CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

An effective tool for the global analysis of both DNA methylation status and protein–chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein–chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements.

[1]  Tim Hui-Ming Huang,et al.  Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer. , 2003, Cancer research.

[2]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[3]  Tim Hui-Ming Huang,et al.  Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. , 2002, Genes & development.

[4]  F. Wardle,et al.  Identifying transcriptional targets , 2004, Genome Biology.

[5]  Kirby D. Johnson,et al.  Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation. , 2004, Methods in molecular biology.

[6]  T. Efferth,et al.  Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation. , 2002, Methods.

[7]  S. Knudsen,et al.  A new non-linear normalization method for reducing variability in DNA microarray experiments , 2002, Genome Biology.

[8]  Nicola J. Rinaldi,et al.  Control of Pancreas and Liver Gene Expression by HNF Transcription Factors , 2004, Science.

[9]  L. Kuras.  Characterization of protein-DNA association in vivo by chromatin immunoprecipitation. , 2004, Methods in molecular biology.

[10]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[11]  Pearlly Yan,et al.  Chromatin Immunoprecipitation (ChIP) on Chip Experiments Uncover a Widespread Distribution of NF-Y Binding CCAAT Sites Outside of Core Promoters* , 2005, Journal of Biological Chemistry.

[12]  Michael Q. Zhang,et al.  Large-scale human promoter mapping using CpG islands , 2000, Nature Genetics.

[13]  Michael Q. Zhang,et al.  A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Martin W. Simmen,et al.  CpG island libraries from human Chromosomes 18 and 22: landmarks for novel genes , 2000, Mammalian Genome.

[15]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[16]  M. Gerstein,et al.  GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[17]  A. Bird,et al.  Number of CpG islands and genes in human and mouse. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Peggy J. Farnham,et al.  Analysis of Myc Bound Loci Identified by CpG Island Arrays Shows that Max Is Essential for Myc-Dependent Repression , 2003, Current Biology.

[19]  Tim Hui-Ming Huang,et al.  Differential methylation hybridization using CpG island arrays. , 2002, Methods in molecular biology.

[20]  F. Antequera,et al.  Structure, function and evolution of CpG island promoters , 2003, Cellular and Molecular Life Sciences CMLS.

[21]  Toshio Kojima,et al.  Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression , 2004, BMC Genomics.

[22]  Patrick Yau,et al.  High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. , 2004, Methods in enzymology.

[23]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[24]  S. Cross,et al.  Isolation of CpG islands from large genomic clones. , 1999, Nucleic acids research.

[25]  Michael Q. Zhang,et al.  Use of Chromatin Immunoprecipitation To Clone Novel E2F Target Promoters , 2001, Molecular and Cellular Biology.

[26]  S. Cawley,et al.  Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs , 2004, Cell.

[27]  T. Volkert,et al.  E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. , 2002, Genes & development.

[28]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[29]  A. Bird,et al.  The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[31]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[32]  A. Bird.  DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[33]  Daiya Takai,et al.  Comprehensive analysis of CpG islands in human chromosomes 21 and 22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[34]  T. Huang,et al.  Methylation profiling of CpG islands in human breast cancer cells. , 1999, Human molecular genetics.

[35]  C. M. Chen,et al.  Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. , 2001, Cancer research.

[36]  S. Cross,et al.  Purification of CpG islands using a methylated DNA binding column , 1994, Nature Genetics.

[37]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[38]  Bradley P. Coe,et al.  A tiling resolution DNA microarray with complete coverage of the human genome , 2004, Nature Genetics.