Daniel Cifuentes, PhD
Associate Professor
Boston University Chobanian & Avedisian School of Medicine
Biochemistry & Cell Biology

PhD, Universidad de Barcelona
BS, Universidad de Barcelona



Our research goals in the Cifuentes laboratory aim to understand the molecular mechanisms of RNA regulation. In particular, we focus on the study of RNA-binding proteins, microRNAs, and RNA modifications to uncover their impact on small RNA biogenesis and mRNA post-transcriptional regulation. To address these goals, the lab combines high-throughput genetic, genomic, and proteomic approaches applied to two independent but technically interconnected areas: vertebrate development and viral replication, using zebrafish and filoviruses as primary model systems.

Role of post-transcriptional regulation during vertebrate embryogenesis:
The beginning of a new life is one of the most enigmatic and dynamic events in Biology. Right after fertilization, multiple cell division occur without any contribution of the transcriptionally silent genome. Therefore, the first embryonic processes are organized at post-transcriptional level. Our laboratory focuses on the study of how small RNA and RNA-binding proteins regulate mRNA stability and decay. To this end, we use zebrafish as a model system to dissect the process of post-transcriptional reprogramming within the context of a whole organism. The combination of fish embryo microinjections, together with powerful genetic, genomic, and proteomic approaches provides a unique platform to address this central question in biology.

Regulation of transcription, replication and translation in RNA viruses:
Filovirus and Arenavirus belong to the group of Viruses of Concern (VOCs) with epidemic and pandemic potential as identified by the World Health Organization. Their common feature is that these viruses have an RNA genome, and as such, RNA regulation take center stage in orchestrating the infection cycle of these viruses. In our laboratory, we investigate 1) how small RNAs and RNA binding protein govern the balance between transcription and replication in Filovirus (Ebola and Marburg virus) and 2) how secondary RNA structures and cellular factors regulate translation of viral mRNAs in Arenavirus (Lassa virus). To this end, we capitalize in our long-standing collaboration with the group of Prof. Mühlberger at the National Emerging Disease Laboratory (NEIDL) at Boston University.

Assistant Professor
Boston University Chobanian & Avedisian School of Medicine
Virology, Immunology & Microbiology


Member
Boston University
Genome Science Institute




Boston University RNA Club
11/01/2023 - 10/31/2025 (PI)
RNA Society


Uncovering the RNA regulatory mechanisms driving pathogenicity of mass-casualty viruses: Merging the technologies of RNA biology and enhanced biosafety to create the next generation of broad spectrum
10/01/2022 - 09/30/2025 (Multi-PI)
PI: Daniel Cifuentes, PhD
Howard Hughes Medical Institute


Analysis of non-canonical functions of microRNAs
03/01/2019 - 02/28/2025 (PI)
NIH/National Institute of General Medical Sciences
3R01GM130935-05S1

Boston University School of Medicine RNA Club
11/01/2018 - 10/31/2024 (PI)
RNA Society


RNA Salon at Boston University
11/01/2016 - 10/31/2024 (PI)
RNA Society


Student Intern Agreement with Universidad Francisco de Vitoria - Covadonga Lopez Ramos
02/01/2018 - 07/31/2024 (Co-Investigator)
PI: Mikel Garcia-Marcos, PhD
Universidad Francisco de Vitoria


BU RNA Salon
11/01/2021 - 10/31/2023 (PI)
RNA Society


Developing a high-throughput method to validate microRNA biogenesis in vivo.
08/01/2020 - 12/31/2022 (PI)
NIH/National Institute of General Medical Sciences
5R21GM138951-02

Deep characterization of the biogenesis and function of Ebola virus microRNAs
07/01/2019 - 06/30/2022 (Multi-PI)
PI: Daniel Cifuentes, PhD
NIH/National Institute of Allergy & Infectious Diseases
5R21AI147285-02

Boston University RNA Club
11/01/2019 - 10/31/2021 (PI)
RNA Society


Showing 10 of 13 results. Show All Results


Title


Yr Title Project-Sub Proj Pubs
2023 Analysis of non-canonical functions of microRNAs 3R01GM130935-05S1
2023 Analysis of non-canonical functions of microRNAs 5R01GM130935-05
2022 Analysis of non-canonical functions of microRNAs 5R01GM130935-04
2022 Analysis of non-canonical functions of microRNAs 3R01GM130935-04S1
2021 Developing a high-throughput method to validate microRNA biogenesis in vivo. 5R21GM138951-02
2021 Analysis of non-canonical functions of microRNAs 5R01GM130935-03
2020 Developing a high-throughput method to validate microRNA biogenesis in vivo. 1R21GM138951-01
2020 Deep characterization of the biogenesis and function of Ebola virus microRNAs 5R21AI147285-02
2020 Analysis of non-canonical functions of microRNAs 3R01GM130935-02S1
2020 Analysis of non-canonical functions of microRNAs 5R01GM130935-02
Showing 10 of 17 results. Show All Results

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.

iCite Analysis       Copy PMIDs To Clipboard

  1. Ross SJ, Hume AJ, Olejnik J, Turcinovic J, Honko AN, McKay LGA, Connor JH, Griffiths A, Mühlberger E, Cifuentes D. Low-Input, High-Resolution 5' Terminal Filovirus RNA Sequencing with ViBE-Seq. Viruses. 2024 Jul 01; 16(7).View Related Profiles. PMID: 39066227; PMCID: PMC11281615; DOI: 10.3390/v16071064;
     
  2. Kretov DA, Folkes L, Mora-Martin A, Walawalkar IA, Imrat, Syedah N, Vanuytsel K, Moxon S, Murphy GJ, Cifuentes D. The miR-144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. Nat Commun. 2024 May 07; 15(1):3821.View Related Profiles. PMID: 38714702; PMCID: PMC11076586; DOI: 10.1038/s41467-024-47982-2;
     
  3. Nelson EV, Ross SJ, Olejnik J, Hume AJ, Deeney DJ, King E, Grimins AO, Lyons SM, Cifuentes D, Mühlberger E. The 3' Untranslated Regions of Ebola Virus mRNAs Contain AU-Rich Elements Involved in Posttranscriptional Stabilization and Decay. J Infect Dis. 2023 Nov 13; 228(Supplement_7):S488-S497.View Related Profiles. PMID: 37551415; PMCID: PMC10651315; DOI: 10.1093/infdis/jiad312;
     
  4. Kretov DA, Folkes L, Mora-Martin A, Syedah N, Walawalkar IA, Vanyustel K, Moxon S, Murphy GJ, Cifuentes D. The miR-144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. bioRxiv. 2023 Jul 19.View Related Profiles. PMID: 37503141; PMCID: PMC10370056; DOI: 10.1101/2023.07.18.549576;
     
  5. Shang R, Kretov DA, Adamson SI, Treiber T, Treiber N, Vedanayagam J, Chuang JH, Meister G, Cifuentes D, Lai EC. Regulated dicing of pre-mir-144 via reshaping of its terminal loop. Nucleic Acids Res. 2022 Jul 22; 50(13):7637-7654.View Related Profiles. PMID: 35801921; PMCID: PMC9303283; DOI: 10.1093/nar/gkac568;
     
  6. Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Correction: Recombinant Lloviu virus as a tool to study viral replication and host responses. PLoS Pathog. 2022 Jun; 18(6):e1010659.View Related Profiles. PMID: 35749346; PMCID: PMC9231773; DOI: 10.1371/journal.ppat.1010659;
     
  7. Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Recombinant Lloviu virus as a tool to study viral replication and host responses. PLoS Pathog. 2022 02; 18(2):e1010268.View Related Profiles. PMID: 35120176; PMCID: PMC8849519; DOI: 10.1371/journal.ppat.1010268;
     
  8. Floro J, Dai A, Metzger A, Mora-Martin A, Ganem NJ, Cifuentes D, Wu CS, Dalal J, Lyons SM, Labadorf A, Flynn RL. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Res. 2021 09 20; 49(16):9424-9443.View Related Profiles. PMID: 34365507; PMCID: PMC8450105; DOI: 10.1093/nar/gkab647;
     
  9. Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell. 2021 Jan 07; 81(1):212.View Related Profiles. PMID: 33417854; PMCID: PMC7831449; DOI: 10.1016/j.molcel.2020.12.028;
     
  10. Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Ythdf m6A Readers Function Redundantly during Zebrafish Development. Cell Rep. 2020 12 29; 33(13):108598. PMID: 33378672; DOI: 10.1016/j.celrep.2020.108598;
     
Showing 10 of 30 results. Show More

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

Bar chart showing 30 publications over 16 distinct years, with a maximum of 3 publications in 2010 and 2016 and 2020 and 2022

YearPublications
20031
20051
20061
20072
20081
20103
20111
20131
20163
20182
20192
20203
20212
20223
20232
20242


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The Brink 2/17/2023

From the Lab to Your Life

BU Today 6/6/2022

2016-2019 Boston University: Peter Paul Career Development Professorship
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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