RNA Molecular Biology Laboratory

Markus Hafner, Ph.D.

    Overview

    Research Areas (IRP Lab Groups)

    Genetics and Genomics,
    Molecular Biology and Biochemistry,
    RNA Biology,
    Systems Biology

    The RNA Molecular Biology Laboratory (RMBL) studies the impact of RNA binding proteins (RBPs) on posttranscriptional gene regulation (PTGR). PTGR summarizes various processes acting upon coding and non-coding RNA and includes RNA maturation, ribonucleoprotein (RNP) assembly, transport, translation, and turnover (Figure 1).

    The recent introduction of large-scale quantitative methods, such as next-generation sequencing (NGS) and modern mass spectrometry (MS), allows for the first-time determination of the functional impact of RBPs on a systems-wide level and has sparked a renewed interest in the systematic characterization of PTGR processes.

    Members of the RMBL focus on elucidating the function and molecular mechanisms of RNA binding proteins involved in RNA transport, RNA stability and turnover, and RNA translation. Broadly, we are pursuing four interdependent projects:

    A rough categorization of interconnected posttranscriptional gene regulatory processes based on cellular compartmentalization.
    Figure 1
    • Investigate the role of predicted AU-rich element binding proteins in determining mRNA turnover.
    • Identify and characterize the interaction network of mRNA binding transport and shuttling proteins and their RNA targets at a sequence and functional level.
    • Investigate the impact of select RBPs on translation initiation and elongation.
    • Integrate the results from our systems-level determination of cis-acting elements into high-resolution maps of posttranscriptional regulatory events.

    Related NIAMS Labs

    Scientific Advances

    The Metabolic Enzyme PKM2 Enters the Nucleus and Plays a Gene Regulatory Role
    PACCE Is a Novel Method for Using Mass Spectrometry to Identify Cellular Proteins That Bind RNA

    Core Research Facilities

    Labs at the NIAMS are supported by the following state-of-the-art facilities and services:

    Staff

    Former Lab Members

    Research Fellows

    • James Marks, Ph.D., 2019-2024; Research Assistant Professor, Vanderbilt University
    • Daniel Benhalevy, Ph.D., 2016-2022; Assistant Professor (Tenure-Track), Tel Aviv University, Israel
    • Amir Manzourolajdad, Ph.D., 2019-2021; Visiting Assistant Professor, Colgate University

    Postdoctoral Fellows

    • Aishe Angeletti Sarshad, Ph.D., 2014-2018; Assistant Professor (Tenure-Track), Gothenburg University, Sweden
    • Suman Ghosal, Ph.D., 2016-2017; Clinical Genomics Specialist, Guidehouse/NIAID
    • Tara Dutka, Ph.D., 2014-2016; Program Director, NIH

    Predoctoral Fellows

    • Alexandra Balvey Gil, 2023;  Pre-doctoral Fellow, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain
    • Arwa Fallatah, M.Sc., 2017-2021; Postdoctoral Fellow, CCR/NCI

    Postbaccalaureate Fellows

    • Emma Young, 2021 - 2023; Graduate Student, UCLA
    • Delaney Ahn, 2021-2022
    • Duncan Claypool, 2018-2020; M.D./Ph.D. student, University of Illinois in Chicago
    • Alexis Jacob, 2018-2020; Ph.D. student, Northwestern University
    • Nicole Johnson, 2017-2019; Research Program Coordinator, Johns Hopkins University School of Medicine
    • Ana I. Correa Muler, 2016-2018; Ph.D. student, Gothenburg University, Sweden
    • Hannah L. McFarland, 2015-2017; Senior Healthcare Consultant, Deloitte
    • Charles Danan, 2014-2016; M.D/Ph.D. student, University of Pennsylvania
    • Sudhir Manickavel, 2014-2015; Resident, University of Alabama Medical School

    Image & Media Gallery

    gloved hand places sample under imaging microscope
    Dr. Markus Hafner on the importance of RNA and RNA-binding proteins in gene expression and disease

    Scientific Publications

    Selected Recent Publications

    The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3' UTRs.

    Suzawa M, Qiu C, Polash AH, Yamaji M, Jacob AA, Horikawa W, Farroha EM, Barua M, Feng X, Liu C, Williams JG, Randazzo D, Sartorelli V, Valkov E, Yamaji M, Hall TMT, Hafner M
    bioRxiv.
    2025 Sep 25;
    pii: 2025.09.25.678639. doi: 10.1101/2025.09.25.678639
    PMID: 41040373

    Discovery and therapeutic delivery of microRNAs targeting deregulated glioblastoma pathways inhibits tumor growth in mice.

    Saha S, Zhang Y, Gibert MK Jr, Dube C, Hanif F, Mulcahy EQX, Bednarek S, Sun Y, Marcinkiewicz P, Wang X, Kwak G, Polash AH, Li H, Hudson K, Dinda M, Saha T, McCord M, Guessous F, Cruickshanks N, Rivera Colon R, Dell'Olio L, Anbu R, Liu W, Choi S, Kefas B, Kumar P, Klibanov AL, Schiff D, Suk JS, Hanes J, Mata J, Hafner M, Abounader R
    J Clin Invest.
    2026 Jun 30;
    pii: e195639. doi: 10.1172/JCI195639
    PMID: 42378058

    PCLIPtools: a robust framework for identifying RNA-protein interaction sites from PAR-CLIP experiments.

    Polash AH, Hafner M
    Nucleic Acids Res.
    2026 Jan 22;
    54(3).
    doi: 10.1093/nar/gkag062
    PMID: 41631485

    Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B.

    Muys BR, Shrestha RL, Anastasakis DG, Pongor L, Li XL, Grammatikakis I, Polash A, Chari R, Gorospe M, Harris CC, Aladjem MI, Basrai MA, Hafner M, Lal A
    Cell Rep.
    2023 Mar 28;
    42(3).
    doi: 10.1016/j.celrep.2023.112260
    PMID: 36924503

    A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.

    Anastasakis DG, Jacob A, Konstantinidou P, Meguro K, Claypool D, Cekan P, Haase AD, Hafner M
    Nucleic Acids Res.
    2021 May 7;
    49(8).
    doi: 10.1093/nar/gkab011
    PMID: 33503264

    Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3.

    Wang S, Chim B, Su Y, Khil P, Wong M, Wang X, Foroushani A, Smith PT, Liu X, Li R, Ganesan S, Kanellopoulou C, Hafner M, Muljo SA
    Genes Dev.
    2019 Aug 1;
    33(15-16).
    doi: 10.1101/gad.325100.119
    PMID: 31221665

    DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions.

    Sauer M, Juranek SA, Marks J, De Magis A, Kazemier HG, Hilbig D, Benhalevy D, Wang X, Hafner M, Paeschke K
    Nat Commun.
    2019 Jun 3;
    10(1).
    doi: 10.1038/s41467-019-10432-5
    PMID: 31160600

    Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.

    Benhalevy D, Anastasakis DG, Hafner M
    Nat Methods.
    2018 Dec;
    15(12).
    doi: 10.1038/s41592-018-0220-y
    PMID: 30478324

    Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells.

    Sarshad AA, Juan AH, Muler AIC, Anastasakis DG, Wang X, Genzor P, Feng X, Tsai PF, Sun HW, Haase AD, Sartorelli V, Hafner M
    Mol Cell.
    2018 Sep 20;
    71(6).
    doi: 10.1016/j.molcel.2018.07.020
    PMID: 30146314

    The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation.

    Benhalevy D, Gupta SK, Danan CH, Ghosal S, Sun HW, Kazemier HG, Paeschke K, Hafner M, Juranek SA
    Cell Rep.
    2017 Mar 21;
    18(12).
    doi: 10.1016/j.celrep.2017.02.080
    PMID: 28329689

    DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs.

    Yamaji M, Jishage M, Meyer C, Suryawanshi H, Der E, Yamaji M, Garzia A, Morozov P, Manickavel S, McFarland HL, Roeder RG, Hafner M, Tuschl T
    Nature.
    2017 Mar 23;
    543(7646).
    doi: 10.1038/nature21690
    PMID: 28297718

    Key Publications

    Nuclear PKM2 binds pre-mRNA at folded G-quadruplexes and reveals their gene regulatory role. 

    Anastasakis DG, Apostolidi M, Garman KA, Polash AH, Umar MI, Meng Q, Scutenaire J, Jarvis JE, Wang X, Haase AD, Brownell I, Rinehart J, Hafner M
    Mol Cell.
    2024 Oct 3;
    84(19).
    doi: 10.1016/j.molcel.2024.07.025
    PMID: 39153475

    Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. 

    Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR
    Cell.
    2021 May 27;
    184(11).
    doi: 10.1016/j.cell.2021.04.012
    PMID: 33979654

    Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.

    Benhalevy D, Anastasakis DG, Hafner M
    Nat Methods.
    2018 Dec;
    15(12).
    doi: 10.1038/s41592-018-0220-y
    PMID: 30478324

    Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells.

    Sarshad AA, Juan AH, Muler AIC, Anastasakis DG, Wang X, Genzor P, Feng X, Tsai PF, Sun HW, Haase AD, Sartorelli V, Hafner M
    Mol Cell.
    2018 Sep 20;
    71(6).
    doi: 10.1016/j.molcel.2018.07.020
    PMID: 30146314

    DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs.

    Yamaji M, Jishage M, Meyer C, Suryawanshi H, Der E, Yamaji M, Garzia A, Morozov P, Manickavel S, McFarland HL, Roeder RG, Hafner M, Tuschl T
    Nature.
    2017 Mar 23;
    543(7646).
    doi: 10.1038/nature21690
    PMID: 28297718

    News & Highlights

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    Last Updated: July 2026
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