A map of cis-regulatory elements and 3D genome structures in zebrafish

Yang, Hongbo; Luan, Yu; Liu, Tingting; Lee, Hyung Joo; Li, Fang; Wang, Yanli; Wang, Xiaotao; Zhang, Bo; Jin, Qiushi; Ang, K.C.; Xing, Xiaoyun; Wang, Juan; Xu, Jie; Song, Fan; Iyyanki, Sriranga; Khunsriraksakul, Chachrit; Salameh, T.; Li, Daofeng; Choudhary, Mayank; Topczewski, Jacek; Wang, Kai; Gerhard, Glenn S.; Hardison, R; Wang, Ting; Cheng, Keith C.; Yue, Feng

doi:10.1038/s41586-020-2962-9

Cited by 109 publications

(114 citation statements)

References 76 publications

Supporting

Mentioning

106

Contrasting

Order By: Relevance

“…We show in the present study that the highly conserved RAR site in the 4 th intron of the zebrafish skap1 gene drives expression in the neural tube and gut in a pattern reminiscent to hoxb1b expression, suggesting that this RARE controls the expression of the neighbouring hoxbb cluster. This is further supported by recent chromosome conformation capture (Hi-C) data obtained from adult zebrafish muscle tissue (Yang et al 2020); mining these data show that the 4 th intron skap1 CNE interacts with several hoxbb genes (not shown). Thus, this indicates that hox regulation by RA involved additional RAR sites located very far downstream from the HoxB cluster (i.e.…”

Section: Discussionsupporting

confidence: 59%

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

López-Pérez

Balwierz

Lenhard

et al. 2020

Preprint

View full text Add to dashboard Cite

Retinoic acid (RA) is a key signaling molecule required for the specification of the pancreatic field within the endodermal germ layer. Still, the gene regulatory cascade triggered by RA in endoderm remains poorly characterized. In this study, we investigated the gene regulatory network induced by RA signaling in zebrafish endodermal cells by a combination of RNA-seq, RAR ChIP-seq and ATAC-seq experiments. By analysing the effect of RA and BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signaling. Localization of RAR binding sites in the zebrafish genome by ChIP-seq highlighted the putative direct RAR target genes. Among them, Hnf1ba and Gata6, two known pancreatic regulatory factors activated by RA treatment, play a crucial role in opening chromatin at many genomic loci as revealed by the strong enrichment of their sequence binding motifs in RA-induced nucleosome-free regions. Furthermore, comparison of RAR ChIP-seq data obtained in zebrafish and in mice highlights the evolutionary-conserved direct targets, comprising the well-known Cyp26a or Hox genes but also Hnf1b and Gata6. Some RAR binding sites are located in highly conserved noncoding regions revealing the strong evolutionary constraint to maintain the function of such regulatory sequences. Among them, we identify a novel RA-induced enhancer located far upstream from the Hoxb Locus. In conclusion, our data reveal the central role of HNF1ba and Gata6 as pioneer transcription factors for the RA-dependent specification of the pancreatic field and highlight the RAR sites conserved from fish to mammals.

show abstract

Section: Discussionsupporting

confidence: 59%

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

López-Pérez

Balwierz

Lenhard

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…LTR, LINE, etc.) (Chalopin et al, 2015;Gao et al, 2016;Yang et al, 2020). However, different TE families within the same TE class can behave very differently when it comes to their genomic distribution or expression patterns (Feschotte et al, 2002;Ishiuchi et al, 2015;Rodriguez-Terrones and Torres-Padilla, 2018;Stitzer et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

Chang

Rovira

Wells

et al. 2021

Preprint

View full text Add to dashboard Cite

There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos, and by the relative scarcity of active TEs in these organisms. Zebrafish is an outstanding model for the study of vertebrate development and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2,000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whilst short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. While two thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched amongst transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides an important resource for using zebrafish as a model to study the impact of TEs on vertebrate development.

show abstract

“…Moreover, how the PCH-driven compartmentalization impacts gene regulation in the zig-zag eel remains elusive. Epigenetic profiling from multiple tissues with various markers other than H3K9me3 should promote the understanding of the regulatory landscape and mechanisms of gene expression across the chromosome (Yang et al 2020;Robson, Ringel, and Mundlos 2019).…”

Section: Discussionmentioning

confidence: 99%

Pericentromeric heterochromatin impacts genome compartmentalization and sex chromosome evolution in a fish

Xue

et al. 2021

Preprint

View full text Add to dashboard Cite

Compartmentalization is one of the principles of chromosome 3D organization and has been suggested to be driven by the attraction of heterochromatin. The extent to which the pericentromeric heterochromatin (PCH) impacts chromosome compartmentalization is yet unclear. Here we produced a chromosome-level and fully phased diploid genome of an aquaculture fish, zig-zag eel (Mastacembelus armatus), and identified the centromeric and pericentromeric regions in the majority of chromosomes of both haploid genomes. The PCH is on average 4.2 Mb long, covering 17.7% of the chromosomes, and is the major target of histone 3 lysine 9 trimethylation (H3K9me3). In nearly half of the chromosomes, the PCH drives the chromosomes into two or three megascale chromatin domains with the PCH being a single one. We further demonstrate that PCH has a major impact in submetacentric, metacentric and small telocentric chromosomes in which the PCH drives the distribution of active and inactive compartments along the chromosomes. Additionally, we identified the young and homomorphic XY sex chromosomes that are submetacentric with the entire short-arm heterochromatinized. Interestingly, the sex-determining region seems to arise within the PCH that had been in place prior to the X-Y divergence and recombination suppression. Together, we demonstrate that the PCH can cover a considerably large portion of the chromosomes, and when it does so, it drives chromosome compartmentalization; and we propose a new model for the origin and evolution of homomorphic sex chromosomes in fish.

show abstract

A map of cis-regulatory elements and 3D genome structures in zebrafish

Cited by 109 publications

References 76 publications

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

A genomic portrait of zebrafish transposable elements and their spatiotemporal embryonic expression

Pericentromeric heterochromatin impacts genome compartmentalization and sex chromosome evolution in a fish

Contact Info

Product

Resources

About