Palindromes on the human X chromosome : testis-biased transcription, gene conversion and evolution

Recent genomic studies of the Y chromosome revealed massive, testis-specific palindromes that span 30% of the chromosome and are subject to gene conversion. We conducted studies to determine whether similar palindromes exist on the human X chromosome and, if they exist, to what degree they share the features of the Y chromosome palindromes. We performed an electronic search for palindromes on the human X chromosome resulting in the identification of 24 palindromes comprising 1.8% of the chromosome. The palindromes consist of sequences 9.5 to more than 140 kilobases long duplicated in inverted orientation separated by a 0.2 to 164 kilobase spacer. The paired palindrome arms display greater than 99 percent nucleotide identity. We determined the palindrome associated gene content and experimentally evaluated their transcription range. All the genes residing in palindrome arms and spacers are transcribed in the testis, with almost two thirds predominantly testis-transcribed. To determine if the testis-transcription bias is due to a chromosome-wide enrichment for testis-transcribed genes, we used publicly available expression data to compare the ratio of palindrome-associated X-linked testis genes with non-palindrome-associated X-linked testis genes. We confirmed that the proportion of testis genes in palindromes is significantly different than that of testis genes on the entire X chromosome. We pursued a comparative sequencing strategy to trace the evolution of the X chromosome palindromes. We sequenced bacterial artificial chromosomes (BACs) from chimpanzee, orangutan and rhesus monkey genomic libraries containing sequence orthologous to several of the human X chromosome palindromes. We found some of the palindromes conserved in all species

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Saionz, Jennifer R., 1976-

Advisor dc:contributor.advisor

• David C. Page.

• Biology.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/35754

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/35754