Y Chromosome Genome Project

Y Chromosome
Image source: Barbara Trask and Cynthia Friedman, Fred Hutchinton Cancer Research Center

About the Project

The BCM-HGSC is sequencing several mammalian Y chromosomes in collaboration with the Page Laboratory to study Y linked traits. The Y chromosome genes have been linked to spermatogenesis, cancer, developmental disorders, graft versus host disease, locomotion, high blood pressure, and the stress response. Often the first phase of a genome sequencing project does not adequately address the Y chromosome. This project specifically targets mammalian Y chromosomes for additional sequencing and sequence finishing.

The white paper describing these projects can be found at the Page Laboratory.

The mapping for these projects is provided by the Page Laboratory. Fingerprint contigs for the BAC libraries are developed by the Michael Smith Genome Sciences Centre. Individual BACs are sequenced and submitted to GenBank. 

Project Progress
Bos taurus (bull) Y chromosome The source of the CH240 BAC library DNA was Hereford bull L1 Domino 99375, registration number 41170496. Dr. Michael MacNeil's laboratory, USDA-ARS, Miles City, MT provided the blood. L1 Domino 99375 is the sire of the cow L1 Dominette 01449, American Hereford Association registration number 42190680, the donor for the WGS library for the genome sequencing.
Rattus norvegicus (rat) Y chromosome The Brown Norway rat that was sequenced for the genome project has a particularly large Y chromosome, most likely due to the presence of expanded repetitive sequences. For this reason, the Y chromosome is being sequenced using a different rat strain. The SRY strain was chosen due to the interest in the Y linked hypertensive phenotype.
Macaca mulatta (rhesus monkey) Y chromosome The rhesus monkey genome project is a collaboration with the Washington University in St. Louis School of Medicine Genome Sequencing Center. BAC sequences are being finished at both institutions.

Genomic Resources

 

Related Publications

Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho T-J, et al. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014 ;508(7497):494-9.

Midorikawa Y, Takayama T, Yamamoto S, Ueda H, Sonoda K, Takane K, et al. Genome-wide analysis of stepwise hepatocarcinogenesis using next generation sequencer. In AACR 104th Annual Meeting 2013. Washington, DC: Cancer Res; 2013.

Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, et al. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature. 2012 ;483(7387):82-6.

Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, et al. European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. Eur J Hum Genet. 2010 ;18(3):309-16.

Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, et al. The DNA sequence of the human X chromosome. Nature. 2005 ;434(7031):325-37.

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier LD, Brown LG, et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003 ;423(6942):825-37.