Blood-Brain Barrier; Cardiovascular System; Neurons; Zebrafish; MicroRNAs
Small RNAs in Development
Stem Cell Center, Yale: Stem Cells and Tissue Repair
Using Zebrafish, my laboratory's goal is to understand how small non-coding RNAs coordinate cardiovascular and neuronal development.
Extensive Research Description
The vascular system is fundamental for embryonic development and adult life, and aberrant vascularization is associated with numerous diseases, including cancer,atherosclerosis and stroke. Since the processes that govern blood vessel formation are conserved, it is possible to use model systems to gain novel insights on vascular development and function. The Zebrafish (Danio rerio) is an ideal model to study blood vessel formation during embryonic development. The transparency and external development of the zebrafish embryo allow an unprecedented level of observation and experimental manipulation. In parallel, numerous techniques allow forward and reverse genetic analysis of signaling pathways in the zebrafish.These genetic approaches coupled with the ability to easily visualize circulatory patterns and blood vessel morphology, make the zebrafish an ideal in vivo platform to assay gene function during vascular development.
microRNAs (miRNAs) are highly conserved non-coding small RNAs that post-transcriptionally regulate gene expression by binding to the 3’UTR of target mRNAs and inhibit their translation, or promote their degradation. miRNAs are autonomously transcribed in a large mRNA transcript (pri-mRNA), or are found in introns of coding genes. In both cases,mature miRNAs are formed by sequential processing into a primary stem loop precursor (pre-miRNAs) by the endonucleases Drosha and Dicer. In vertebrates,the 22 base pair duplex miRNAs are unwound and a single mature strand is loaded onto Argonaute 2 (Ago2). The Ago2/miRNA complex (the RNA-induced silencing complex, or RISC), leads to translational repression and decreased transcript stability, through deadenylation. miRNAs function in a number of different biological processes, including cardiogenesis, muscle development, oncogenesis, brain morphogenesis, and hematopoiesis.
Despite recent findings, several critical barriers remain that hamper the study of miRNAs. First, identification of relevant miRNA targets, especially cell-specific target transcripts in vivo,can be difficult. Second, genetic manipulation (i.e. targeted knockout) of miRNA sequences in the vertebrate genome can be challenging and, until recently, had been limited to mice. Third, in many cases loss of miRNA function leads to subtle phenotypic changes, which can be difficult to observe and characterize during embryonic stages in mouse. Finally, the genetic interaction of miRNAs and their targets can be difficult to dissect in vivo in the mouse system.
The lab takes advantage of the zebrafish as a model system to overcome these barriers. Our goal is to elucidate how miRNAs participated in the genetic network driving arteries-veins differentiation, angiogenesis, neuro-vascular development.
Full List of PubMed Publications
- Hirschi KK, Nicoli S, Walsh K: Hematopoiesis Lineage Tree Uprooted: Every Cell Is a Rainbow. Dev Cell. 2017 Apr 10. PMID: 28399402
- Kasper DM, Moro A, Ristori E, Narayanan A, Hill-Teran G, Fleming E, Moreno-Mateos M, Vejnar CE, Zhang J, Lee D, Gu M, Gerstein M, Giraldez A, Nicoli S: MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos. Dev Cell. 2017 Mar 27. PMID: 28350988
- Narayanan A, Hill-Teran G, Moro A, Ristori E, Kasper DM, A Roden C, Lu J, Nicoli S: In vivo mutagenesis of miRNA gene families using a scalable multiplexed CRISPR/Cas9 nuclease system. Sci Rep. 2016 Aug 30; 2016 Aug 30. PMID: 27572667
- Lopez-Ramirez MA, Calvo CF, Ristori E, Thomas JL, Nicoli S: Isolation and Culture of Adult Zebrafish Brain-derived Neurospheres. J Vis Exp. 2016 Feb 29; 2016 Feb 29. PMID: 26967835
- Fortuna V, Pardanaud L, Brunet I, Ola R, Ristori E, Santoro MM, Nicoli S, Eichmann A: Vascular Mural Cells Promote Noradrenergic Differentiation of Embryonic Sympathetic Neurons. Cell Rep. 2015 Jun 23; 2015 Jun 11. PMID: 26074079
- Kallakuri S, Yu JA, Li J, Li Y, Weinstein BM, Nicoli S, Sun Z: Endothelial cilia are essential for developmental vascular integrity in zebrafish. J Am Soc Nephrol. 2015 Apr; 2014 Sep 11. PMID: 25214579
- Ristori E, Lopez-Ramirez MA, Narayanan A, Hill-Teran G, Moro A, Calvo CF, Thomas JL, Nicoli S: A Dicer-miR-107 Interaction Regulates Biogenesis of Specific miRNAs Crucial for Neurogenesis. Dev Cell. 2015 Mar 9; 2015 Feb 5. PMID: 25662174
- Baeyens N, Nicoli S, Coon BG, Ross TD, Van den Dries K, Han J, Lauridsen HM, Mejean CO, Eichmann A, Thomas JL, Humphrey JD, Schwartz MA: Vascular remodeling is governed by a VEGFR3-dependent fluid shear stress set point. Elife. 2015 Feb 2; 2015 Feb 2. PMID: 25643397
- Ristori E, Nicoli S: miRNAs expression profile in zebrafish developing vessels. Methods Mol Biol. 2015. PMID: 25468601
- Lopez-Ramirez MA, Nicoli S: Role of miRNAs and epigenetics in neural stem cell fate determination. Epigenetics. 2014 Jan; 2013 Dec 16. PMID: 24342893