XENOPUS LAEVIS PEROXIREDOXINS ARE EXPRESSED IN DISTINCT TISSUES DURING EARLY EMBRYOGENESIS

Development in the frog, Xenopus laevis, requires the utilization of yolk glyco- lipo-proteins in a temporally- and spatially-dependent manner. The metabolism of the yolk produces H20 2, a potent Reactive Oxygen Species (ROS). Peroxiredoxins (Prdxs) are a family of 6 anti-oxidant enzymes that, amongst other roles, reduce H20 2. Prdxs reduce H20 2through a thiol-redox reaction at conserved cysteine residues, which results in the creation of disulfide bonds. Recently the thiol-redox reaction of Prdxs has also been implicated in several cell signaling systems. Herein is a report of the cloning and expression patterns during development of 6 peroxiredoxin homologs from the frog X. laevis. Sequence analysis has confirmed their identity as well as their evolutionary relationship with peroxiredoxins from several other species. Using RT-PCR and in situ hybridization analysis we have shown that there is early, robust and unique expression patterns for all six homologs during development. All six X. laevis peroxiredoxins are expressed in neural regions including the brain, and eyes, as well as the somites. Different expression patterns for each peroxiredoxin are also observed in the pronephric region, including the proximal and distal tubules and the Wolffian duct. Expression of several peroxiredoxins was also observed in the blood precursors and the olfactory placode. These results suggest important roles for all six peroxiredoxins during early development. These roles may be restricted to their functions as anti-oxidant enzymes, but may also be related to their emerging roles in redox signaling, which is discussed herein

Gene family evolution underlies cell type diversification in the hypothalamus of teleosts

Hundreds of cell types form the vertebrate brain but it is largely unknown how similar cellular repertoires are between or within species or how cell-type diversity evolves. To examine cell-type diversity across and within species, we performed single-cell RNA sequencing of similar to 130,000 hypothalamic cells from zebrafish (Danio rerio) and surface and cave morphs of Mexican tetra (Astyanax mexicanus). We found that over 75% of cell types were shared between zebrafish and Mexican tetra, which diverged from a common ancestor over 150 million years ago. Shared cell types displayed shifts in paralogue expression that were generated by subfunctionalization after genome duplication. Expression of terminal effector genes, such as neuropeptides, was more conserved than the expression of their associated transcriptional regulators. Species-specific cell types were enriched for the expression of species-specific genes and characterized by the neofunctionalization of expression patterns of members of recently expanded or contracted gene families. Comparisons between surface and cave morphs revealed differences in immune repertoires and transcriptional changes in neuropeptidergic cell types associated with genomic differences. The single-cell atlases presented here are a powerful resource to explore hypothalamic cell types and reveal how gene family evolution and shifts in paralogue expression contribute to cellular diversity

Expanded encyclopaedias of DNA elements in the human and mouse genomes

AbstractThe human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.11Nsciescopu

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.11Nsciescopu