Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis

Abstract

Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. Integrating these datasets, we constructed a much-improved gene model set including about 17,000 novel isoforms, identified 1600 transcription factors, 1100 long non-coding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series datasets provided another dimension of information. With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, regulatory logic between accessible elements and genes during embryogenesis. We built a user-friend medaka omics data portal to present these datasets. This resource provides the first comprehensive omics datasets of medaka embryogenesis. Ultimately, we term these three assays as the minimum ENCODE toolbox and propose the use of it as the initial and essential profiling genomic assays for model organisms that have limited data available. This work will be of great value for the research community using medaka as the model organism and many others as well.

The bowfin genome illuminates the developmental evolution of ray-finned fishes

“…Currently, beyond zebrafish and medaka (for example, refs. 66 , 67 ), there are limited gene-regulatory resources for fishes, rendering comparative analyses across species or whole-genome duplications difficult. Our bowfin ATAC-seq atlas provides a key platform to further connect gene-regulatory homology across vertebrates while strengthening the utility of non-teleost fishes for examining genome function in the context of long-standing questions about vertebrate evolution and development.…”

The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes

“…Currently, beyond zebra sh and medaka (e.g. 76,77 ), there are limited gene regulatory resources for shes, making comparative analyses across species or whole genome duplications di cult. Our bow n ATAC-Seq atlas is the rst for any non-teleost and provides a critical platform to further connect gene regulatory homology across vertebrates while strengthening the utility of non-teleost shes for examining genome function in the context of long-standing questions about vertebrate evolution and development.…”

Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua

“…In our study, ADS (AA425620), a key enzyme for artemisinin biosynthesis, was highly expressed in GT but no nearby ACR was detected. This discrepancy of DEG and DAR was actually common and has been reported in other biological processes, such as flower bud induction in Arabidopsis thaliana and early embryo development in Oryzias latipes [ 51 , 52 ]. One possible explanation is the dynamic chromatin remodeling event during gene regulation.…”