title: Genetic landscape of open chromatin in yeast.
abstract: Chromatin regulation underlies a variety of DNA metabolism processes, including transcription, recombination, repair, and replication. To perform a quantitative genetic analysis of chromatin accessibility, we obtained open chromatin profiles across 96 genetically different yeast strains by FAIRE (formaldehyde-assisted isolation of regulatory elements) assay followed by sequencing. While 5∼10% of open chromatin region (OCRs) were significantly affected by variations in their underlying DNA sequences, subtelomeric areas as well as gene-rich and gene-poor regions displayed high levels of sequence-independent variation. We performed quantitative trait loci (QTL) mapping using the FAIRE signal for each OCR as a quantitative trait. While individual OCRs were associated with a handful of specific genetic markers, gene expression levels were associated with many regulatory loci. We found multi-target trans-loci responsible for a very large number of OCRs, which seemed to reflect the widespread influence of certain chromatin regulators. Such regulatory hotspots were enriched for known regulatory functions, such as recombinational DNA repair, telomere replication, and general transcription control. The OCRs associated with these multi-target trans-loci coincided with recombination hotspots, telomeres, and gene-rich regions according to the function of the associated regulators. Our findings provide a global quantitative picture of the genetic architecture of chromatin regulation.
authors: Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
authors: Kibaick
authors: K
authors: Lee
authors: Sang Cheol
authors: SC
authors: Kim
authors: Inkyung
authors: I
authors: Jung
authors: Kwoneel
authors: K
authors: Kim
authors: Jungmin
authors: J
authors: Seo
authors: Heun-Sik
authors: HS
authors: Lee
authors: Gireesh K
authors: GK
authors: Bogu
authors: Dongsup
authors: D
authors: Kim
authors: Sanghyuk
authors: S
authors: Lee
authors: Byungwook
authors: B
authors: Lee
authors: Jung Kyoon
authors: JK
authors: Choi
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D015966:Gene Expression Regulation, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D016615:Telomere / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D014157:Transcription Factors