Project description:3D structure of chromatin is thought to be critical for the regulation of gene expression during development. Here we employ the Micro-C assay to achieve 100 bp resolution for the genome organization of Drosophila melanogaster throughout the first half of embryogenesis. The resulting contact maps enable the identification of fine-scaled structures such as individual loops and boundaries delineating TADs. We observe that 3D structures form prior to zygotic genome activation in precellular embryos, and many of these organizational features persist during successive mitotic cycles. 3D structures are classified through the use of 149 ChIP-seq datasets. We present evidence for specialized elements associated with housekeeping genes that are enriched for BEAF-32 but not CTCF. We also characterize a distinct class of elements associated with developmental gene regulation that are enriched with GAF and Zld binding. This binding is maintained during mitotic cycles and exhibits evolutionary conservation of both sequence and 3D structures. In sum, this work provides a comprehensive genome-wide characterization at unprecedented resolution of the role of 3D chromatin organization in gene regulation during development. We propose that the 3D organization of the pre-cellular embryo facilitates deployment of the developmental control genes defining the Drosophila fate map.
Project description:The zebrafish has been widely used for the study of human disease and development, as ~70% of the protein-coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome, however, has lagged behind that of other model systems such as mouse and Drosophila. Based on multi-omics approaches taken in the ENCODE and Roadmap Epigenomics projects, we performed RNA-seq, ATAC-seq, ChIP-seq and Hi-C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall, we have identified 235,596 cis-regulatory elements, which potentially shape the tissue-specific and developmental-stage-specific gene expression in zebrafish. A comparison of zebrafish, human, and mouse regulatory elements allowed us to identify both evolutionarily conserved and species-specific regulatory sequences. Furthermore, through the analysis of Hi-C data in zebrafish brain and muscle, we observed different levels of 3D genome organization, including compartment, topological associating domains (TADs), and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization.
Project description:This project is based on visualizing the chemical and microbiological composition of individuals of Colostethus panamensis (Dendrobatidae), through the creation of a topographic map of the surface of their skin in 3D
Project description:RNA molecules not only carry genetic information like DNA, but also folds into exquisite 3D structures like proteins. Despite strong interests in RNA biology and their medical applications, RNA structure determination in vivo remained a long-standing problem. Here we developed a new technology to directly determine RNA structures in vivo, termed SHARC-seq. Applying SHARC-seq, spatial distances among nucleotides can be measured and used to rebuild in vivo RNA 3D structure and dynamics.
Project description:This project is based on visualizing the chemical and microbiological composition of individuals of Colostethus panamensis (Dendrobatidae), through the creation of a topographic map of the surface of their skin in 3D
Project description:Acetylome and proteome of WT (5905), gcn5 loss-of-function, and GCN5 overexpression Drosophila at age of 3d Acetylome and proteome of WT (5905) Drosophila during aging (at age of 3d, 15d, 30d, and 45d)
Project description:Cross-linking mass spectrometry (XL-MS) has made significant progress in understanding the structure of protein and elucidating architectures of larger protein complexes. Current XL-MS applications are limited to targeting lysine, glutamic acid, aspartic acid, and cysteine residues. There remains a need for the development of novel cross-linkers enabling selectively target other amino-acid residues in proteins. Here, a novel simple cross-linker, namely [4,4'-(disulfanediylbis(ethane-2,1-diyl)) bis(1,2,4-triazolidine-3,5-dione)] (DBB), has been designed, synthesized, and characterized. This cross-linker can react selectively with tyrosine residues in protein through electrochemical click reaction. Upon tandem mass spectrometry, the DBB cross-links produced the characteristic fragments, thus permitting the simplified data analysis and accurate identification for the cross-linked products. This is the first time developing a cross-linker for targeting tyrosine residue on protein without using photoirradiation or metal catalyst. This strategy might potentially be used as a complementary tool for XL-MS to probe protein 3D structures, protein complexes, and protein-protein interaction.