Antonio Giraldez, PhD
Fergus F. Wallace Professor of Genetics
Research & Publications
Biography
News
Research Summary
In our laboratory we investigate the gene regulatory code that shapes vertebrate embryonic development using zebrafish, mouse and human as a model system. We combine genomics, genetics, embryology, imaging 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.
Research Interests
Microscopy; Developmental Biology; Gene Expression Regulation, Developmental; Computational Biology; Genomics; Systems Biology; Autism Spectrum Disorder; RNA Recognition Motif
Public Health Interests
Child/Adolescent Health
Research Images
Selected Publications
- The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activationMiao L, Tang Y, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation. Molecular Cell 2022, 82: 986-1002.e9. PMID: 35182480, PMCID: PMC9327391, DOI: 10.1016/j.molcel.2022.01.024.
- Abstract 706: Changes in Translational Efficacy During Zebrafish Heart RegenerationGoldman J, Bazzini A, Giraldez A, Poss K. Abstract 706: Changes in Translational Efficacy During Zebrafish Heart Regeneration. Circulation Research 2019, 125 DOI: 10.1161/res.125.suppl_1.706.
- Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafishVejnar CE, Messih M, Takacs C, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee M, Beaudoin JD, Musaev D, Darwich-Codore H, Walther T, Tavazoie S, Cifuentes D, Giraldez A. Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Research 2019, 29: 1100-1114. PMID: 31227602, PMCID: PMC6633259, DOI: 10.1101/gr.245159.118.
- Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome ActivationChan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation. Developmental Cell 2019, 49: 867-881.e8. PMID: 31211993, PMCID: PMC7201981, DOI: 10.1016/j.devcel.2019.05.037.
- Analyses of mRNA structure dynamics identify embryonic gene regulatory programsBeaudoin 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 resolutionYartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nature Methods 2016, 14: 201-207. PMID: 28024160, PMCID: PMC5423094, DOI: 10.1038/nmeth.4121.
- 5.32 A ZEBRAFISH MODEL FOR IDENTIFYING COMMON BIOLOGICAL MECHANISMS AND PHARMACOLOGICAL PATHWAYS IN AUTISM SPECTRUM DISORDERSIjaz S, Ghosh M, Wilson S, Rihel J, Giraldez A, State M, Hoffman E. 5.32 A ZEBRAFISH MODEL FOR IDENTIFYING COMMON BIOLOGICAL MECHANISMS AND PHARMACOLOGICAL PATHWAYS IN AUTISM SPECTRUM DISORDERS. Journal Of The American Academy Of Child & Adolescent Psychiatry 2016, 55: s194. DOI: 10.1016/j.jaac.2016.09.291.
- Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transitionBazzini AA, del Viso F, Moreno‐Mateos M, 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.
- Upstream ORFs are prevalent translational repressors in vertebratesJohnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. The EMBO Journal 2016, 35: 706-723. PMID: 26896445, PMCID: PMC4818764, DOI: 10.15252/embj.201592759.
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivoMoreno-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: 982-988. PMID: 26322839, PMCID: PMC4589495, DOI: 10.1038/nmeth.3543.
- Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservationBazzini 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: 981-993. PMID: 24705786, PMCID: PMC4193932, DOI: 10.1002/embj.201488411.
- Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transitionLee 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: 360-364. PMID: 24056933, PMCID: PMC3925760, DOI: 10.1038/nature12632.
- Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in ZebrafishBazzini AA, Lee MT, Giraldez AJ. Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish. Science 2012, 336: 233-237. PMID: 22422859, PMCID: PMC3547538, DOI: 10.1126/science.1215704.
- A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic ActivityCifuentes 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 2010, 328: 1694-1698. PMID: 20448148, PMCID: PMC3093307, DOI: 10.1126/science.1190809.
- MicroRNAs in Development and DiseaseStaton A, Giraldez A. MicroRNAs in Development and Disease. 2008 DOI: 10.1002/9780470015902.a0020863.
- Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAsGiraldez 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 2006, 312: 75-79. PMID: 16484454, DOI: 10.1126/science.1122689.
- MicroRNAs Regulate Brain Morphogenesis in ZebrafishGiraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP, Schier AF. MicroRNAs Regulate Brain Morphogenesis in Zebrafish. Science 2005, 308: 833-838. PMID: 15774722, DOI: 10.1126/science.1109020.