruaki Okada, Hiroshi Masumoto (2 December 2002). "CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA". The Journal of Cell Biology. 159 (5): 765. doi:10.1083/jcb.200207112. Retrieved 2017-02-05.

External links

Template:Sisterlinks

Retrieved from "https://www.wikidoc.org/index.php?title=CENP-B_box_gene_transcriptions&oldid=1736106"