Autistic Disorder; Zebrafish; Developmental Biology; Gene Expression Regulation, Developmental; Computational Biology; Genomics; Systems Biology
Public Health Interests
Stem Cell Center, Yale: Stem Cell Genetics
In our laboratory we investigate how gene regulation shapes vertebrate embryonic development using zebrafish as a model system. We combine genomics, genetics, embryology, chemical 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 focused on understanding the mechanisms that activate the genome soon after fertilization and how this universal transition drives post-transcriptional regulation of the maternal instructions to allow one of the central developmental transitions to occur. Our research is focusing in four main areas: Analysis of Genome activation, mechanisms of post-transcriptional regulation, computational modeling of gene expression and animal models to understand autism.
- RESA identifies mRNA regulatory sequences with high resolution. Yartseva V,Takacs CM, Vejnar CE, Lee MT‡, Giraldez AJ‡. Nature Methods. in press.
- 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‡. EMBO J. 2016 Oct 4;35(19):2087-2103
- Upstream ORFs are prevalent translational repressors in vertebrates. Johnstone TG, Bazzini AA, Giraldez AJ‡. EMBO J. 2016 Apr 1;35(7)
- 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‡ Neuron. 2016 Feb 17
Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition
Lee MT#, Ashley R#. Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ‡. Nature, 2013 Sep 22. doi: 10.1038/nature12632
Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish.
Bazzini AA, Lee MT, Giraldez AJ‡. Science. 13 April 2012: 233-23
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. Neuron. 2016 Feb 17;89(4):725-33. doi: 10.1016/j.neuron.2015.12.039. Epub 2016 Jan 28.
Upstream ORFs are prevalent translational repressors in vertebrates.
Johnstone TG, Bazzini AA, Giraldez AJ. EMBO J. 2016 Feb 19. pii: e201592759.
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. Science. 2010 Jun 25;328(5986):1694-8. Epub 2010 May 6.
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.
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. Nat Methods. 2015 Oct;12(10):982-8. doi: 10.1038/nmeth.3543. Epub 2015 Aug 31.
miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration.
Staton AA, Knaut H and Giraldez AJ. Nature Genetics. 2011 Mar;43(3):204-11. Epub 2011 Jan 23.