Antonio Giraldez, PhD
Fergus F. Wallace Professor of Genetics; Chair, Genetics
Research & Publications
Biography
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Research Summary
In our laboratory we investigate the gene regulatory code that shapes vertebrate embryonic development using zebrafish as a model system. We combine genomics, genetics, embryology, machine learning and computational biology to address a central question in biology: how does a fertilized egg develop into a complex multicellular embryo. This process requires a precise spatial and temporal regulation of gene expression. We are primarily focus on understanding i) the mechanisms that activate the genome after fertilization, ii) the post-transcriptional regulatory code that shapes mRNA stability and translation across vertebrates using the maternal to zygotic transition as a model, and iii) the gene regulatory code that specifies different cell types during embryogenesis. Our research is focusing in four main areas: Mechanisms of Genome activation, mechanisms of post-transcriptional regulation, computational modeling of gene expression and animal models to understand autism.
Coauthors
Research Interests
Developmental Biology; Gene Expression Regulation, Developmental; Computational Biology; Genomics; Systems Biology; Autism Spectrum Disorder; RNA Recognition Motif
Public Health Interests
Child/Adolescent Health
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Selected Publications
- Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nature Structural & Molecular Biology 2018, 25: 677-686. PMID: 30061596, PMCID: PMC6690192, DOI: 10.1038/s41594-018-0091-z.
- RESA identifies mRNA-regulatory sequences at high resolution.Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nature Methods 2017, 14: 201-207. PMID: 28024160, PMCID: PMC5423094, DOI: 10.1038/nmeth.4121.
- Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. The EMBO Journal 2016, 35: 2087-2103. PMID: 27436874, PMCID: PMC5048347, DOI: 10.15252/embj.201694699.
- Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition.Lee MT, Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature 2013, 503: 360-4. PMID: 24056933, PMCID: PMC3925760, DOI: 10.1038/nature12632.
- Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish.Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science (New York, N.Y.) 2012, 336: 233-7. PMID: 22422859, PMCID: PMC3547538, DOI: 10.1126/science.1215704.
- Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2.Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJ, Wilson SW, Rihel J, State MW, Giraldez AJ. Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2. Neuron 2016, 89: 725-33. PMID: 26833134, PMCID: PMC4766582, DOI: 10.1016/j.neuron.2015.12.039.
- Upstream ORFs are prevalent translational repressors in vertebrates.Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal 2016, 35: 706-23. PMID: 26896445, PMCID: PMC4818764, DOI: 10.15252/embj.201592759.
- A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science (New York, N.Y.) 2010, 328: 1694-8. PMID: 20448148, PMCID: PMC3093307, DOI: 10.1126/science.1190809.
- Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. The EMBO Journal 2014, 33: 981-93. PMID: 24705786, PMCID: PMC4193932, DOI: 10.1002/embj.201488411.
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nature Methods 2015, 12: 982-8. PMID: 26322839, PMCID: PMC4589495, DOI: 10.1038/nmeth.3543.
- miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration.Staton AA, Knaut H, Giraldez AJ. miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration. Nature Genetics 2011, 43: 204-11. PMID: 21258340, PMCID: PMC3071589, DOI: 10.1038/ng.758.
- Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs.Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science (New York, N.Y.) 2006, 312: 75-9. PMID: 16484454, DOI: 10.1126/science.1122689.
- MicroRNAs regulate brain morphogenesis in zebrafish.Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP, Schier AF. MicroRNAs regulate brain morphogenesis in zebrafish. Science (New York, N.Y.) 2005, 308: 833-8. PMID: 15774722, DOI: 10.1126/science.1109020.