1
|
Buono L, Annona G, Magri MS, Negueruela S, Sepe RM, Caccavale F, Maeso I, Arnone MI, D’Aniello S. Conservation of cis-Regulatory Syntax Underlying Deuterostome Gastrulation. Cells 2024; 13:1121. [PMID: 38994973 PMCID: PMC11240583 DOI: 10.3390/cells13131121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Throughout embryonic development, the shaping of the functional and morphological characteristics of embryos is orchestrated by an intricate interaction between transcription factors and cis-regulatory elements. In this study, we conducted a comprehensive analysis of deuterostome cis-regulatory landscapes during gastrulation, focusing on four paradigmatic species: the echinoderm Strongylocentrotus purpuratus, the cephalochordate Branchiostoma lanceolatum, the urochordate Ciona intestinalis, and the vertebrate Danio rerio. Our approach involved comparative computational analysis of ATAC-seq datasets to explore the genome-wide blueprint of conserved transcription factor binding motifs underlying gastrulation. We identified a core set of conserved DNA binding motifs associated with 62 known transcription factors, indicating the remarkable conservation of the gastrulation regulatory landscape across deuterostomes. Our findings offer valuable insights into the evolutionary molecular dynamics of embryonic development, shedding light on conserved regulatory subprograms and providing a comprehensive perspective on the conservation and divergence of gene regulation underlying the gastrulation process.
Collapse
Affiliation(s)
- Lorena Buono
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Research Infrastructure for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarollo (CABD), Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | | | - Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 80133 Naples, Italy
| | - Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| |
Collapse
|
2
|
Srdanović S, Þorsteinsson H, Friðriksson Þ, Pétursson SÓ, Maier VH, Karlsson KÆ. Transient knock-down of kcna2 reduces sleep in larval zebrafish. Behav Brain Res 2017; 326:13-21. [PMID: 28223099 DOI: 10.1016/j.bbr.2017.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 11/19/2022]
Abstract
In the current study we set out to determine the effects of morpholino oligonucleotide (MO) knock-down of kcna2 on sleep-wake cycles in zebrafish. The results were compared to a non-overlapping MO injection, Dec2, who's mutant is also linked with a short sleep phenotype. Four groups of fish were used in the experiment: naïve fish, and fish injected with either control, kcna2, or Dec2 MO. All groups underwent 24-h behavioral monitoring of sleep-wake cycles at four and seven days-post-fertilization (dpf). First, we established an immobility dependent, sleep related, increase in arousal thresholds at both 4 and 7 dpf. Secondly, we show that kcna2 MO injected fish exhibit significantly less sleep behavior than controls and naïve fish, whereas Dec2 MO injections had similar but less severe effects. Finally, using kcna2 MO injected fish only, we turn to local field recordings at the level of the telencephalon and tectum opticum and rule out that the knock-down resulted in a non-specific increase in neural excitability that would mask sleep behavior.
Collapse
Affiliation(s)
| | | | - Þ Friðriksson
- Biomedical Center, University of Iceland, Læknagarður, 101, Reykjavik, Iceland
| | - S Ó Pétursson
- Biomedical Center, University of Iceland, Læknagarður, 101, Reykjavik, Iceland
| | - V H Maier
- Biomedical Center, University of Iceland, Læknagarður, 101, Reykjavik, Iceland
| | - K Æ Karlsson
- Department of Biomedical Engineering, School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.
| |
Collapse
|
3
|
Ow JR, Tan YH, Jin Y, Bahirvani AG, Taneja R. Stra13 and Sharp-1, the Non-Grouchy Regulators of Development and Disease. Curr Top Dev Biol 2014; 110:317-38. [DOI: 10.1016/b978-0-12-405943-6.00009-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
4
|
Ling BMT, Gopinadhan S, Kok WK, Shankar SR, Gopal P, Bharathy N, Wang Y, Taneja R. G9a mediates Sharp-1-dependent inhibition of skeletal muscle differentiation. Mol Biol Cell 2012; 23:4778-85. [PMID: 23087213 PMCID: PMC3521685 DOI: 10.1091/mbc.e12-04-0311] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sharp-1, a basic helix-loop-helix transcription factor, is a potent repressor of skeletal muscle differentiation and is dysregulated in muscle pathologies. However, the mechanisms by which it inhibits myogenesis are not fully understood. Here we show that G9a, a lysine methyltransferase, is involved in Sharp-1-mediated inhibition of muscle differentiation. We demonstrate that G9a directly interacts with Sharp-1 and enhances its ability to transcriptionally repress the myogenin promoter. Concomitant with a differentiation block, G9a-dependent histone H3 lysine 9 dimethylation (H3K9me2) and MyoD methylation are apparent upon Sharp-1 overexpression in muscle cells. RNA interference-mediated reduction of G9a or pharmacological inhibition of its activity erases these repressive marks and rescues the differentiation defect imposed by Sharp-1. Our findings provide new insights into Sharp-1-dependent regulation of myogenesis and identify epigenetic mechanisms that could be targeted in myopathies characterized by elevated Sharp-1 levels.
Collapse
Affiliation(s)
- Belinda Mei Tze Ling
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | | | | | | | | | | | | | | |
Collapse
|