Project description:Rapid advances in biochemical technologies have enabled several strategies for typing candidate HLA alleles, but linking them into a single MHC haplotype structure remains challenging. Here we have developed a multi-loci haplotype phasing technique and demonstrate its utility towards phasing of MHC and KIR loci in human samples. We accurately (~99%) reconstruct the complete haplotypes for over 90% of sequence variants spanning the 4-megabase region of these two loci. By haplotyping a majority of coding and non-coding alleles at the MHC and KIR loci in a single assay, this method has the potential to assist transplantation matching and facilitate investigation of the genetic basis of human immunity and disease. Complete haplotype phasing of 2 loci (MHC and KIR) in 1 human cell line.
Project description:Rapid advances in biochemical technologies have enabled several strategies for typing candidate HLA alleles, but linking them into a single MHC haplotype structure remains challenging. Here we have developed a multi-loci haplotype phasing technique and demonstrate its utility towards phasing of MHC and KIR loci in human samples. We accurately (~99%) reconstruct the complete haplotypes for over 90% of sequence variants spanning the 4-megabase region of these two loci. By haplotyping a majority of coding and non-coding alleles at the MHC and KIR loci in a single assay, this method has the potential to assist transplantation matching and facilitate investigation of the genetic basis of human immunity and disease.
Project description:How transcription factors (TFs) and their binding sites organize and engage nucleosomes at natural genomic locations remains poorly understood. Here we develop Benzonase-seq to measure the rotational phasing of nucleosomes in human cells, and enhance ChIP-exo (v6) to measure rotational phasing on the same DNA molecule bound by a TF. Unbound CTCF sites were found to be rotationally accessible on nucleosomes and this rotational accessibility is encoded by classical dinucleotide periodicities. CTCF binding results in nucleosome displacement to adjacent DNA phasing sequences. Examining 40 TF classes, their unbound sites were phased inward, outward, or lacked phasing. In all examined cases, TF binding (e.g. NFIA and FoxA) results in adjacent rotational and translational phasing, which is not dinucleotide encoded. Benzonase-seq also more robustly maps nucleosome and subnucleosome positions in hard-to-map CpG islands. These findings provide a clearer view of how TFs engage and position nucleosomes to shape the natural chromatin landscape.
Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1.
Project description:How transcription factors (TFs) and their binding sites organize and engage nucleosomes at natural genomic locations remains poorly understood. Here we develop Benzonase-seq to measure the rotational phasing of nucleosomes in human cells, and enhance ChIP-exo (v6) to measure rotational phasing on the same DNA molecule bound by a TF. Unbound CTCF sites were found to be rotationally accessible on nucleosomes and this rotational accessibility is encoded by classical dinucleotide periodicities. CTCF binding results in nucleosome displacement to adjacent DNA phasing sequences. Examining 40 TF classes, their unbound sites were phased inward, outward, or lacked phasing. In all examined cases, TF binding (e.g. NFIA and FoxA) results in adjacent rotational and translational phasing, which is not dinucleotide encoded. Benzonase-seq also more robustly maps nucleosome and subnucleosome positions in hard-to-map CpG islands. These findings provide a clearer view of how TFs engage and position nucleosomes to shape the natural chromatin landscape.
Project description:Copy number variations (CNVs) constitute the largest portion of the human genome variation. We determined a genome-wide high resolution SNP/CNV haplotype structure of Asians, by analyzing a collection of complete hydatidiform moles (CHMs) of Japanese, using high-density DNA arrays. CHMs are tissues carrying duplicated haploid genomes derived from single sperms, and are suitable material for the detection of CNVs, because they are expected to reveal greater signal to noise ratio in hybridization experiments. Also, the absence of heterozygosity ensures straightforward CNV interpretation without being bothered by overlapping CNV segments. We genotyped 100 CHM genomes using Affymetrix SNP 6.0 and Illumina 1M-duo, created a definitive haplotype map including 1.7 million SNPs and 2339 CNV region (CNVR) that is presented as D-HaploDB Phase 4.1. Illumina Human1M-Duov3 BeadChip analyses were performed according to the manufacturer's directions on DNA extracted from 97 complete hydatidiform moles (CHMs) tissues collected throughout Japan.
Project description:<p>Integrated analyses of transcriptomic, proteomic and metabolomic data sets consistently highlights the crucial involvement of protein function and retinol metabolism pathways in the heat-resistant strain of S. subcrenata. These findings underscore the significance of these pathways in enabling the strain's ability to withstand high temperatures and adapt to heat stress. The haplotype-resolved female and male genomes and multiomics data presented in this study provide a solid foundation for investigating the molecular mechanisms of sex in S. subcrenata.</p>