A histone map of human chromosome 20q13.12.
BACKGROUND
We present a systematic search for regulatory elements in a 3.5 Mb region on human chromosome 20q13.12, a region associated with a number of medical conditions such as type II diabetes and obesity.


RESULTS
We profiled six histone modifications alongside RNA polymerase II (PolII) and CTCF in two cell lines, HeLa S3 and NTERA-2 clone D1 (NT2/D1), by chromatin immunoprecipitation using an in-house spotted DNA array, constructed with 1.8 kb overlapping plasmid clones. In both cells, more than 90% of transcription start sites (TSSs) of expressed genes showed enrichments with PolII, di-methylated lysine 4 of histone H3 (H3K4me2), tri-methylated lysine 4 of histone H3 (H3K4me3) or acetylated H3 (H3Ac), whereas mono-methylated lysine 4 of histone H3 (H3K4me1) signals did not correlate with expression. No TSSs were enriched with tri-methylated lysine 27 of histone H3 (H3K27me3) in HeLa S3, while eight TSSs (4 expressed) showed enrichments in NT2/D1. We have also located several CTCF binding sites that are potential insulator elements.


CONCLUSIONS
In summary, we annotated a number of putative regulatory elements in 20q13.12 and went on to verify experimentally a subset of them using dual luciferase reporter assays. Correlating this data to sequence variation can aid identification of disease causing variants.
Akan
Pelin
P
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. pa2@sanger.ac.uk
Sahlén
Martin
M
Deloukas
Panagiotis
P
D000076246:CCCTC-Binding Factor; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping / Q000379:methods*; D002890:Chromosomes, Human, Pair 20; D004268:DNA-Binding Proteins / Q000032:analysis; D004742:Enhancer Elements, Genetic; D006657:Histones; D006801:Humans; D008745:Methylation; D012319:RNA Polymerase II / Q000032:analysis; D012097:Repressor Proteins / Q000032:analysis
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D004268:DNA-Binding Proteins; D006657:Histones; D012097:Repressor Proteins; D012319:RNA Polymerase II