ChIP-chip and ChIP-seq

1. ChIP-chip and ChIP-seq Vishy Iyer

2. Origins of ChIP� 1978 Jackson V. Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell 15: 945-954. 1988 Solomon MJ, Larsen PL, Varshavsky A. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that H4 is retained on a highly transcribed gene. Cell 53: 937-947 1991 Dedon PC, Soults JA, Allis CD, Gorovsky MA. Formaldehyde cross-linking and immunoprecipitation demonstrate developmental changes in H1 association with transcriptionally active genes. Mol. Cell Biol. 11: 1729-1733 1993 Orlando V, Paro R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell 75: 1187-1198. 1996 Hecht A, Strahl-Bolsinger S, Grunstein M. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383: 92-96 1998 Boyd KE, Wells J, Gutman J, Bartley SM, Farnham PJ. c-Myc target gene specificity is determined by a post-DNA binding mechanism. PNAS 95: 13887-13892

3. � and ChIP-chip Phimister B (1998) Getting hip to the chip. Nature Genetics. 18: 195 Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. (2000) Genome-wide location and function of DNA binding proteins. Science. 290: 2306-2309 Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409: 533-538 Kim TH, Barrera LO, Zheng L, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B, (2005). A high-resolution map of active promoters in the human genome. Nature 436: 876-880

4. Strategy for ChIP-chip