Showing papers by "Lingyun Song published in 2010"

DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells

Abstract: Identification of active gene regulatory elements is a key to understanding transcriptional control governing biological processes like cell-type specificity, differentiation, development, proliferation, and response to the environment. Mapping DNase I hypersensitive (HS) sites has historically been a valuable tool for identifying all different types of regulatory elements, including promoters, enhancers, silencers, insulators and locus control regions. This method utilizes DNase I to selectively digest nucleosome-depleted DNA (presumably by transcription factors), whereas DNA regions tightly wrapped in nucleosome and higher order structures are more resistant. The traditional low-throughput method for identifying DNase I HS sites uses Southern blots. Here, we describe the complete and improved protocol for DNase-seq, a high-throughput method that identifies DNase I HS sites across the whole genome by capturing DNase-digested fragments and sequencing them by high-throughput next generation sequencing. In a single experiment, DNase-seq can identify most active regulatory regions from potentially any cell type from any species with a sequenced genome.

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

Abstract: The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans.