What is found at the end of a chromosome?

The ends of chromosomes are composed of telomeres and subtelomeres, they are essential structures for genome integrity. However, they are very difficult to study because they are made of repeated DNA sequences. This work, conducted by Zhou Xu's team (Computational and Quantitative Biology Laboratory) was published in the journal Nucleic Acids Research. In this paper, the researchers use long-read sequencing data to comprehensively map subtelomeres in the green alga Chlamydomonas reinhardtii and identify specific repeated elements, providing information about the function and evolution of these regions.

For eukaryotes, proper stabilization of chromosome ends is crucial. Because they are linear, the machinery that carries out their replication cannot reach the end of the chromosome and they tend to get shorter with each division of the cell. A dedicated reverse transcriptase, telomerase, is able to add repeats of a short sequence (e.g. TTAGGG in humans) called telomeres to the end of the chromosome, which are recognized by specialized proteins. Together they form a protective structure that prevents the end of the chromosome from being recognized as a DNA break.

But telomeres are not the only important structure at the end of the chromosome. The adjacent region, called the subtelomere, is also involved in genome integrity and evolution. Subtelomeres are often made up of repeated sequences that include transposons, gene families involved in adaptation to the environment, satellite sequences or ribosomal DNA. Because of their length and complex repetitive structure, they are generally difficult to sequence and assemble correctly as part of the complete genome. This feat has been achieved in humans only very recently, thanks to the development of sequencing methods that can read a DNA strand over a very long length.

Using data from this type of sequencing, a group of French and Scottish researchers was able to map and analyze in detail the subtelomeres of the 17 chromosomes of Chlamydomonas reinhardtii. This small unicellular green alga, a cousin of plants, is used as an experimental model in many studies. Its telomeres, usually a few hundred nucleotides long, consist of a TTTTAGGG repeat. At 31 of the 34 chromosomal ends, downstream of the telomere, there are no transposon, but a specific repeat that the authors called Sultan, for "SUbtelomeric Long TANdem repeat". It is about 850 nucleotides long and repeated between 2 and 46 times per subtelomere, and is present exclusively in these regions. Downstream, there is usually a promoter directing the transcription of a long non-coding RNA toward the centromere, followed by either transposons or expressed genes. In some cases, the researchers have identified signatures of repair events at the subtelomere level, or even the appearance between the telomere and the Sultans of block of other complex repetitive sequences. They called them Subtile ("SUBTelomeric repeats of Intermediate Length") and Suber ("SUBtelomeric Extra-long Repeat"). These three repeats (Sultan, Subtile and Suber) are associated with marks of heterochromatin, a condensed DNA structure that potentially plays a role in protecting chromosome ends.

Further investigating the origin and diversity of these repeats, they observed that each subtelomere carries a specific signature in its Sultans, indicating that the repeat is locally propagated by tandem duplications. Subtiles and Subers propagate in the same way, although it also seems clear that all of these repeats can jump from one chromosome to another, explaining their presence at almost all ends except the three that consist of ribosomal DNA repeats. The organization of subtelomeric repeat sequences is thus the result of a complex and dynamic history, whose mechanisms and evolutionary constraints remain to be explored.

What about other algae? The researchers examined a range of more or less closely related species, and to their surprise they observed that while the repetitive nature of subtelomeres seems conserved, each species uses one (or more) repeats of its own. Could the subtelomere play a role in speciation? This is what genomic sequencing of various wild isolates of Chlamydomonas reinhardtii should soon reveal.

Figure: Map of the ends of the 17 chromosomes in the model microalga C. reinhardtii, established by long-read sequencing and careful assembly. Telomeric repeats (TTTTAGGG/CCCTAAAA, in black) systematically cap each chromosome arm ('_L' for the left,'_R' for the right). Downstream, the "subtelomeres" are mostly made up of repeats of a new element specific to each arm, Sultan (in green, classes A, B and C) and, more rarely, also of other repeats, Subtile and Suber (in light pink, class C). Three subtelomeres consist of repeats encoding ribosome RNA subunits (rDNA, in purple), covering several million base pairs at the right end of chromosomes 8 and 14. The symbol'//' indicates a truncated representation relative to the scale, shown in thousands of base pairs (kb).


Team lead by Zhou Xu (Biology Computational and Quantitative) : Telomere and Genome Stability

F. Chaux-JukicS. O’Donnell, R. J. Craig, S. Eberhard, O. Vallon, et Z. Xu, « Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii », Nucleic Acids Research, vol. 49, no 13, p. 7571?7587, juill. 2021, doi: 10.1093/nar/gkab534.