ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Dardaillon, Justine; Dauga, Delphine; Simion, Paul; Faure, Emmanuel; Onuma, Takeshi A.; DeBiasse, Melissa B.; Louis, Alexandra; Nitta, Kazuhiro R.; Naville, Magali; Besnardeau, Lydia; Reeves, Wendy; Wang, Kai; Fagotto, Marie; Guéroult-Bellone, Marion; Fujiwara, Shigeki; Dumollard, Rémi; Veeman, Michael; Volff, Jean‐Nicolas; Crollius, Hugues Roest; Douzery, Emmanuel J. P.; Ryan, Joseph F.; Davidson, Brad; Nishida, Hiroki; Dantec, Christelle Le; Lemaire, Patrick

doi:10.1093/nar/gkz955

Cited by 51 publications

(78 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For in situ hybridization, embryos were treated with 10 micromolar Cytochalasin B at the 112 cell stage after U0126/DMSO treatment at the 32 cell stage, then fixed at stage 16 as described in (Reeves et al, 2014) RNAseq analysis and bioinformatics: Tophat (Trapnell et al, 2013(Trapnell et al, , 2012 was used to align reads to the Ciona KH2012 gene models (KH.KHGene.2012.gff3, retrieved from ANISEED, http://www.aniseed.cnrs.fr/) (Brozovic et al, 2016;Dardaillon et al, 2020). The standard DEseq pipeline (Love et al, 2014) was used to calculate read counts and test for differential expression.…”

Section: Calculation Of Theoretical Maximum Decrease By Bra Crisprmentioning

confidence: 99%

See 1 more Smart Citation

Brachyury controlsCionanotochord fate as part of a feedforward network and not as a unitary master regulator

Reeves

Shimai

Winkley

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators and find that combinatorial cocktails are more effective at reprograming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a and other components of the notochord gene regulatory network and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classicallydefined master regulator.

show abstract

Section: Calculation Of Theoretical Maximum Decrease By Bra Crisprmentioning

confidence: 99%

“…The red lines show the best fit linear regressions. (Dardaillon et al, 2020) and/or single cell RNAseq (Cao et al, 2019). See supplemental table 4 for more details.…”

Section: Work Citedmentioning

confidence: 99%

Brachyury controlsCionanotochord fate as part of a feedforward network and not as a unitary master regulator

Reeves

Shimai

Winkley

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Genome scaffolds, predicted genes, and transcriptome assembly were incorporated into ANISEED, a web-based and publicly available genome database (Brozovic et al, 2018;Dardaillon et al, 2020). It includes the genome information of 13 ascidian species as well as larvacean species (present data).…”

Section: Genome Browsermentioning

confidence: 99%

“…This genome assembly, named OSKA2016, was compared with the OikoBase to estimate sequence variation between the two O. dioica populations. These resources have been incorporated into a publicly available genome database of tunicates, ANISEED (https://www.anise ed.cnrs.fr/; Brozovic et al, 2018;Dardaillon et al 2020), an open database for developmental, evolutionary, and comparative genome research involving this small chordate species. Using the genome scaffolds, we lastly tried to characterize male-specific scaffolds and gain insight into the male-specific Y-region of the Japanese O. dioica.…”

Section: Introductionmentioning

confidence: 99%

A genome database for a Japanese population of the larvacean Oikopleura dioica

et al. 2020

Self Cite

View full text Add to dashboard Cite

The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non‐redundant transcripts were assembled using RNA‐seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male‐ or female‐specific genome libraries yielded male‐specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male‐specific Y‐region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.

show abstract

“…Publicly available ATAC-seq data from Ciona robusta embryos (Madgwick et al, 2019) viewed through the genome browser on the ANISEED database (Dardaillon et al, 2020)…”

Section: Enhancer Identification and Cloningmentioning

confidence: 99%

Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships

Harder

Hix

Reeves

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Many genes are regulated by two or more enhancers that drive similar expression patterns. Evolutionary theory suggests that these seemingly redundant enhancers must have functionally important differences. In the simple ascidian chordate Ciona, the transcription factor Brachyury is induced exclusively in the presumptive notochord downstream of lineage specific regulators and FGF-responsive Ets family transcription factors. Here we exploit the ability to finely titrate FGF signaling activity via the MAPK pathway using the MEK inhibitor U0126 to quantify the dependence of transcription driven by different Brachyury reporter constructs on this direct upstream regulator. We find that the more powerful promoter-adjacent proximal enhancer and a weaker distal enhancer have fundamentally different dose-response relationships to MAPK inhibition. The Distal enhancer is more sensitive to MAPK inhibition but shows a less cooperative response, whereas the Proximal enhancer is less sensitive and more cooperative. A longer construct containing both enhancers has a complex dose-response curve that supports the idea that the proximal and distal enhancers are moderately super-additive. We show that the overall expression loss from intermediate doses of U0126 is not only a function of the fraction of cells expressing these reporters, but also involves graded decreases in expression at the single-cell level. Expression of the endogenous gene shows a comparable dose-response relationship to the full length reporter, and we find that different notochord founder cells are differentially sensitive to MAPK inhibition. Together, these results indicate that although the two Brachyury enhancers have qualitatively similar expression patterns, they respond to FGF in quantitatively different ways and act together to drive high levels of Brachyury expression with a characteristic input/output relationship. This indicates that they are fundamentally not redundant genetic elements.

show abstract

ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Cited by 51 publications

References 36 publications

Brachyury controlsCionanotochord fate as part of a feedforward network and not as a unitary master regulator

Brachyury controlsCionanotochord fate as part of a feedforward network and not as a unitary master regulator

A genome database for a Japanese population of the larvacean Oikopleura dioica

Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships

Contact Info

Product

Resources

About