Overview

DNA serves as the substrate for three biological processes: replication, genetic recombination and gene transcription. Our group is presently concerned with genetic recombination, exploring the mechanisms that determine the location of genetic recombination sites and the complex rules of DNA binding specificity. We are 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 binding protein variants, partner protein interactions, and the influences of sex affect recombination.

Scientific report

Recombination mechanisms

In meiosis, genetic recombination serves a dual function. It assures the proper assortment of chromatids at the first meiotic division and in doing so creates the genetic diversity that makes individuals unique, providing the raw material for evolutionary processes. In mammals, including humans and mice, recombination occurs at specialized sites along chromosomes known as hotspots. As we and others have previously shown, recombination at both human and mouse hotspots is determined by the zinc finger protein, PRDM9, which binds to hotspot DNA sequences and locally trimethylates histone H3 lysine4, a chromatin activating reaction. The combined presence of PRDM9 and H3K4me3 provides the signal for translocating hotspots to the chromatid axis and recruiting the DNA topoisomerase SPO11, which creates the DNA double strand break required for the exchange of DNA sequences between chromatids that eventually give rise to genetic crossovers. Our research is focused on several aspects of PRDM9 function.

In vitro studies of DNA binding by PRDM9 expressed in E. coli are being used to identify the genome wide distribution of potential PRDM9 binding sites and to analyze the complex rules governing PRDM9s DNA binding specificity. This last has significance beyond the field of recombination biology as there are over 800 zinc finger protein genes in mammalian genomes; they serve as the most ubiquitous DNA recognition device in biology, and over half of them, like PRDM9, have 10 or more fingers. The rules governing their DNA binding specificities are poorly understood, and PRDM9 with its tens of thousands of potential binding sites in mammalian genomes, combined with the availability of multiple alleles of PRDM9, each with different binding specificities, makes this a favorable model system for understanding the rules governing this most common DNA recognition device in biological systems.

Using ChIP-SEQ to identify sites of PRDM9 dependent H3K4 trimethylation we have identified ~20,000 sites of PRDM9 action during early meiosis, showing that PRDM9 binding first serves to reorient nucleosomes locally, creating a nucleosome free zone in which double strand break formation can occur. The span of trimethylated nucleosomes then determines the migration limits of the Holliday junctions between recombining DNA strands and hence the locations of genetic crossovers. We are presently using this assay to characterize allelic variation in PRDM9 function, the competition that ensues when more than one PRDM9 allele is active in the same cell, and the influences of sex and of other chromatin modifying enzymes on initiation of recombination.

Inferring that PRDM9 cannot act in isolation, we are searching for interacting partners using both physical and genetic strategies, testing physical interactions of PRDM9 with other proteins in vitro and in vivo and using selected genetic crosses searching for modifiers of PRDM9 function.

Our long-term goals are providing a detailed understanding of how PRDM9 serves as the signaling device to initiate recombination and how the locations, relative activity and fate of recombination hotspots are determined.

Dr. Petko Petkov shares full responsibility for our research group. Other members include a bioinformatics specialist, three long serving technicians and a group of rotating postdoctoral fellows.

Several representative publications are listed below; see the Publication listings tab for the complete list.

  • Billings T, Parvanov ED, Baker CL, Walker M, Paigen K, Petkov PM. 2013. DNA binding specificities of the long zinc-finger recombination protein PRDM9. Genome Biol 14(4):R35.
  • Parvanov ED, Petkov PM, Paigen K. 2010. Prdm9 controls activation of mammalian recombination hotspots. Science 327(5967):835. PMCID: PMC2821451.
  • Paigen K, Petkov P. 2010. Mammalian recombination hotspots: properties, control and evolution. Nat Genet Rev 11:221-233 (Review).
  • Paigen K, Szatkiewicz, et al.. 2008. The recombinational anatomy of a mouse chromosome. PLoS Genet 4(7):e1000119. PMCID: PMC2440539.
  • 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.

Lab staff

Principal Investigator: Kenneth Paigen, Ph.D.
Co-Principal Investigator: Petko M. Petkov, Ph.D.
Associate Research Scientist: Emil Parvanov, Ph.D., Ruth Saxl, Ph.D.
Postdoctoral Associates: Christopher Baker, Ph.D., Pavlina Petkova, Ph.D., Natalie Powers, Ph.D.
Research Assistant III: Tim Billings, B.S., Catrina Spruce, B.S.
Laboratory Technician IV: Anita Adams, Dylan Rausch, B.S.
Bioinformatics Specialist: Michael B. Walker, B.S.
Research Administrative Assistant: Patricia Cherry

Publication listings

Baker CL, Kajita S, Walker M, Petkov PM, Paigen K. 2014. PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration. Genome Res 24(5):724-732. PMCID: PMC4009602

Billings T, Parvanov ED, Baker CL, Walker M, Paigen K, Petkov PM. 2013. DNA binding specificities of the long zinc-finger recombination protein PRDM9. Genome Biol 14(4):R35.

Paigen K, Petkov P. 2012. Meiotic DSBs and the control of mammalian recombination. Cell Res 22(12):1624-1626. PMCID: PMC3515751

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 oncogene 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 Mol 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 gametes. 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.

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