Gene transcriptions/Boxes/CENP-Bs

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

Methylations

Main resources: Genes/Methylations and Methylations

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

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

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."

Centromeres

Main resource: 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]."

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."

"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)."

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

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]."

Minichromosomes

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

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]."

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])."

Nucleosomes

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

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."

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)."

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.

See also

• Gene transcriptions/A1BG/Core promoters