Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation

Abstract

Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1–4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.

Molecular cytogenetics and St-chromosome-specific molecular markers development of novel stripe rust resistant wheat–Thinopyrum intermedium as well as wheat–Thinopyrum ponticum substitution lines

“…Because of no severe effects on viability of ES-25, the subtelomeric region elimination presumably contributed to genome diversity [48].…”

Subtelomeric Chromatin in the Fission Yeast S. pombe

“…Chr I and II have subtelomeric regions adjacent to the telomere repeat sequences at both ends; Chr III has rDNA repeats, which code for ribosomal RNA, replacing the subtelomeric regions in the 972h − strain. Some strains possess partial subtelomeric sequences adjacent to the telomeres of Chr III [5,6]. The nuclear envelope (NE) remains intact throughout the cell cycle (closed mitosis) unlike higher animals and plants, in which the NE disassembles during mitosis (open mitosis).…”

“…They can be separated into two 50 kb domains: the subtelomere homologous domains (SH) which lie adjacent to the telomeric repeats, and the subtelomere unique domains (SU or ST, which we will hereon refer to as ST), which lie internal to the SH domains. Recent work from the Kanoh lab has revealed the exact sequences of the elusive portions of subtelomeric domains [6].…”

“…Even though the S. pombe genome sequence was published in 2002 [2], there remained uncertainty and gaps within the SH sequence assemblies which has slowed research on these domains. Many groups have contributed to the elucidation of chromosomal arrangement of subtelomeric sequences, including sequencing of a telomere plasmid library [3], sequence identification and mapping [57,58], and the heroic efforts of the Kanoh group who finally completed the subtelomeric sequence assemblies by mapping using their comprehensive series of strains bearing deletions of subtelomeric sequences [5,6]. These efforts have also highlighted the propensity for accumulation of mutations within SH sequences and suggest that these domains are a rich source of genetic variation.…”

“…TAS sequences are highly complex mosaic structures consisting of elements shared between the four subtelomeres but in mixed order and exhibiting nucleotide changes within the motifs. These characteristics indicate that these domains are hot spots for recombination and rearrangement [6]. TAS sequences are unusual with strong enrichment for poly [dA:dT] tracts, which have been shown to preclude nucleosome assembly [54].…”