Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Abstract

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

Genome-Wide Identification and Analysis of the Cryptochrome/Photolyase Family in brown algae Saccharina japonica

“…Three major categories of proteins are included in CPF family: the cyclobutene pyrimidine dimer (CPD) photolyases, the (6-4) pyrimidine-pyrimidone adduct [(6-4) photoproduct] photolyases, and the cryptochromes (CRY) (Paola et al, 2014). The number of CPF genes varies little among different lineages, generally not more than ten, i. g. 5 in A. thaliana, 10 in Danio rerio, 6 in P. tricornutum (Baranasic et al, 2022, The Arabidopsis Genome Initiative, 2000, Martino et al, 2007. The number of CPF in three brown algae in this study is 4, which may indicate that the number of CPF in brown algae is conservative.…”

The cap epitranscriptome: Early directions to a complex life as mRNA

“…The data that support the findings of this study are openly available. [39][40][41][42] ORCID Yuan W. Tian https://orcid.org/0000-0002-4752-1933 Matthias Soller https://orcid.org/0000-0003-3844-0258…”

Promoting validation and cross-phylogenetic integration in model organism research

“…These Encyclopedia of DNA Elements (ENCODE) projects focused largely on human, C. elegans , D. melanogaster and mouse ( ENCODE Project Consortium, 2012 ; Celniker et al, 2009 ; ENCODE Project Consortium et al, 2020 ). DANIO-CODE is an inspiring bottom-up community effort of more than 30 laboratories that has integrated published and unpublished zebrafish epigenomic data ( Baranasic et al, 2022 ; Lawson, 2022 ). An integrated analysis of more than 1800 remapped data sets from 15 distinct developmental stages using chromatin immunoprecipitation with sequencing (ChIP-seq; Robertson et al, 2007 ), assay for transposase-accessible chromatin with sequencing (ATAC-seq; Buenrostro et al, 2013 ), RNA sequencing ( Emrich et al, 2006 ), cap analysis gene expression (CAGE; Shiraki et al, 2003 ), high-throughput chromosome conformation capture (Hi-C; Lieberman-Aiden et al, 2009 ) and circularized chromosome conformation capture sequencing (4C-seq; Zhao et al, 2006 ) yielded over 140,000 predicted regulatory elements associated with development and organogenesis.…”