Ken Paigen

Functional Clustering in the Mammalian Genome


The manner in which the location and arrangement of genes along chromosomes relates to their biological functions and to other features of genome organization remains a largely open question. Acquiring experimental tools for mapping these relationships and determining the extent to which functionally related genes are in physical proximity are matters of considerable importance for efforts to identify genetic factors important in human health and disease, as well as for enhancing our understanding of the evolutionary processes underlying genome organization. We are developing tools to address these problems.

An important aspect of this project is to integrate information coming from other Center projects. We are working with Drs. Ron Korstanje and Karen Svenson, for example, to evaluate whether there is genomic clustering among the quantitative trait loci determining various phenotypic traits. We believe this is especially important as evolution selects directly on phenotypes and only indirectly on their underlying molecular biology. We are also working with Dr. Petkov to evaluate the relationship between the genomic organization of recombination hotspots and chromosome features such as gene density, repeat elements, domains of linkage disequilibrium, GC content and purine/pyrimidine strand bias.

Center related publications

Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species
Walker MB, King BL, Paigen K.
PLoS One. 2012;7(4):e35274. PMCID: PMC3338513 [ Full Text ] [ datasets ]

Mammalian recombination hot spots: properties, control and evolution
Paigen K, Petkov P.
Nat Rev Genet. 2010 Mar;11(3):221-33.

Prdm9 controls activation of mammalian recombination hotspots
Parvanov ED, Petkov PM, Paigen K.
Science. 2010 Feb 12;327(5967):835. PMCID: PMC2821451. [ Full Text ]

Parental origin of chromosomes influences crossover activity within the Kcnq1 transcriptionally imprinted domain of Mus musculus
Ng SH, Madeira R, Parvanov ED, Petros LM, Petkov PM, Paigen K.
BMC Mol Biol. 2009 May 13;10:43. PMCID: PMC2689222. [ Full Text ]

Trans-regulation of mouse meiotic recombination hotspots by Rcr1
Parvanov ED, Ng SHS, Petkov PM, Paigen K.
PLoS Biol. 2009 Feb 17;7(2):e36. PMCID: PMC2642880. [ Full Text ]

A quantitative assay for crossover and noncrossover molecular events at individual recombination hotspots in both male and female gametes
Ng SH, Parvanov E, Petkov PM, Paigen K.
Genomics. 2008 Oct;92(4):204-9. PMCID: PMC2610674 [ Full Text ]

The recombinational anatomy of a mouse chromosome
Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SH, Graber JH, Broman KW, Petkov PM.
PLoS Genet. 2008 Jul 11;4(7):e1000119. PMCID: PMC2440539 [ Full Text ]

Crossover interference underlies sex differences in recombination rates
Petkov PM, Broman KW, Szatkiewicz JP, Paigen K.
Trends Genet. 2007 Nov;23(11):539-42.

Evidence of a large-scale functional organization of mammalian chromosomes
Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K.
PLoS Biol. 2007 May;5(5):e127; author reply e128. PMCID: PMC1868061 [ Full Text ]

Patterns and mechanisms of genome organization in the mouse
Graber JH, Churchill GA, Dipetrillo KJ, King BL, Petkov PM, Paigen K.
J Exp Zoolog A Comp Exp Biol. 2006 Sep 1;305(9):683-8.


Ken Paigen