Zinc finger gene clusters and tandem gene duplication

Zinc finger genes in mammalian genomes are frequently found to occur in clusters with cluster members appearing in a tandem array on the chromosome. It has been suggested that in situ gene duplication events are primarily responsible for the evolution of such clusters. The problem of inferring the series of duplication events responsible for producing clustered families is different from the standard phylogeny problem. In this paper we study this inference problem using a graph called Duplication Model that captures the series of duplication events while taking into account the observed order of the genes on the chromosome. We provide algorithms to reconstruct a duplication model for a given data set. We use our method to hypothesise the series of duplication events that may have produced the ZNF45 family that appears on human chromosome 19.

[1]  J R Desjarlais,et al.  Toward rules relating zinc finger protein sequences and DNA binding site preferences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Daniel H. Huson,et al.  Hybrid tree reconstruction methods , 1999, JEAL.

[3]  M. Nei,et al.  MOLECULAR POPULATION GENETICS AND EVOLUTION , 1976 .

[4]  L. Ashworth,et al.  Tandem zinc-finger gene families in mammals: insights and unanswered questions. , 1998, DNA sequence : the journal of DNA sequencing and mapping.

[5]  Daniel S. Weld.  Comparative Analysis , 1987, IJCAI.

[6]  E. Davidson,et al.  The hardwiring of development: organization and function of genomic regulatory systems. , 1997, Development.

[7]  Wen-Hsiung Li,et al.  Fundamentals of molecular evolution , 1990 .

[8]  H. Thiesen,et al.  Krüppel-associated boxes are potent transcriptional repression domains. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Gary Benson,et al.  Reconstructing the Duplication History of a Tandem Repeat , 1999, ISMB.

[10]  Tom Slezak,et al.  An integrated metric physical map of human chromosome 19 , 1995, Nature Genetics.

[11]  P F Little,et al.  High-resolution localization of 69 potential human zinc finger protein genes: a number are clustered. , 1992, Genomics.

[12]  A Klug,et al.  Repetitive zinc‐binding domains in the protein transcription factor IIIA from Xenopus oocytes. , 1985, The EMBO journal.

[13]  Robert R. Sokal,et al.  A statistical method for evaluating systematic relationships , 1958 .

[14]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[15]  N. Pavletich,et al.  Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.

[16]  E Branscomb,et al.  Comparative analysis of a conserved zinc finger gene cluster on human chromosome 19q and mouse chromosome 7. , 1996, Genomics.

[17]  Lusheng Wang,et al.  Improved Approximation Algorithms for Tree Alignment , 1996, J. Algorithms.