Abstract
Mapping DNase I hypersensitive (HS) sites is an accurate method of
identifying the location of genetic regulatory elements, including
promoters, enhancers, silencers, insulators, and locus control regions.
We employed high-throughput sequencing and whole-genome tiled array
strategies to identify DNase I HS sites within human primary CD4+
T cells. Combining these two technologies, we have created a comprehensive
and accurate genome-wide open chromatin map. Surprisingly, only 16%-21%
of the identified 94,925 DNase I HS sites are found in promoters
or first exons of known genes, but nearly half of the most open sites
are in these regions. In conjunction with expression, motif, and
chromatin immunoprecipitation data, we find evidence of cell-type-specific
characteristics, including the ability to identify transcription
start sites and locations of different chromatin marks utilized in
these cells. In addition, and unexpectedly, our analyses have uncovered
detailed features of nucleosome structure.
- algorithms
- area_under_curve
- binding_sites
- cd4-positive_t-lymphocytes,_cytology
- cell_nucleus,_metabolism
- chromatin,_genetics
- chromatin_immunoprecipitation
- chromosomes,_human
- chromosome_mapping,_methods
- deoxyribonuclease_i,_chemistry/pharmacology
- genome,_human,_genetics/immunology
- histones,_chemistry
- humans
- nucleosomes,_chemistry
- oligonucleotide_array_sequence_analysis
- promoter_regions,_genetic
- roc_curve
- sensitivity_and_specificity
- sequence_analysis,_dna
- transcription_factors,_metabolism
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