Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription.

G-quadruplex or G4 DNA, a four-stranded DNA structure formed in G-rich sequences, has been hypothesized to be a structural motif involved in gene regulation. In this study, we examined the regulatory role of potential G4 DNA motifs (PG4Ms) located in the putative transcriptional regulatory region (TRR, -500 to +500) of genes across the human genome. We found that PG4Ms in the 500-bp region downstream of the annotated transcription start site (TSS; PG4M(D500)) are associated with gene expression. Generally, PG4M(D500)-positive genes are expressed at higher levels than PG4M(D500)-negative genes, and an increased number of PG4M(D500) provides a cumulative effect. This observation was validated by controlling for attributes, including gene family, function, and promoter similarity. We also observed an asymmetric pattern of PG4M(D500) distribution between strands, whereby the frequency of PG4M(D500) in the coding strand is generally higher than that in the template strand. Further analysis showed that the presence of PG4M(D500) and its strand asymmetry are associated with significant enrichment of RNAP II at the putative TRR. On the basis of these results, we propose a model of G4 DNA-mediated stimulation of transcription with the hypothesis that PG4M(D500) contributes to gene transcription by maintaining the DNA in an open conformation, while the asymmetric distribution of PG4M(D500) considerably reduces the probability of blocking the progression of the RNA polymerase complex on the template strand. Our findings provide a comprehensive view of the regulatory function of G4 DNA in gene transcription.

[1]  R. Wells,et al.  Unusual DNA Structures , 2011, Springer New York.

[2]  S. Darst,et al.  A Structural Model of Transcription Elongation , 2000 .

[3]  F. Alt,et al.  Class-switch recombination: interplay of transcription, DNA deamination and DNA repair , 2004, Nature Reviews Immunology.

[4]  Yan Xu,et al.  Formation of the G-quadruplex and i-motif structures in retinoblastoma susceptibility genes (Rb) , 2006, Nucleic acids research.

[5]  Michael Fry,et al.  Tetraplex DNA and its interacting proteins. , 2007, Frontiers in bioscience : a journal and virtual library.

[6]  C. D. Lewis,et al.  An erythrocyte-specific protein that binds to the poly(dG) region of the chicken beta-globin gene promoter. , 1988, Genes & development.

[7]  Daekyu Sun,et al.  Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1alpha promoter. , 2005, Biochemistry.

[8]  Sarah W. Burge,et al.  Quadruplex DNA: sequence, topology and structure , 2006, Nucleic acids research.

[9]  C. D. Lewis,et al.  Properties of BGP1, a poly(dG)-binding protein from chicken erythrocytes. , 1990, Nucleic acids research.

[10]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[11]  C. Turro,et al.  Stabilization of duplex DNA structure and suppression of transcription in vitro by bis(quinone diimine) complexes of rhodium(III) and ruthenium(II). , 2003, Inorganic chemistry.

[12]  T. Simonsson,et al.  G-Quadruplex DNA Structures Variations on a Theme , 2001, Biological chemistry.

[13]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[14]  R. Shafer,et al.  Biological aspects of DNA/RNA quadruplexes , 2000, Biopolymers.

[15]  Stephen Neidle,et al.  Putative DNA quadruplex formation within the human c-kit oncogene. , 2005, Journal of the American Chemical Society.

[16]  L. Hurley,et al.  G-quadruplex DNA: a potential target for anti-cancer drug design. , 2000, Trends in pharmacological sciences.

[17]  Steven Hahn,et al.  A transcription reinitiation intermediate that is stabilized by activator , 2000, Nature.

[18]  S. Mirkin,et al.  Transcriptionally driven cruciform formation in vivo. , 1992, Nucleic acids research.

[19]  D. Cosman,et al.  The leukocyte immunoglobulin‐like receptors (LIRs): a new family of immune regulators , 1999, Journal of leukocyte biology.

[20]  Jean-Louis Mergny,et al.  Kinetics of tetramolecular quadruplexes , 2005, Nucleic acids research.

[21]  Paul T. Groth,et al.  The ENCODE (ENCyclopedia Of DNA Elements) Project , 2004, Science.

[22]  E. Birney,et al.  EnsMart: a generic system for fast and flexible access to biological data. , 2003, Genome research.

[23]  S. Greive,et al.  Thinking quantitatively about transcriptional regulation , 2005, Nature Reviews Molecular Cell Biology.

[24]  N. Maizels,et al.  Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. , 2004, Genes & development.

[25]  W. Rutter,et al.  Pur-1, a zinc-finger protein that binds to purine-rich sequences, transactivates an insulin promoter in heterologous cells. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[26]  D. Davies,et al.  Helix formation by guanylic acid. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Mitali Mukerji,et al.  Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. , 2006, Genome research.

[28]  N. Maizels,et al.  High Affinity Interactions of Nucleolin with G-G-paired rDNA* , 1999, The Journal of Biological Chemistry.

[29]  S. Cogoi,et al.  G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription , 2006, Nucleic acids research.

[30]  S. Neidle,et al.  Highly prevalent putative quadruplex sequence motifs in human DNA , 2005, Nucleic acids research.

[31]  R. Moyzis,et al.  Structure-function correlations of the insulin-linked polymorphic region. , 1996, Journal of molecular biology.

[32]  M. Campbell,et al.  PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.

[33]  W. Rutter,et al.  Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Barbara E. Wright,et al.  Stress‐directed adaptive mutations and evolution , 2004, Molecular microbiology.

[35]  Stephen Neidle,et al.  A conserved quadruplex motif located in a transcription activation site of the human c-kit oncogene. , 2006, Biochemistry.

[36]  Dipankar Sen,et al.  A sodium-potassium switch in the formation of four-stranded G4-DNA , 1990, Nature.

[37]  Max A. Keniry,et al.  Quadruplex structures in nucleic acids , 2000, Biopolymers.

[38]  H. Heumann,et al.  Translocation of the Escherichia coli transcription complex observed in the registers 11 to 20: "jumping" of RNA polymerase and asymmetric expansion and contraction of the "transcription bubble". , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Yiqiang Zhao,et al.  Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals , 2007, FEBS letters.

[40]  Shankar Balasubramanian,et al.  Prevalence of quadruplexes in the human genome , 2005, Nucleic acids research.

[41]  Roger A. Jones,et al.  NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region , 2006, Nucleic acids research.

[42]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[43]  L. Hurley,et al.  The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. , 2004, Journal of the American Chemical Society.

[44]  S. Balasubramanian,et al.  DNA Quadruplexes and Gene Regulation , 2006 .

[45]  Ning Li,et al.  Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome. , 2007, Biochemical and biophysical research communications.

[46]  D. Thiele,et al.  Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA. , 1990, Journal of biomolecular structure & dynamics.

[47]  N. Maizels,et al.  Dynamic roles for G4 DNA in the biology of eukaryotic cells , 2006, Nature Structural &Molecular Biology.

[48]  Michael R. Green,et al.  A role for activator-mediated TFIIB recruitment in diverse aspects of transcriptional regulation , 1995, Current Biology.

[49]  Marc Drolet,et al.  Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R‐loop formation and DNA topology , 2006, Molecular microbiology.

[50]  D. Reinberg,et al.  Recycling of the general transcription factors during RNA polymerase II transcription. , 1995, Genes & development.

[51]  J. Wang,et al.  Supercoiling of the DNA template during transcription. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Clifford A. Meyer,et al.  Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells , 2005, Genome Biology.

[53]  Haiyong Han,et al.  The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo. , 2002, Molecular cancer therapeutics.

[54]  Laurence H. Hurley,et al.  Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents , 2005, Nucleic acids research.

[55]  Roger A. Jones,et al.  Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization. , 2005, Biochemistry.

[56]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[57]  M. Fry,et al.  Formation and properties of hairpin and tetraplex structures of guanine-rich regulatory sequences of muscle-specific genes , 2005, Nucleic acids research.

[58]  Shankar Balasubramanian,et al.  G-quadruplexes in promoters throughout the human genome , 2006, Nucleic acids research.

[59]  M. Lieber,et al.  R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells , 2003, Nature Immunology.

[60]  D. Bearss,et al.  Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription , 2002, Proceedings of the National Academy of Sciences of the United States of America.