Daniel Cifuentes, PhD

Assistant Professor, Biochemistry

Daniel Cifuentes
617.358.4521
72 E. Concord St Silvio Conte (K)

Biography

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.

Other Positions

  • Member, Genome Science Institute, Boston University

Education

  • Universidad de Barcelona, PhD
  • Universidad de Barcelona, BS

Classes Taught

  • GMSBI777
  • GMSGE701
  • GMSMM730

Publications

  • Published on 7/22/2022

    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. PMID: 35801921.

    Read at: PubMed
  • Published on 6/24/2022

    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. PMID: 35749346.

    Read at: PubMed
  • Published on 2/4/2022

    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. PMID: 35120176.

    Read at: PubMed
  • Published on 9/20/2021

    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. PMID: 34365507.

    Read at: PubMed
  • Published on 1/7/2021

    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. PMID: 33417854.

    Read at: PubMed
  • Published on 12/29/2020

    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.

    Read at: PubMed
  • Published on 11/19/2020

    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. 2020 12 17; 80(6):1104-1122.e9. PMID: 33259812.

    Read at: PubMed
  • Published on 3/18/2020

    Kretov DA, Walawalkar IA, Mora-Martin A, Shafik AM, Moxon S, Cifuentes D. Ago2-Dependent Processing Allows miR-451 to Evade the Global MicroRNA Turnover Elicited during Erythropoiesis. Mol Cell. 2020 04 16; 78(2):317-328.e6. PMID: 32191872.

    Read at: PubMed
  • Published on 6/21/2019

    Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Res. 2019 07; 29(7):1100-1114. PMID: 31227602.

    Read at: PubMed
  • Published on 4/4/2019

    Marivin A, Morozova V, Walawalkar I, Leyme A, Kretov DA, Cifuentes D, Dominguez I, Garcia-Marcos M. GPCR-independent activation of G proteins promotes apical cell constriction in vivo. J Cell Biol. 2019 05 06; 218(5):1743-1763. PMID: 30948426.

    Read at: PubMed

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