@article {124, title = {Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish.}, journal = {Nat Commun}, volume = {13}, year = {2022}, month = {2022 Sep 20}, pages = {5520}, abstract = {

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3{\textquoteright}-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis of adar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the\ innate immune response, respectively.

}, keywords = {Adenosine, Animals, Immunity, Innate, Inosine, Mammals, RNA, RNA-Binding Proteins, Zebrafish}, issn = {2041-1723}, doi = {10.1038/s41467-022-33260-6}, author = {Niescierowicz, Katarzyna and Pryszcz, Leszek and Navarrete, Cristina and Tralle, Eugeniusz and Sulej, Agata and Abu Nahia, Karim and Kasprzyk, Marta El{\.z}bieta and Misztal, Katarzyna and Pateria, Abhishek and Paku{\l}a, Adrianna and Bochtler, Matthias and Winata, Cecilia} } @article {125, title = {Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.}, journal = {Nat Genet}, volume = {54}, year = {2022}, month = {2022 Jul}, pages = {1037-1050}, 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.

}, keywords = {Animals, Chromatin, Databases, Genetic, Gene Expression Regulation, Developmental, Genome, Genomics, Humans, Mice, Molecular Sequence Annotation, Organogenesis, Regulatory Sequences, Nucleic Acid, Zebrafish, Zebrafish Proteins}, issn = {1546-1718}, doi = {10.1038/s41588-022-01089-w}, author = {Baranasic, Damir and H{\"o}rtenhuber, Matthias and Balwierz, Piotr J and Zehnder, Tobias and Mukarram, Abdul Kadir and Nepal, Chirag and V{\'a}rnai, Csilla and Hadzhiev, Yavor and Jimenez-Gonzalez, Ada and Li, Nan and Wragg, Joseph and D{\textquoteright}Orazio, Fabio M and Relic, Dorde and Pachkov, Mikhail and D{\'\i}az, Noelia and Hern{\'a}ndez-Rodr{\'\i}guez, Benjam{\'\i}n and Chen, Zelin and Stoiber, Marcus and Dong, Micha{\"e}l and Stevens, Irene and Ross, Samuel E and Eagle, Anne and Martin, Ryan and Obasaju, Oluwapelumi and Rastegar, Sepand and McGarvey, Alison C and Kopp, Wolfgang and Chambers, Emily and Wang, Dennis and Kim, Hyejeong R and Acemel, Rafael D and Naranjo, Silvia and {\L}api{\'n}ski, Maciej and Chong, Vanessa and Mathavan, Sinnakaruppan and Peers, Bernard and Sauka-Spengler, Tatjana and Vingron, Martin and Carninci, Piero and Ohler, Uwe and Lacadie, Scott Allen and Burgess, Shawn M and Winata, Cecilia and van Eeden, Freek and Vaquerizas, Juan M and G{\'o}mez-Skarmeta, Jos{\'e} Luis and Onichtchouk, Daria and Brown, Ben James and Bogdanovic, Ozren and van Nimwegen, Erik and Westerfield, Monte and Wardle, Fiona C and Daub, Carsten O and Lenhard, Boris and M{\"u}ller, Ferenc} } @article {119, title = {Cardiac-specific β-catenin deletion dysregulates energetic metabolism and mitochondrial function in perinatal cardiomyocytes.}, journal = {Mitochondrion}, volume = {60}, year = {2021}, month = {2021 09}, pages = {59-69}, abstract = {

β-Catenin signaling pathway regulates cardiomyocytes proliferation and differentiation, though its involvement in metabolic regulation of cardiomyocytes remains unknown. We used one-day-old mice with cardiac-specific knockout of β-catenin and neonatal rat ventricular myocytes treated with β-catenin inhibitor to investigate the role of β-catenin metabolism regulation in perinatal cardiomyocytes. Transcriptomics of perinatal β-catenin-ablated hearts revealed a dramatic shift in the expression of genes involved in metabolic processes. Further analysis indicated an inhibition of lipolysis and glycolysis in both in vitro and in vivo models. Finally, we showed that β-catenin deficiency leads to mitochondria dysfunction via the downregulation of Sirt1/PGC-1α pathway. We conclude that cardiac-specific β-catenin ablation disrupts the energy substrate shift that is essential for postnatal heart maturation, leading to perinatal lethality of homozygous β-catenin knockout mice.

}, issn = {1872-8278}, doi = {10.1016/j.mito.2021.07.005}, author = {Balatskyi, Volodymyr V and Vaskivskyi, Vasyl O and Myronova, Anna and Avramets, Diana and Nahia, Karim Abu and Macewicz, Larysa L and Ruban, Tetiana P and Kucherenko, Dar{\textquoteright}ya Yu and Soldatkin, Oleksandr O and Lushnikova, Iryna V and Skibo, Galyna G and Winata, Cecilia L and Dobrzyn, Pawel and Piven, Oksana O} } @article {120, title = {Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region.}, journal = {Cell Mol Life Sci}, volume = {78}, year = {2021}, month = {2021 Oct}, pages = {6669-6687}, abstract = {

The atrioventricular canal (AVC) is the site where key structures responsible for functional division between heart regions are established, most importantly, the atrioventricular (AV) conduction system and cardiac valves. To elucidate the mechanism underlying AVC development and function, we utilized transgenic zebrafish line sqet31Et expressing EGFP in the AVC to isolate this cell population and profile its transcriptome at 48 and 72 hpf. The zebrafish AVC transcriptome exhibits hallmarks of mammalian AV node, including the expression of genes implicated in its development and those encoding connexins forming low conductance gap junctions. Transcriptome analysis uncovered protein-coding and noncoding transcripts enriched in AVC, which have not been previously associated with this structure, as well as dynamic expression of epithelial-to-mesenchymal transition markers and components of TGF-β, Notch, and Wnt signaling pathways likely reflecting ongoing AVC and valve development. Using transgenic line Tg(myl7:mermaid) encoding voltage-sensitive fluorescent protein, we show that abolishing the pacemaker-containing sinoatrial ring (SAR) through Isl1 loss of function resulted in spontaneous activation in the AVC region, suggesting that it possesses inherent automaticity although insufficient to replace the SAR. The SAR and AVC transcriptomes express partially overlapping species of ion channels and gap junction proteins, reflecting their distinct roles. Besides identifying conserved aspects between zebrafish and mammalian conduction systems, our results established molecular hallmarks of the developing AVC which underlies its role in structural and electrophysiological separation between heart chambers. This data constitutes a valuable resource for studying AVC development and function, and identification of novel candidate genes implicated in these processes.

}, keywords = {Animals, Animals, Genetically Modified, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Genome, Genomics, Heart Septal Defects, Heart Valves, Myocardium, Organogenesis, Pacemaker, Artificial, Wnt Signaling Pathway, Zebrafish, Zebrafish Proteins}, issn = {1420-9071}, doi = {10.1007/s00018-021-03939-y}, author = {Abu Nahia, Karim and Migda{\l}, Maciej and Quinn, T Alexander and Poon, Kar-Lai and {\L}api{\'n}ski, Maciej and Sulej, Agata and Liu, Jiandong and Mondal, Shamba S and Pawlak, Micha{\l} and Bugajski, {\L}ukasz and Piwocka, Katarzyna and Brand, Thomas and Kohl, Peter and Korzh, Vladimir and Winata, Cecilia} } @article {122, title = {Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift.}, journal = {BMC Genomics}, volume = {22}, year = {2021}, month = {2021 Dec 18}, pages = {904}, abstract = {

BACKGROUND: Liver fibrosis is a wound-healing response to tissue injury and inflammation hallmarked by the extracellular matrix (ECM) protein deposition in the liver parenchyma and tissue remodelling. Different cell types of the liver are known to play distinct roles in liver injury response. Hepatocytes and liver endothelial cells receive molecular signals indicating tissue injury and activate hepatic stellate cells which produce ECM proteins upon their activation. Despite the growing knowledge on the molecular mechanism underlying hepatic fibrosis in general, the cell-type-specific gene regulatory network associated with the initial response to hepatotoxic injury is still poorly characterized.

RESULTS: In this study, we used thioacetamide (TAA) to induce hepatic injury in adult zebrafish. We isolated three major liver cell types - hepatocytes, endothelial cells and hepatic stellate cells - and identified cell-type-specific chromatin accessibility and transcriptional changes in an early stage of liver injury. We found that TAA induced transcriptional shifts in all three cell types hallmarked by significant alterations in the expression of genes related to fatty acid and carbohydrate metabolism, as well as immune response-associated and vascular-specific genes. Interestingly, liver endothelial cells exhibit the most pronounced response to liver injury at the transcriptome and chromatin level, hallmarked by the loss of their angiogenic phenotype.

CONCLUSION: Our results uncovered cell-type-specific transcriptome and epigenome responses to early stage liver injury, which provide valuable insights into understanding the molecular mechanism implicated in the early response of the liver to pro-fibrotic signals.

}, keywords = {Animals, Endothelial Cells, Epigenomics, Liver, Zebrafish}, issn = {1471-2164}, doi = {10.1186/s12864-021-08173-1}, author = {Migda{\l}, Maciej and Tralle, Eugeniusz and Nahia, Karim Abu and Bugajski, {\L}ukasz and K{\k e}dzierska, Katarzyna Zofia and Garbicz, Filip and Piwocka, Katarzyna and Winata, Cecilia Lanny and Pawlak, Micha{\l}} } @article {121, title = {Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemaker.}, journal = {BMC Genomics}, volume = {22}, year = {2021}, month = {2021 Oct 02}, pages = {715}, abstract = {

BACKGROUND: Sinoatrial Node (SAN) is part of the cardiac conduction system, which controls the rhythmic contraction of the vertebrate heart. The SAN consists of a specialized pacemaker cell population that has the potential to generate electrical impulses. Although the SAN pacemaker has been extensively studied in mammalian and teleost models, including the zebrafish, their molecular nature remains inadequately comprehended.

RESULTS: To characterize the molecular profile of the zebrafish sinoatrial ring (SAR) and elucidate the mechanism of pacemaker function, we utilized the transgenic line sqet33mi59BEt to isolate cells of the SAR of developing zebrafish embryos and profiled their transcriptome. Our analyses identified novel candidate genes and well-known conserved signaling pathways involved in pacemaker development. We show that, compared to the rest of the heart, the zebrafish SAR overexpresses several mammalian SAN pacemaker signature genes, which include hcn4 as well as those encoding calcium- and potassium-gated channels. Moreover, genes encoding components of the BMP and Wnt signaling pathways, as well as members of the Tbx family, which have previously been implicated in pacemaker development, were also overexpressed in the SAR. Among SAR-overexpressed genes, 24 had human homologues implicated in 104 different ClinVar phenotype entries related to various forms of congenital heart diseases, which suggest the relevance of our transcriptomics resource to studying human heart conditions. Finally, functional analyses of three SAR-overexpressed genes, pard6a, prom2, and atp1a1a.2, uncovered their novel role in heart development and physiology.

CONCLUSION: Our results established conserved aspects between zebrafish and mammalian pacemaker function and revealed novel factors implicated in maintaining cardiac rhythm. The transcriptome data generated in this study represents a unique and valuable resource for the study of pacemaker function and associated heart diseases.

}, keywords = {Animals, Heart Rate, Humans, Sinoatrial Node, Transcriptome, Zebrafish}, issn = {1471-2164}, doi = {10.1186/s12864-021-08016-z}, author = {Minhas, Rashid and Loeffler-Wirth, Henry and Siddiqui, Yusra H and Obr{\k e}bski, Tomasz and Vashisht, Shikha and Nahia, Karim Abu and Paterek, Alexandra and Brzozowska, Angelika and Bugajski, Lukasz and Piwocka, Katarzyna and Korzh, Vladimir and Binder, Hans and Winata, Cecilia Lanny} } @article {115, title = {Targeted RNA Knockdown by a Type III CRISPR-Cas Complex in Zebrafish.}, journal = {CRISPR J}, volume = {3}, year = {2020}, month = {2020 08}, pages = {299-313}, abstract = {

RNA interference is a powerful experimental tool for RNA knockdown, but not all organisms are amenable. Here, we provide a proof of principle demonstration that a type III Csm effector complex can be used for programmable mRNA transcript degradation in eukaryotes. In zebrafish, Csm complex (StCsm) proved effective for knockdown of maternally expressed in germ cells of fish. It also led to significant, albeit less drastic, fluorescence reduction at one day postfertilization in and ( fish that express zygotically. StCsm targeted against the endogenous elicited the characteristic one-eyed phenotype with greater than 50\% penetrance, and hence with similar efficiency to morpholino-mediated knockdown. We conclude that Csm-mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts, in some cases reaching comparable efficiency to morpholino-based knockdown without significant off-target effects.

}, issn = {2573-1602}, doi = {10.1089/crispr.2020.0032}, author = {Fricke, Thomas and Smalakyte, Dalia and Lapinski, Maciej and Pateria, Abhishek and Weige, Charles and Pastor, Michal and Kolano, Agnieszka and Winata, Cecilia and Siksnys, Virginijus and Tamulaitis, Gintautas and Bochtler, Matthias} } @article {116, title = {The zebrafish as a model for developmental and biomedical research in Poland and beyond.}, journal = {Dev Biol}, volume = {457}, year = {2020}, month = {2020 01 15}, pages = {167-168}, keywords = {Animals, Biomedical Research, Developmental Biology, Disease Models, Animal, Poland, Zebrafish}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2019.11.003}, author = {Winata, Cecilia Lanny and Dodzian, Joanna and Bialek-Wyrzykowska, Urszula} } @article {112, title = {Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.}, journal = {Genome Res}, volume = {29}, year = {2019}, month = {2019 03}, pages = {506-519}, abstract = {

Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mechanism still exist because little is known about their downstream targets and interactive regulatory network. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption in vivo, we performed time-series analyses of the transcriptome and genome-wide chromatin accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of the corresponding TFs. Loss of function of cardiac TFs Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in chromatin accessibility profile, indicating their role in heart development. Among regions with differential chromatin accessibility in mutants were highly conserved noncoding elements that represent putative enhancers driving heart development. The most prominent gene expression changes, which correlated with chromatin accessibility modifications within their proximal promoter regions, occurred between heart tube morphogenesis and looping, and were associated with metabolic shift and hematopoietic/cardiac fate switch during CM maturation. Our results revealed the dynamic regulatory landscape throughout heart development and identified interactive molecular networks driving key events of heart morphogenesis.

}, keywords = {Animals, Cells, Cultured, Chromatin, Chromatin Assembly and Disassembly, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Heart, Myocytes, Cardiac, Transcription Factors, Transcriptome, Zebrafish, Zebrafish Proteins}, issn = {1549-5469}, doi = {10.1101/gr.244491.118}, author = {Pawlak, Michal and Kedzierska, Katarzyna Z and Migdal, Maciej and Nahia, Karim Abu and Ramilowski, Jordan A and Bugajski, Lukasz and Hashimoto, Kosuke and Marconi, Aleksandra and Piwocka, Katarzyna and Carninci, Piero and Winata, Cecilia L} } @article {113, title = {A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.}, journal = {Dev Dyn}, volume = {248}, year = {2019}, month = {2019 09}, pages = {837-849}, abstract = {

BACKGROUND: Identifying enhancers and deciphering their putative roles represent a major step to better understand the mechanism of metazoan gene regulation, development, and the role of regulatory elements in disease. Comparative genomics and transgenic assays have been used with some success to identify critical regions that are involved in regulating the spatiotemporal expression of genes during embryogenesis.

RESULTS: We identified two novel tetrapod-teleost conserved noncoding elements within the vicinity of the zic3 and zic6 loci in the zebrafish genome and demonstrated their ability to drive tissue-specific expression in a transgenic zebrafish assay. The syntenic analysis and robust green fluorescent expression in the developing habenula in the stable transgenic line were correlated with known sites of endogenous zic3 and zic6 expression.

CONCLUSION: This transgenic line that expresses green fluorescent protein in the habenula is a valuable resource for studying a specific population of cells in the zebrafish central nervous system. Our observations indicate that a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression.

}, keywords = {Animals, Animals, Genetically Modified, Conserved Sequence, Embryonic Development, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Green Fluorescent Proteins, Habenula, Homeodomain Proteins, Humans, Nervous System, Repressor Proteins, Transcription Factors, Zebrafish, Zebrafish Proteins}, issn = {1097-0177}, doi = {10.1002/dvdy.69}, author = {Minhas, Rashid and Paterek, Aleksandra and {\L}api{\'n}ski, Maciej and Baza{\l}a, Micha{\l} and Korzh, Vladimir and Winata, Cecilia L} } @article {pmid29229769, title = {Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition}, journal = {Development}, volume = {145}, year = {2018}, month = {01/2018}, abstract = {

In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs. Pan-embryonic CPA inhibition disrupted the maternal-to-zygotic transition (MZT), causing a failure of developmental progression beyond the mid-blastula transition and changes in global gene expression that indicated a failure of ZGA and maternal mRNA clearance. Among the genes that were differentially expressed were those encoding chromatin modifiers and key transcription factors involved in ZGA, including nanog, pou5f3 and sox19b, which have distinct CPA dynamics. Our results establish the necessity of CPA for ensuring progression of the MZT. The RNA-seq data generated in this study represent a valuable zebrafish resource for the discovery of novel elements of the early embryonic transcriptome.

}, author = {Winata, C. L. and {\L}api{\'n}ski, M. and Pryszcz, L. and Vaz, C. and Bin Ismail, M. H. and Nama, S. and Hajan, H. S. and Lee, S. G. P. and Korzh, V. and Sampath, P. and Tanavde, V. and Mathavan, S.} } @article {36, title = {Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.}, journal = {Genome Res}, volume = {21}, year = {2011}, month = {2011 Aug}, pages = {1328-38}, abstract = {

Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50\%-60\%. Taken together, our data constitute a useful genomic information and valuable transcriptome resource for gene discovery and for understanding the mechanisms of early embryogenesis in zebrafish.

}, keywords = {Animals, Base Sequence, Genome, RNA, Messenger, RNA, Messenger, Stored, Sequence Analysis, RNA, Transcriptome, Zebrafish, Zebrafish Proteins, Zygote}, issn = {1549-5469}, doi = {10.1101/gr.116012.110}, author = {Aanes, H{\r a}vard and Winata, Cecilia L and Lin, Chi Ho and Chen, Jieqi P and Srinivasan, Kandhadayar G and Lee, Serene G P and Lim, Adrian Y M and Hajan, Hajira Shreen and Collas, Philippe and Bourque, Guillaume and Gong, Zhiyuan and Korzh, Vladimir and Alestr{\"o}m, Peter and Mathavan, Sinnakaruppan} }