Several uses of Y chromosome testing are listed in Table 9.1. The Y chromosome has become a popular tool for tracing historical human migration patterns through male lineages (Jobling and Tyler-Smith 1995, Jobling and Tyler-Smith 2003). Anthropological, historical, and genealogical questions can be answered through Y chromosome results. For example, as will be discussed later in the chapter, Y chromosome results in 1998 linked modern day descendants of Thomas Jefferson and Eston Hemings leading to the controversial conclusion that Jefferson fathered the slave.
A detailed analysis of the 'finished' reference Y chromosome sequence was described in the 19 June 2003 issue of Nature by researchers from the Whitehead Institute and Washington University. Although it is stated as being a 'finished' sequence, Skaletsky et al. (2003) report on only 23 Mb of the roughly 50 Mb present in a typical human Y chromosome. The unreported and as yet unsequenced ~30 Mb portion is a heterochromatin region located on the long arm of the Y chromosome (Figure 9.4) that is not transcribed and is composed of highly repetitive sequences, which are impossible to sequence reliably with current technology. At 50 Mb, the Y chromosome is the third smallest human chromosome - only slightly larger than chromosome 21 (47 Mb) and chromosome 22 (49 Mb).
The non-recombining region of the human Y chromosome (NRY) comprises approximately 95% of the chromosome (Figure 9.4a). The two tips of the
Areas of use in Y chromosome testing (adapted from Butler 2003).
Forensic casework on Male-specific amplification (can avoid differential sexual assault evidence extraction to separate sperm and epithelial cells)
Analysis of multiple regions along the Y chromosome that should not be affected by deletion of the amelogenin region (see Thangaraj et al. 2002, Steinlechner et al. 2002)
Male children can be tied to fathers in motherless paternity cases or testing of male relatives if father is unavailable
Missing persons investigations
Patrilineal male relatives may be used for reference samples
Human migration and Lack of recombination enables comparison of male evolutionary studies individuals separated by large periods of time
Historical and genealogical research
Surnames usually retained by males; can make links where paper trail is limited
(a) Schematic of X and Y sex chromosomes. The two tips of the Y chromosome known as the pseudo-autosomal region 1 (PAR1) and 2 (PAR2) recombine with the tips of the X chromosome. The remaining 95% of the Y chromosome is referred to as the non-recombining portion of the Y chromosome (NRY) or male-specific region of the Y (MSY). (b) The Y chromosome is composed of both euchromatic and heterochromatic regions of which only the 23Mb of euchromatin has been sequenced.
Y chromosome, known as pseudo-autosomal regions (PAR), recombine with X chromosome homologous regions. PARI located at the tip of the short arm (Yp) of the Y chromosome is approximately 2.5 Mb in length while PAR2 at the tip of the long arm (Yq) is less than 1 Mb in size (Graves et al. 1998). Skaletsky et al. (2003) renamed the NRY the male-specific region (MSY) because of evidence of frequent gene conversion or intrachromosomal recombination. A total of 156 known transcription units including 78 protein-coding genes are present on MSY The Y chromosome is highly duplicated either with itself or with the X chromosome. Three classes of sequences have been characterized in the Y chromosome: X-transposed, X-degenerate, and ampliconic (Skaletsky et al. 2003). Two blocks on the short arm of the Y chromosome with a combined length of 3.4 Mb make up the X-transposed sequences. These sequences are 99% identical to sequences found in Xq21, contain two coding genes, and do not participate in X-Y crossing over during male meiosis. X-degenerate segments of MSY occur in eight blocks on both the short arm and the long arm of the Y chromosome with an aggregate length of 8.6 Mb. These X-degenerate segments possess up to 96% nucleotide sequence identity to their X-linked homologues. These X-homologous regions can make it challenging to design Y chromosome assays that generate male-specific DNA results. If portions of an X-homologous region of the Y chromosome are examined inadvertently, then female DNA, which possesses two X chromosomes, will be detected. Thus, when testing Y chromosome-specific assays it is important to examine them in the presence of female DNA (high levels) to verify that there is little-to-no cross talk with X-homologous regions of the Y chromosome (Hall and Ballantyne 2003a).
The ampliconic segments are composed of seven large blocks scattered across both the short arm and the long arm and covering about 10.2 Mb of the Y chromosome (Skaletsky et al. 2003). Some 60% of these ampliconic sequences have intrachromosomal identities of 99.9% or greater. In other words, it is very difficult to tell these sequences apart from one another. Another interesting feature of these ampliconic segments is that many of them are palindromes - that is, the almost exact duplicate sequences are inverted with respect to each other's sequence essentially as mirror images. Eight large palindromes collectively comprise 5.7 Mb of Yq with at least six of these palindromes containing testis genes. Genetic markers within these palindromic regions will exist as multi-copy PCR products from single primer sets. For example, the DAZ (deleted in azosper-mic) gene occurs in four copies at ~24Mb along the reference sequence (Saxena et al. 1996, Skaletsky et al. 2003).
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