Project description:Allelic differences between the two sets of chromosomes can affect the propensity of inheritance in humans, but the extent of such differences in the human genome has yet to be fully explored. Here, we delineate allelic chromatin modifications and transcriptomes amongst a broad set of human tissues, enabled by a chromosome-span haplotype reconstruction strategy1. The resulting haplotype-resolved epigenomic maps reveal extensive allele bias in the transcription of human genes as well as chromatin state, allowing us to infer cis-regulatory relationships between genes and their control sequences. These maps also uncover a new class of cis regulatory elements and detail activities of repetitive elements in various human tissues. The rich datasets described here will enhance our understanding of the mechanisms controlling tissue-specific gene expression programs. One replicate of Hi-C experiment in four human tissues with four different individuals (Thymus STL001, Aorta STL002, Leftventricle STL003, and Liver STL011).
Project description:Allelic differences between the two sets of chromosomes can affect the propensity of inheritance in humans, but the extent of such differences in the human genome has yet to be fully explored. Here, we delineate allelic chromatin modifications and transcriptomes amongst a broad set of human tissues, enabled by a chromosome-span haplotype reconstruction strategy1. The resulting haplotype-resolved epigenomic maps reveal extensive allele bias in the transcription of human genes as well as chromatin state, allowing us to infer cis-regulatory relationships between genes and their control sequences. These maps also uncover a new class of cis regulatory elements and detail activities of repetitive elements in various human tissues. The rich datasets described here will enhance our understanding of the mechanisms controlling tissue-specific gene expression programs.
Project description:Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
Project description:Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
2022-11-15 | GSE192499 | GEO
Project description:Chromosome-scale, haplotype-resolved genome assembly of a tetraploid potato cultivar