Supplementary Table 4. Known sequence motifs
Motif Abbrev
Motif
IVR
VDJ
CACAGTG-N12/23-ACAAAAACC
VDJ-RSS7
Comments
inverted
repeats
V(D)J joining
signal
Reference
Lewis et al 1997
VDJ-RSS9
ERO
WAWTTDDWWWDHWGWHMAWTT
Translin-major
Major: GCNCWSSW-N0-2-GCCCWSSW
Translin-minor
Minor: MTGCAG- N0-4-GCCCWSSW
TopoII
RNYNNCNNGYNGKTNYNY
GTNWAYAYYNATNNG
miniSatellite
GGGCAGGARG
SatIII
YMCNTACSYCCKYYTNNC
Chi
GCWGGWGG
SAR-A1
AATAAAYAAA
SAR-A2
WADAWAYAWW
SAR-T1
TTWTWTTWTT
SAR-T2
TWWTDTTWWW
MAR
AATATTTTT
PYR
Y12
GAGA
(GA)6
Eukaryotes
replication
origin
sequence
Translin
binding site
Dobbs et al 1994
Topoisomerase
II binding site
Broeker et al
1996;
Spitzner &
Muller 1988;
Sander & Hsieh
1985
Human
minisatellite
core sequence
Satellite III
core
Chi-like
sequence
Scaffold
associated
sequence
(SAR)
Wahls et al 1990
Matrix
attachment
sequence
(MAR)
Pyrimidine
tract
Cockerill and
Garrad 1986;
Cockerill et al
1987
Yamaguchi et al
1985; Suzuki et
al 1993
Putative triple
helices
Caddle et al
1990; Lyamichev
et al 1986; Wells
1988
Aoki et al, 1995
Kas & Laemmli
1992
Krowczynska et
al 1990
Gasser et al
1989; Liebich et
al 2002
ARS-Sc
WTTTAYRTTTW
PurI
GGNNGAGGGAGARRRR
unwind
AATATATTT
Autonomous
Replication
Sequence
(S.cerevisiae)
Pur I binding
sequence
core
unwinding
element
Newlon et al
1991;Stinchcomb
et al 1982
Bergemann &
Johnson 1992
References
(1) Aoki, K., Suzuki, K., Sugano, T., Tasaka, T., Nakahara, K., Kuge, O., Omori, A. and Kasai,
M. A novel gene, Translin, encodes a recombination hotspot binding protein associated with
chromosomal translocations. Nat Genet 1995, 10, 167-74.
(2) Bergemann, A.D. and Johnson, E.M. The HeLa Pur factor binds single-stranded DNA at a
specific element conserved in gene flanking regions and origins of DNA replication. Mol Cell
Biol 1992, 12, 1257-65.
(3) Broeker, P.L., Super, H.G., Thirman, M.J., Pomykala, H., Yonebayashi, Y., Tanabe, S.,
Zeleznik-Le, N. and Rowley, J.D. Distribution of 11q23 breakpoints within the MLL breakpoint
cluster region in de novo acute leukemia and in treatment-related acute myeloid leukemia:
correlation with scaffold attachment regions and topoisomerase II consensus binding sites. Blood
1996, 87, 1912-22.
(4) Caddle, M.S., Lussier, R.H., Heintz, N.H. Intramolecular DNA triplexes, bent DNA and DNA
unwinding elements in the initiation region of an amplified dihydrofolate reductase replicon. J
Mol Biol 1990, 211, 19-33.
(5) Cockerill, P.N. and Garrard, W.T. Chromosomal loop anchorage of the kappa
immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites.
Cell 1986, 44, 273-82.
(6) Cockerill, P.N., Yuen, M.H. and Garrard, W.T. The enhancer of the immunoglobulin heavy
chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem 1987,
262, 5394-7.
(7) Dobbs, D.L., Shaiu, W.L. and Benbow, R.M. Modular sequence elements associated with
origin regions in eukaryotic chromosomal DNA. Nucleic Acids Res 1994, 22, 2479-89.
(8) Gasser, S.M., Amati, B.B., Cardenas, M.E. and Hofmann, J.F. Studies on scaffold attachment
sites and their relation to genome function. Int Rev Cytol 1989, 119, 57-96.
(9) Kas, E. and Laemmli, U.K. In vivo topoisomerase II cleavage of the Drosophila histone and
satellite III repeats: DNA sequence and structural characteristics. EMBO J 1992, 11, 705-16.
(10) Krowczynska, A.M., Rudders, R.A., Krontiris, T.G. The human minisatellite consensus at
breakpoints of oncogene translocations. Nucleic Acids Res 1990, 18, 1121-7.
(11) Lewis, S.M., Agard, E, Suh, S. and Czyzyk, L. Cryptic signals and the fidelity of V(D)J
joining. Mol Cell Biol 1997, 17, 3125-36.
(12) Liebich, I., Bode, J., Frisch, M. and Wingender, E. S/MARt DB: a database on
scaffold/matrix attached regions. Nucleic Acids Res 2002, 30, 372-4.
(13) Lyamichev, V.I., Mirkin, S.M., Frank-Kamenetskii, M.D. Structures of homopurinehomopyrimidine tract in superhelical DNA. J Biomol Struct Dyn 1986, 3, 667-9.
(14) Newlon, C.S., Lipchitz, L.R., Collins, I., Deshpande, A., Devenish, R.J., Green, R.P., Klein,
H.L., Palzkill, T.G., Ren, R.B., Synn, S. and et al. Analysis of a circular derivative of
Saccharomyces cerevisiae chromosome III: a physical map and identification and location of
ARS elements. Genetics 1991, 129, 343-57.
(15) Sander, M. and Hsieh, T.S. Drosophila topoisomerase II double-strand DNA cleavage:
analysis of DNA sequence homology at the cleavage site. Nucleic Acids Res 1985, 13, 1057-72.
(16) Spitzner, J.R. and Muller, M.T. A consensus sequence for cleavage by vertebrate DNA
topoisomerase II. Nucleic Acids Res 1988, 16, 5533-56.
(17) Stinchcomb, D.T., Mann, C. and Davis, R.W. Centromeric DNA from Saccharomyces
cerevisiae. J Mol Biol 1982, 158, 157-90.
(18) Suzuki, M., Savoysky, E., Izuta, S., Tatebe, M., Okajima, T. and Yoshida, S. RNA priming
coupled with DNA synthesis on natural template by calf thymus DNA polymerase alpha-primase.
Biochemistry 1993, 32, 12782-92.
(19) Wahls, W.P., Wallace, L.J., Moore, P.D. Hypervariable minisatellite DNA is a hotspot for
homologous recombination in human cells. Cell 1990, 60, 95-103.
(20) Wells, R.D. Unusual DNA structures. J Biol Chem 1988, 263, 1095-8.
(21) Yamaguchi, M., Hendrickson, E.A. and DePamphilis, M.L. DNA primase-DNA polymerase
alpha from simian cells: sequence specificity of initiation sites on simian virus 40 DNA. Mol Cell
Biol 1985, 5, 1170-83.