The subtelomeric region of the Arabidopsis thaliana chromosome
IIIR contains potential genes and duplicated fragments
from other chromosomes
Chi-Ting Wang
•
Chia-Hsing Ho
•
Ming-Jhy Hseu
•
Chung-Mong Chen
Received: 13 May 2010 / Accepted: 5 July 2010 / Published online: 22 July 2010
Ó Springer Science+Business Media B.V. 2010
Abstract The subtelomere and a portion of the associated
telomeric region (together named 3RTAS) of chromosome
IIIR from the Arabidopsis thaliana ecotypes Columbia
(Col) and Wassilewskija (Ws) were specifically amplified
by polymerase chain reaction and subsequently cloned and
sequenced. The centromere-proximal portion of 3RTAS
from both ecotypes contained two newly identified poten-
tial genes, one encoding the chloroplast luminal 19-kDa
protein precursor and the other encoding three potential
alternatively spliced CCCH-type zinc finger proteins. The
telomere-proximal portion of 3RTAS from the Col ecotype
contained short duplicated fragments derived from chro-
mosomes I, II, and III, and that from the Ws ecotype
contained a duplicated fragment derived from chromosome
V. Each duplicated fragment has diverged somewhat in
sequence from that of the ectopic template. Small patches
of homologous nucleotides were found within the flanking
sequences of both the duplicated fragments and the corre-
sponding ectopic template sequences. The structural char-
acteristics of these duplicated fragments suggest that they
are filler DNAs captured by non-homologous end joining
during double-strand break repair. Our characterization of
3RTAS not only filled up a gap in the chromosome IIIR
sequence of A. thaliana but also identified new genes with
unknown functions.
Keywords Single-telomere length analysis Á
Arabidopsis thaliana Á Genome structure Á Subtelomere Á
Telomere-associated sequence Á Gene identification
Abbreviations
DIG Digoxigenin
DSB Double-strand break
NCBI National Center for Biotechnology Information
NHEJ Non-homologous end joining
PCR Polymerase chain reaction
STELA Single-telomere length analysis
TAIR The Arabidopsis Information Resources
TAS Telomere-associated sequence
Introduction
Telomeres, the nucleoprotein complexes found at chro-
mosome ends, are essential for chromosome stability. They
prevent the ends from fusing together or being recognized
and treated as damaged DNA. Most eukaryotic telomeres
consist of short, tandemly repeated nucleotide sequences,
with one strand (5
0
? 3
0
in the direction of the chromo-
some end) being guanine rich (G-rich strand) (Zakian
1995).
In contrast to the simplicity and short lengths of telo-
meric repeats, the organization of subtelomeric sequences,
i.e., those that are proximal to the telomeres, is complex
and variable among eukaryotes (Pryde et al. 1997).
Repetitive sequences (Alkhimova et al. 2004; Chen et al.
C.-T. Wang Á C.-M. Chen (&)
Institute of Plant and Microbial Biology, Academia Sinica,
Taipei 115, Taiwan, Republic of China
e-mail: chen922@gate.sinica.edu.tw
C.-H. Ho
Institute of Biochemical Sciences, College of Life Science,
National Taiwan University, Taipei 106, Taiwan,
Republic of China
M.-J. Hseu
Institute of Biological Chemistry, Academia Sinica,
Taipei 115, Taiwan, Republic of China
123
Plant Mol Biol (2010) 74:155–166
DOI 10.1007/s11103-010-9664-x