Intramural Research Online Research Resources DNaseHS Sites

Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites

Gregory E. Crawford¹, Ingeborg E. Holt¹, James C. Mullikin¹, Denise Tai¹, NIH Intramural Sequencing Center², Eric D. Green^1,2, Tyra G. Wolfsberg¹, and Francis S. Collins¹

¹Genome Technology Branch
²NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD

Abstract

Analysis of the human genome sequence has identified approximately 25,000-30,000 protein-coding genes, but little is known about how most of these are regulated. Mapping DNase I hypersensitive (HS) sites has traditionally represented the gold-standard experimental method for identifying regulatory elements, but the labor-intensive nature of this technique has limited its application to only a small number of human genes. We have developed a novel protocol to generate a genome-wide library of gene regulatory sequences by cloning DNase HS sites. We generated a library of DNase HS sites from quiescent primary human CD4+ T cells and analyzed ~5600 of the resulting clones. Compared to sequences from randomly generated in silico libraries, sequences from these clones were found to map more frequently to regions of the genome known to contain regulatory elements, such as regions upstream of genes, within CpG islands, and in sequences that align between mouse and human. These cloned sites also tend to map near genes that have detectable transcripts in CD4+ T cells, demonstrating that transcriptionally active regions of the genome are being selected. Validation of putative regulatory elements was achieved by repeated recovery of the same sequence and by real-time PCR. This cloning strategy, which can be scaled up and applied to any cell line or tissue, will be useful in identifying regulatory elements controlling global expression differences that delineate tissue types, stages of development, and disease susceptibility.

DNase HS Coordinates

• Chromosome 1

• Chromosome 1_random

• Chromosome 2

• Chromosome 3_random

• Chromosome 3

• Chromosome 4

• Chromosome 4_random

• Chromosome 5

• Chromosome 6_random

• Chromosome 6

• Chromosome 7

• Chromosome 8

• Chromosome 9

• Chromosome 10

• Chromosome 11

• Chromosome 12

• Chromosome 13

• Chromosome 14

• Chromosome 15_random

• Chromosome 15

• Chromosome 16

• Chromosome 17

• Chromosome 18

• Chromosome 19

• Chromosome 20

• Chromosome 21

• Chromosome 22

• Chromosome X

• Chromosome X_random

• Chromosome Y

• All Chromosomes

Last modified: Friday, 29-Apr-2005 12:43:36 EDT

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