RT Journal
A1 Li, Yingshu
A1 Liu, Yongjie
A1 Yang, Hang
A1 Zhang, Ting
A1 Naruse, Kiyoshi
A1 Tu, Qiang
T1 Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
JF Genome Research 
JO Genome Research 
YR 2020 
FD June 01 
VO 30 
IS 6 
SP 924 
OP 937 
DO 10.1101/gr.258871.119 
UL http://genome.cshlp.org/content/30/6/924.abstract 
AB 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. By integrating these data sets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long noncoding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series data sets provided another dimension of information. With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, as well as regulatory logic between accessible elements and genes, during embryogenesis. We built a user-friendly medaka omics data portal to present these data sets. This resource provides the first comprehensive omics data sets 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.