A high-resolution map of active promoters in the human genome

By Tae Hoon Kim, Leah Barrera, Ming Zheng, Chunxu Qu, Michael A. Singer, Todd A. Richmond, Ying N Wu, Roland Green, Bing Ren. Nature, 2005

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A chromatin landmark and transcription initiation at most promoters in human cells. (2007, background): “…with H3K4me3 have been reported at inactive genes within the b -globin locus (Schneider et al., 2004), X-linked genes (Brinkman et al., 2006), certain transcriptional regulatory genes (Azuara et al., 2006; Bernstein et al., 2006; Brink-man et al., 2006), and other genes (Kim et al., 2005).”
Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. (2007, methodology): “Of immunoprecipitated or total genomic LM-PCR DNA, 4 mg was labeled with Cy3 or Cy5 and combined to hybridize to NimbleGen human whole-genome arrays that were manufactured by NimbleGen Systems (www.nimblegen.com) as described (Kim et al., 2005).”
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. (2006, methodology): “Maskless array synthesis and hybridization were carried out with 100 ng of amplified 5C libraries at NimbleGen Systems Inc. as previously described (Singh-Gasson et al. 1999; Nuwaysir et al. 2002; Kim et al. 2005; Selzer et al. 2005).”
The mammalian epigenome. (2007, methodology): “High-resolution tiling oligonucleotide arrays were used to interrogate either all active promoters (Kim et al., 2005) or the nonrepetitive portions of human chromosomes 21 and 22 plus several orthologous human and mouse loci (Bernstein et al., 2005).”