Human genomic Z-DNA segments probed by the Zα domain of ADAR1

Double-stranded DNA is a dynamic molecule that adopts different secondary structures. Experimental evidence indicates Z-DNA plays roles in DNA transactions such as transcription, chromatin remodeling and recombination. Furthermore, our computational analysis revealed that sequences with high Z-DNA forming potential at moderate levels of DNA supercoiling are enriched in human promoter regions. However, the actual distribution of Z-DNA segments in genomes of mammalian cells has been elusive due to the unstable nature of Z-DNA and lack of specific probes. Here we present a first human genome map of most stable Z-DNA segments obtained with A549 tumor cells. We used the Z-DNA binding domain, Zα, of the RNA editing enzyme ADAR1 as probe in conjunction with a novel chromatin affinity precipitation strategy. By applying stringent selection criteria, we identified 186 genomic Z-DNA hotspots. Interestingly, 46 hotspots were located in centromeres of 13 human chromosomes. There was a very strong correlation between these hotspots and high densities of single nucleotide polymorphism. Our study indicates that genetic instability and rapid evolution of human centromeres might, at least in part, be driven by Z-DNA segments. Contrary to in silico predictions, however, we found that only two of the 186 hotspots were located in promoter regions.

[1]  A. Rich,et al.  The Zalpha domain from human ADAR1 binds to the Z-DNA conformer of many different sequences. , 1998, Nucleic acids research.

[2]  David N Cooper,et al.  Breakpoints of gross deletions coincide with non-B DNA conformations. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[3]  P. S. Ho,et al.  Phylogenomic analysis of the emergence of GC-rich transcription elements , 2007, Proceedings of the National Academy of Sciences.

[4]  S. Wölfl,et al.  Transcription of human c‐myc in permeabilized nuclei is associated with formation of Z‐DNA in three discrete regions of the gene. , 1992, The EMBO journal.

[5]  Martha Kirby,et al.  Regulation of CSF1 Promoter by the SWI/SNF-like BAF Complex , 2001, Cell.

[6]  Alexander Rich,et al.  Z-DNA: the long road to biological function , 2003, Nature Reviews Genetics.

[7]  A. Rich,et al.  Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases , 2005, Nature.

[8]  Guliang Wang,et al.  Z-DNA-forming sequences generate large-scale deletions in mammalian cells. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Minou Bina,et al.  The flexibility and topology of simian virus 40 DNA in minichromosomes. , 1987, Nucleic acids research.

[10]  I. Mian,et al.  A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  W P Wahls,et al.  The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture , 1990, Molecular and cellular biology.

[12]  G. Schroth,et al.  Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. , 1992, The Journal of biological chemistry.

[13]  C. Tyler-Smith,et al.  Mapping of a human centromere onto the DNA by topoisomerase II cleavage , 2000, EMBO reports.

[14]  A. Rich,et al.  Structure–function analysis of the Z‐DNA‐binding domain Zα of dsRNA adenosine deaminase type I reveals similarity to the (α + β) family of helix–turn–helix proteins , 1999, The EMBO journal.

[15]  Guliang Wang,et al.  Non-B DNA structure-induced genetic instability. , 2006, Mutation research.

[16]  P. S. Kim,et al.  Construction of a Z-DNA-specific restriction endonuclease. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Michael S. Strano,et al.  Optical Detection of DNA Conformational Polymorphism on Single-Walled Carbon Nanotubes , 2006, Science.

[18]  A. Rich,et al.  Z-DNA-binding proteins can act as potent effectors of gene expression in vivo , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  A. Rich,et al.  Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. , 1999, Science.

[20]  K. Choo,et al.  A rapid method of genomic array analysis of scaffold/matrix attachment regions (S/MARs) identifies a 2.5-Mb region of enhanced scaffold/matrix attachment at a human neocentromere. , 2003, Genome research.

[21]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[22]  H R Drew,et al.  The anatomy of A-, B-, and Z-DNA. , 1982, Science.

[23]  K. Zhao,et al.  Cooperative Activity of BRG1 and Z-DNA Formation in Chromatin Remodeling , 2006, Molecular and Cellular Biology.

[24]  D. Levens,et al.  The functional response of upstream DNA to dynamic supercoiling in vivo , 2008, Nature Structural &Molecular Biology.

[25]  Virgil L. Woods,et al.  An epigenetic mark generated by the incorporation of CENP-A into centromeric nucleosomes , 2007, Proceedings of the National Academy of Sciences.

[26]  Alexander Rich,et al.  Characterization of Z-DNA as a nucleosome-boundary element in yeast Saccharomyces cerevisiae , 2007, Proceedings of the National Academy of Sciences.

[27]  L. Clarke,et al.  A novel cis-acting centromeric DNA element affects S. pombe centromeric chromatin structure at a distance , 1995, The Journal of cell biology.

[28]  S. Zimmerman.  The three-dimensional structure of DNA. , 1982, Annual review of biochemistry.

[29]  P. Dröge.  Protein tracking‐induced supercoiling of DNA: A tool to regulate DNA transactions in vivo? , 1994, BioEssays : news and reviews in molecular, cellular and developmental biology.

[30]  S. Henikoff,et al.  The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA , 2001, Science.

[31]  D. Gurley,et al.  Cloning of the cDNA and gene of mouse mast cell protease-6. Transcription by progenitor mast cells and mast cells of the connective tissue subclass. , 1991, The Journal of biological chemistry.

[32]  Wolfgang Stephan,et al.  The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.

[33]  Gary H. Karpen,et al.  Determining centromere identity: cyclical stories and forking paths , 2001, Nature Reviews Genetics.

[34]  A. Rich,et al.  A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Z. Wang,et al.  Differential control of transcription‐induced and overall DNA supercoiling by eukaryotic topoisomerases in vitro. , 1996, The EMBO journal.

[36]  P. Champ,et al.  Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. , 2004, Nucleic acids research.

[37]  G. Felsenfeld,et al.  Effect of Z-DNA on nucleosome placement. , 1987, Journal of molecular biology.

[38]  S. Wölfl,et al.  Transcription of the human corticotropin-releasing hormone gene in NPLC cells is correlated with Z-DNA formation. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[39]  R. Sinden.  DNA Structure and Function , 1994 .