The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species
. However, studies in ...zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
Ideal three‐dimensional imaging of complex samples made up of micron‐scale structures extending over mm to cm, such as biological tissues, requires both wide field of view and high resolution. For ...existing optics and detectors used for micro‐CT (computed tomography) imaging, sub‐micron pixel resolution can only be achieved for fields of view of <2 mm. This article presents a unique detector system with a 6 mm field‐of‐view image circle and 0.5 µm pixel size that can be used in micro‐CT units utilizing both synchrotron and commercial X‐ray sources. A resolution‐test pattern with linear microstructures and whole adult Daphnia magna were imaged at beamline 8.3.2 of the Berkeley Advanced Light Source. Volumes of 10000 × 10000 × 7096 isotropic 0.5 µm voxels were reconstructed over a 5.0 mm × 3.5 mm field of view. Measurements in the projection domain confirmed a 0.90 µm measured spatial resolution that is largely Nyquist‐limited. This unprecedented combination of field of view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate changes in tissue and cellular morphology in the context of larger, whole, intact model organisms and specimens. This system is also anticipated to benefit micro‐CT imaging in materials science, microelectronics, agricultural science and biomedical engineering.
A custom wide‐field lens and a new‐generation megapixel camera enabled micro‐CT scanning over a 3.5 mm × 5 mm field of view at 1 µm resolution/0.5 µm pixel size at Lawrence Berkeley Laboratory's Advanced Light Source and Argonne National Laboratory's Advanced Photon Source using a phantom with micron‐scale features. This novel combination of resolution and field of view was designed for broad applicability to any setting in which micron‐scale structures need to be characterized comprehensively in three dimensions over mm to cm.
Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 ...gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.
The diversity of human physical characters has long intrigued mankind and is far from being understood. Skin pigmentation shows great variation both within and between human populations, is a ...measurable quantitative trait, and plays a key role in skin cancer susceptibility. The study of admixed populations suggests that the A111T allele of SLC24A5 and the L374F allele of SLC45A2 (MATP) each explain about a quarter of the skin color difference between northern European and West African populations. Neither gene explains the lighter skin pigmentation of East Asian populations, indicating a convergent evolutionary mechanism whose genetic basis is unknown. In order to map the basis of light skin color in East Asians, we collected 565 samples from aboriginal tribes from Malaysia and measured skin pigmentation by reflectance spectroscopy. Skin pigmentation, expressed as Melanin Index, ranged from 28 to 75, with population averages of 56 (Negrito), 46 (Senoi), and 42 (Proto Malay). After exclusion of individuals with significant European admixture using identified SNPs which are ancestry informative markers, genetic analysis will be used to map candidate genes for East Asian skin pigmentation. These genes will subsequently be tested using morpholino oligonucleotide knockdown of orthologues in zebrafish. We will report our plans and progress in these studies. NIH, UKM and JG Cancer Rsrch Foundation fund this research.
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