BIOINFORMATICS ANALYSES TO THE ETIOLOGY OF T(1 ... - Nature

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Supplementary Table 4. Known sequence motifs


Motif Abbrev

Motif

Comments

Reference

IVR


inverted
repeats


VDJ

CACAGTG
-
N12/23
-
ACAAAAACC

V(D)J joining
signal

Lewis et al 1
997

VDJ
-
RSS7


VDJ
-
RSS9


ERO

WAWTTDDWWWDHWGWHMAWTT

Eukaryotes
replication
o
rigin
sequence

Dobbs et al 1994

Translin
-
major

Major: GCNCWSSW
-
N
0
-
2
-
GCCCWSSW

Translin
binding site

Aoki et al, 1995

Translin
-
minor

Minor: MTGCAG
-

N
0
-
4
-
GCCCWSSW

TopoII

RNYNNCNNGYNGKTNYNY

Topoisomerase
II binding site

Broeker et al
1996;

Spitzner &
Mull
er 1988;
Sander & Hsieh
1985


GTNWAYAYYNATNNG



miniSatellite

GGGCAGGARG

Human
minisatellite
core sequence

Wahls et al 1990

SatIII

YMCNTACSYCCKYYTNNC

Satellite III
core

Kas & Laemmli
1992

Chi

GCWGGWGG

Chi
-
like
sequence

Krowczynska et
al 1990

SAR
-
A1

AATAAAYAAA

Scaffold
associated
sequence
(SAR)

Gasser et al
1989; Liebich et
al 2002

SAR
-
A2

WADAWAYAWW

SAR
-
T1

TTWTWTTWTT

SAR
-
T2

TWWTDTTWWW

MAR

AATATTTTT

Matrix
attachment
sequence
(MAR)

Cockerill and
Garrad 1986;
Cockerill et al
1987

PYR

Y
12

Pyrimidine
tract

Yamaguchi et al
1985; Suzuki et
al 1993

GAGA

(GA)
6

Putative triple
helices

Caddle et al
1990; Lyamichev
et al 1986; Wells
1988

ARS
-
Sc

WTTTAYRTTTW

Autonomous
Replication
Sequence
(S.cerevisiae)

Newlon et al
1991;Stinchcomb
et al 1982

Pu
rI

GGNNGAGGGAGARRRR

Pur I binding
sequence

Bergemann &
Johnson 1992

unwind

AATATATTT

core
unwinding
element



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 re
gion 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. Intramolecula
r 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 e
lements. 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 seque
nce 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, 3
72
-
4.


(13) Lyamichev, V.I., Mirkin, S.M., Frank
-
Kamenetskii, M.D. Structures of homopurine
-
homopyrimidine 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. an
d 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
top
oisomerase 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 recombin
ation 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 i
nitiation sites on simian virus 40 DNA. Mol Cell
Biol 1985, 5, 1170
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83.