Daniel Cifuentes, PhD
Assistant Professor
Boston University School of Medicine
Dept of Biochemistry

PhD, Universidad De Barcelona



The beginning of a new life is one of the most enigmatic and dynamic events in Biology. The long term goal of my laboratory is to understand how post-transcriptional regulation of RNA and proteins orchestrates development of a single cell oocyte into a whole embryo and how these mechanisms can be extrapolated to other biological transitions such as cellular reprogramming or malignant transformation.

To address these questions, my laboratory focuses on the mechanisms of post-transcriptional regulation during vertebrate embryogenesis using zebrafish as a model system. This approach allows us to dissect the process of reprogramming in vivo within the context of a whole organism. The combination of fish embryo microinjection together with powerful genetic, genomic, and proteomic approaches provides a unique platform to address these central questions in biology.

2016-2019 Boston University: Peter Paul Career Development Professorship


Analysis of the Molecular Machinery of Micro RNA Processing Pathways
04/08/2016 - 03/31/2018 (PI)
NIH/National Institute of Child Health & Human Development
5R00HD071968-04

RNA Salon at Boston University
11/01/2016 - 10/31/2017 (PI)
RNA Society



Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

  1. Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Optimized CRISPR-Cas9 System for Genome Editing in Zebrafish. Cold Spring Harb Protoc. 2016 Oct 03; 2016(10):pdb.prot086850. PMID: 27698232; DOI: 10.1101/pdb.prot086850;.
  2. Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Optimization Strategies for the CRISPR-Cas9 Genome-Editing System. Cold Spring Harb Protoc. 2016 Oct 03; 2016(10):pdb.top090894. PMID: 27698246; DOI: 10.1101/pdb.top090894;.
  3. 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 Feb 17; 89(4):725-33. PMID: 26833134; PMCID: PMC4766582; DOI: 10.1016/j.neuron.2015.12.039;.
  4. Yoda M, Cifuentes D, Izumi N, Sakaguchi Y, Suzuki T, Giraldez AJ, Tomari Y. Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep. 2013 Nov 14; 5(3):715-26. PMID: 24209750; PMCID: PMC3856240; DOI: 10.1016/j.celrep.2013.09.029;.
  5. Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development. 2011 Oct; 138(20):4555-64. PMID: 21937602; PMCID: PMC3177320; DOI: 10.1242/dev.066779;.
  6. Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods. 2011 Jan; 8(1):67-9. PMID: 21151135; PMCID: PMC3018472; DOI: 10.1038/nmeth.1542;.
  7. 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. 2010 Jun 25; 328(5986):1694-8. PMID: 20448148; PMCID: PMC3093307; DOI: 10.1126/science.1190809;.
  8. Pescador N, Villar D, Cifuentes D, Garcia-Rocha M, Ortiz-Barahona A, Vazquez S, Ordoñez A, Cuevas Y, Saez-Morales D, Garcia-Bermejo ML, Landazuri MO, Guinovart J, del Peso L. Hypoxia promotes glycogen accumulation through hypoxia inducible factor (HIF)-mediated induction of glycogen synthase 1. PLoS One. 2010; 5(3):e9644. PMID: 20300197; PMCID: PMC2837373; DOI: 10.1371/journal.pone.0009644;.
  9. Flores E, Cifuentes D, Fernández-Novell JM, Medrano A, Bonet S, Briz MD, Pinart E, Peña A, Rigau T, Rodríguez-Gil JE. Freeze-thawing induces alterations in the protamine-1/DNA overall structure in boar sperm. Theriogenology. 2008 Jun; 69(9):1083-94. PMID: 18359506; DOI: 10.1016/j.theriogenology.2008.01.022;.
  10. Cifuentes D, Martínez-Pons C, García-Rocha M, Galina A, Ribas de Pouplana L, Guinovart JJ. Hepatic glycogen synthesis in the absence of glucokinase: the case of embryonic liver. J Biol Chem. 2008 Feb 29; 283(9):5642-9. PMID: 18165236; DOI: 10.1074/jbc.M706334200;.
Showing 10 of 14 results. Show More

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 14 publications over 9 distinct years, with a maximum of 3 publications in 2010 and 2016

YearPublications
20031
20051
20061
20072
20081
20103
20111
20131
20163
In addition to these self-described keywords below, a list of MeSH based concepts is available here.

CRISPR
iCLIP
microinjection
microRNA
zebrafish
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72 E. Concord St Silvio Conte (K)
Boston MA 02118
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