Found: Missing sequence of the human Y chromosome

Sequence may contain genes controlling stature and tumor development

Scientists report on Friday in the journal Genome Research that they have successfully cloned and characterized a previously intractable DNA sequence: a 554-kilobase-pair genomic segment near the centromere of the human Y chromosome. This sequence contains eight putatively active genes that could be implicated in sex-associated height differences and gonadal tumor development.

This pericentromeric gap was one of the few holes remaining in the “finished” sequence of the human genome reported last October by the International Human Genome Sequencing Consortium. This “finished” sequence was the culmination of a 13-year effort to elucidate the order and orientation of 2.85 billion basepairs that comprise the human genome. The high-quality sequence spanned more than 99% of the euchromatic (gene-containing) portion of the genome with an accuracy of 99.999%, but despite this accomplishment, substantial sections of chromosomal sequences were still missing.

The Y chromosome, a sex chromosome that is specific to the human male, has posed a particular challenge to researchers attempting to decode its sequence. It contains an extraordinary abundance of repetitive elements, including transposons and tandem arrays of satellite sequences. This highly repetitive, transcriptionally dormant genomic landscape, termed “heterochromatin,” defines approximately two-thirds of the Y chromosome, including a section spanning the centromere. Such repetitive sequences, although not recalcitrant to cloning, are laborious to assemble, requiring meticulous analysis of complex repeated sequences.

In this case, the challenge was undertaken by a team of scientists led by Gudrun Rappold, Ph.D., Professor of Human Genetics at the University of Heidelberg in Germany. Their manuscript describing this work, published online today and in the February print issue of Genome Research (www.genome.org), presents the sequencing and analysis of 554 kilobases of previously uncharacterized sequence from the pericentromeric region of the Y chromosome. This sequence contains a 450-kilobase “euchromatic island” with eight presumably active genes flanked by repetitive satellite sequences.

To ensure that this 554-kilobase sequence was in fact missing from the “finished” human genome sequence and was not a structural polymorphism present only in a subset of males in the human population, members of Rappold’s laboratory – including Stefan Kirsch, Ph.D., lead author on the paper – tested 100 men of different ethnic origin for the presence of this 554-kilobase fragment. Indeed, the sequence was present in all 100 individuals tested, but not in any female controls, confirming that this sequence was a fundamental part of the Y chromosome.

More surprising, however, was Rappold’s finding that this “missing” sequence was not unique to the Y chromosome. Rather, this sequence exhibited between 95-99% homology to sequences on exactly half (11 of 22) of the other chromosomes in the human genome, including the pericentromeric regions of autosomes (non-sex chromosomes) 1, 2, 3, 4, 9, 10, 11, 14, 15, 16, and 22. This remarkable similarity can be attributed to segmental duplications, a phenomenon whereby large portions of the genome are copied during evolution. Segmental duplications, which emerged during the past 30 million years of primate evolution, are significantly enriched in subtelomeric and pericentromeric sequences, and now comprise approximately 5% of the human genome, were considered to be one of the biggest obstacles to finishing the human genome sequence. “The identification of these segmental duplications suggests an underrepresentation of pericentromeric regions of the acrocentric chromosomes in the current human genome sequence,” Rappold pointed out.

The current study was designed as part of a long-term effort to characterize the molecular genetic basis for Y-chromosome-linked phenotypes. Rappold and colleagues had previously physically mapped the GCY locus, which is thought to be the genetic determinant of sex-related stature differences in humans and is in close proximity to the Y centromere. In addition, the GBY, or gonadoblastoma locus, which is responsible for development of tumors associated with the undifferentiated gonad, has been genetically mapped to the region. Because the “missing” sequence described in this study contained eight putatively active genes, further functional testing of these genes may reveal insights into the genetic basis for stature and gonadoblastoma.