DNA serves as the substrate for three biological processes: replication, genetic recombination and gene transcription. Our group is presently concerned with the latter two, exploring the mechanisms that determine the location of genetic recombination sites and the extent to which the physical organization of genes along chromosomes is related to their biological function. We have now begun identifying and characterizing the components of a novel regulatory system controlling the location of recombination hotspots, the sites of genetic recombination and the extent to which recombination is regionally controlled and differs between the sexes. Analyzing the relation between gene function and location, we find that the persistence of ancient gene duplications keeping functionally related genes in proximity is the dominant factor determining genome organization.
Our lab’s focus is understanding the functional organization of mammalian genomes, using both experimental and computational approaches. There are two major areas of endeavor.Recombination hotspots
Meiotic recombination underlies all of genetics and creates the raw material of evolution. In mammals it occurs at highly localized regions, typically 1-2 kb long, called hotspots, which are surrounded by long stretches virtually devoid of recombination tens to hundreds of kilobases long. The issues we are addressing include determining the pattern of hotspot distribution along chromosomes; mapping and cloning trans-acting genes controlling hotspot location and activity; the origin of the greater recombination seen in females compared to males; sex specificity of hotspot activity; and genomic imprinting of hotspot activity.These experiments are carried out using molecular markers to map hotspots among offspring of large-scale mouse crosses of 3,000 male and 3,000 female meioses. We have so far determined the basic pattern of hotspot distribution along the entirety of Chromosomes 1 and 11 in two crosses, learned that only some hotspots are sex-specific, and found that the difference in recombination rates in the two sexes is a consequence of genetic interference that is related to a sex difference in the compaction of chromosomes at the pachytene stage of meiosis I.
We have also demonstrated the existence of a novel regulatory system controlling the activity of specific hotspots by comparing the results of genetic crosses in which the distal region of mouse Chromosome 1 is kept heterozygous for the strains C57BL6/J and CAST/EiJ while the remainder of the genome is either homozygous B6 or heterozygous B6/CAST. Some hotspots require the presence of a CAST allele elsewhere for activity, others are suppressed by the presence of distant CAST alleles, and still others are quantitatively modulated either up or down. The first control gene, which regulates occurrence of the double strand DNA break initiating recombination at a family of hotspots on Chromosome 1, has now been located on Chromosome 17 and identified as a DNA binding protein with chromatin modifying activity.
Studies of the regulatory system are concentrated on characterizing this protein and identifying the additional factors controlling hotspot suppression and quantitative modulation. Additional work is proceeding on the discovery of genomic imprinting affecting recombination and the role of telomere length in controlling recombination rates in adjacent regions.Computational analysis of the human and mouse genomes
There is substantial genomic clustering of functionally related genes in the human and other vertebrate genomes. Nearly one in five human protein coding genes occur in micro clusters composed of ancient duplications that have remained in close proximity. There is considerable variation among gene families that arose prior to the mammalian/avian divergence 310 Mya as to whether they remain in micro clusters, suggesting that persistence of at least some micro clusters reflects evolutionary selection against dispersion rather than lack of opportunity. Among sets of functionally related genes tested for clustering, many show evidence of micro clustering. However, there is little evidence of macro clustering, which results from migration together of structurally unrelated genes that participate in common functions, a phenomenon originally predicted by R.A. Fisher on theoretical grounds that epistatically interacting genes will come to lie in proximity as a means of promoting the co-inheritance of favorable allelic combinations.
These results were obtained using an adaptation of r-scan statistics, which was tested for its sensitivity to the quality of the gene sets following addition of functionally unrelated genes and subtraction of functionally related genes. Probabilities and false discovery rates were determined empirically using 10,000 sets containing equivalent numbers of randomly chosen genes. A software package that performs the necessary calculations for any set of genes and presents the results in both tabular and graphical form is available on the internet server at http://cgd.jax.org/genomic_clustering.do. The methodology is applicable to any organism for which a nearly complete list of protein coding genes and their relative genomic locations is available.
Principal Investigator: Kenneth Paigen, Ph.D.
Co-Principal Investigator: Petko M. Petkov, Ph.D.
Associate Research Scientist: Ruth Saxl, Ph.D.
Postdoctoral Associates: Christopher Baker, Ph.D., Pavlina Ivanova, Ph.D.
Research Assistant IV: Evelyn Sargent, B.S.
Research Assistant III: Tim Billings, B.S.
Laboratory Assistant III: Anita Adams
Bioinformatics Specialist: Michael B. Walker, B.S.
Research Administrative Assistant: Patricia Cherry
Walker M, King B, Paigen K. 2012. 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. PLoS One 7(4):e35274. PMCID: PMC3338513
Paigen K, Petkov P. 2010. Mammalian recombination hotspots: properties, control and evolution. Nat Genet Rev 11:221-233 (Review).
Parvanov ED, Petkov PM, Paigen K. 2010. Prdm9 controls activation of mammalian recombination hotspots. Science 327(5967):835. PMCID: PMC2821451
Harrill AH, Watkins PB, Su S, Ross PK, Harbourt DE, Stylianou IM, Boorman GA, Russo MW, Sackler RS, Harris SC, Smith PC, Tennant R, Bogue M, Paigen K, Harris C, Contractor T, Wiltshire T, Rusyn I, Threadgill DW. 2009. Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans. Genome Res 19(9):1507-1515. PMCID: PMC2752130
Ng SH, Maas SA, Petkov PM, Mills KD, Paigen K. 2009. Co-localization of somatic and meiotic double strand breaks near the Myc onocgene on mouse chromosome 15. Genes Chromosomes Cancer 48(10):925-930. PMCID: PMC2821716
Ng SH, Maderia R, Parvanov ED, Petros LM, Petkov PM, Paigen K. 2009. Parental origin of chromosomes influences crossover activity within the Kcnq1 transcriptionally imprinted domain Mus musculus. BMC Molec Biol 10:43. PMCID: PMC2689222
Parvanov ED, Ng SHS, Petkov PM, Paigen K. 2009. Trans-regulation of mouse meiotic recombination hotspots by Rcr1. PLoS Biol 7:e1000036. PMCID: PMC2642880
Ng SH, Parvanov E, Petkov PM, Paigen K. 2008. A quantitative assay for crossover and noncrossover molecular events at individual recombination hotspots in both male and female gamets. Genomics 92:204-209. PMCID: PMC2610674
Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng S, Graber JH, Broman KW, Petkov PM. 2008. The recombinational anatomy of a mouse chromosome. PLoS Genet 4(7):e1000119. PMCID: PMC2440539
Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K. 2007. Evidence of large-scale functional organization of mammalian chromosomes. PLoS Biol 5(5):2127.
Petkov PM, Broman KW, Szatkiewicz JP, Paigen K. 2007. Crossover interference underlies sex differences in recombination rates. Trend Genet 23(11): doi:10.1016/j.tig.2007.08.015.
Graber JH, Churchill GA, DiPetrillo KJ, King BL, Petkov PM, Paigen K. 2006. Patterns and mechanisms of genome organization in the mouse. J Exp Zool 305A:683-688.
Petkov P, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen. 2005. Evidence of a large scale functional organization of mammalian chromosomes. PLoS Genet 1(3):312-322.
Kelmenson PM, Petkov P, Wang X, Higgins DC, Paigen BJ, Paigen K. 2005. A torrid zone on mouse chromosome 1 containing a cluster of recombinational hotspots. Genetics 169:833-841.
Paigen K. 2004. Understanding the human condition: experimental strategies in mammalian genetics. ILAR J 43: 123-135.
Paigen K. 2003. One hundred years of mouse genetics: An intellectual history. II. The molecular revolution (1981-2002). Genetics 163:1227-1235.
Paigen K. 2003. One hundred years of mouse genetics: An intellectual history. I. The classical period (1902-1980). Genetics 163:1-7.