Principal Investigator

Markus Hafner, Ph.D.

Dr. Markus Hafner leads a team of scientists studying the impact of RNA binding proteins (RBPs) on posttranscriptional gene regulation (PTGR). Dr. Hafner’s research focuses on ribonucleoproteins (RNPs) involved in RNA transport and stability.

The RNA Molecular Biology Group (RMBG) 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 RMBG 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:

  • 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. 
A rough categorization of interconnected posttranscriptional gene regulatory processes based on cellular compartmentalization.
Figure 1


Group Leader
Earl Stadtman Tenure Track Investigator
Visiting Fellow
Visiting Fellow
Postbaccalaureate Fellow
Postbaccalaureate Fellow
Postbaccalaureate Fellow
Research Fellow
Postdoctoral Fellow

Scientific Publications

Giannelou A, Wang H, Zhou Q, Park YH, Abu-Asab MS, Ylaya K, Stone DL, …, Hafner M, Sun HW, Kastner DL, Aksentijevich I.  Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors. Ann Rheum Dis. 2018 Jan 22. pii: annrheumdis-2017-212401. doi: 10.1136/annrheumdis-2017-212401.

Putzbach W, Gao QQ, Patel M, van Dongen S, Haluck-Kangas A, Sarshad AA, Bartom ET, Kim KA, Scholtens DM, Hafner M, Zhao JC, Murmann AE, Peter ME.  Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism. Elife. 2017 Oct 24;6. pii: e29702. doi: 10.7554/eLife.29702.

Mattijssen S, Arimbasseri AG, Iben JR, Gaidamakov S, Lee J, Hafner M, Maraia RJ. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. Elife. 2017 Sep 12;6. pii: e28889. doi: 10.7554/eLife.28889.

Gogakos T, Brown M, Garzia A, Meyer C, Hafner M, Tuschl T.  Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP. Cell Rep. 2017 Aug 8;20(6):1463-1475. doi: 10.1016/j.celrep.2017.07.029.

Benhalevy, D., McFarland, H.L., Sarshad, A.A., and Hafner, M. PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites. Methods. 2017 Apr 15;118-119:41-49. doi: 10.1016/j.ymeth.2016.11.009.

Benhalevy, D., Gupta, S.K., Danan, C.H., Ghosal, S., Sun, H.-W., Kazemier, H.G., Paeschke, K., Hafner, M., and Juranek, S.A. The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation. Cell Rep. 2017 Mar 21;18(12):2979-2990. doi: 10.1016/j.celrep.2017.02.080.

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. DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs. Nature. 2017 Mar 23;543(7646):568-572. doi: 10.1038/nature21690.

Arimbasseri, A.G., Iben, J., Wei, F.-Y., Rijal, K., Tomizawa, K., Hafner, M., and Maraia, R.J.  Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer requires N6-isopentenylation of A37. RNA. 2016 Sep;22(9):1400-10. doi: 10.1261/rna.056259.116.

Faraji, F., Hu, Y., Yang, H.H., Lee, M.P., Winkler, G.S., Hafner, M., and Hunter, K.W. Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7. PLoS Genet. 2016 Jan 25;12(1):e1005820. doi: 10.1371/journal.pgen.1005820.

Hauptmann J, Schraivogel D, Bruckmann A, Manickavel S, Jakob L, Eichner N, Pfaff J, Urban M, Sprunck S, Hafner M, Tuschl T, Deutzmann R, Meister G. Ago-APP: A GW peptide-based Argonaute affinity capture strategy. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11841-5. doi: 10.1073/pnas.1506116112.

Yoon JH, Jo MH, White EJ, De S, Hafner M, Zucconi BE, Abdelmohsen K, Martindale JL, Yang X, Wood WH 3rd, Shin YM, Song JJ, Tuschl T, Becker KG, Wilson GM, Hohng S, Gorospe M. AUF1 promotes let-7b loading on Argonaute 2. Genes Dev. 2015 Aug 1;29(15):1599-604. doi: 10.1101/gad.263749.115.

Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T. ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. Cell Rep. 2014 Dec 24;9(6):2330-43. doi: 10.1016/j.celrep.2014.11.030. Epub 2014 Dec 18.

Gerstberger, S., Hafner, M., Tuschl T. A census of human RNA binding proteins. Nat Rev Genet. 2014 Dec;15(12):829-45. doi: 10.1038/nrg3813. Epub 2014 Nov 4.

Yoon, J.-H, De, S., Srikantan S., Abdelmohsen, K., Grammatikakis, I., Kim, J., Kim, K.M., …, Hafner, M., and Gorospe, M. PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nat Commun. 2014 Nov 4;5:5248. doi: 10.1038/ncomms6248.

Karaca, E., Weitzer, S., Pehlivan, D., Shiraishi, H., Gogakos, T., Hanada, T., Jhangiani, S.N., Wiszniewski, W., Withers, M., Campbell, I.M., …, Hafner M., et al. Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function. Cell. 2014 Apr 24;157(3):636-50. doi: 10.1016/j.cell.2014.02.058.

Wang X, Wang HK, Li Y, Hafner M, Banerjee NS, Tang S, Briskin D, Meyers C, Chow LT, Xie X, Tuschl T, Zheng ZM. microRNAs are biomarkers of oncogenic human papillomavirus infections. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4262-7. doi: 10.1073/pnas.1401430111. Epub 2014 Mar 3.

Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol. 2014 Jan 8;15(1):R12.

Brown M, Suryawanshi H, Hafner M, Farazi TA, Tuschl T. Mammalian miRNA curation through next-generation sequencing. Front Genet. 2013 Aug 2;4:145. doi: 10.3389/fgene.2013.00145.

Renwick N, Cekan P, Masry PA, McGeary SE, Miller JB, Hafner M, Li Z, Mihailovic A, Morozov P, Brown M, Gogakos T, Mobin MB, Snorrason EL, Feilotter HE, Zhang X, Perlis CS, Wu H, Suárez-Fariñas M, Feng H, Shuda M, Moore PS, Tron VA, Chang Y, Tuschl T. Multicolor microRNA FISH effectively differentiates tumor types. J Clin Invest. 2013 Jun 3;123(6):2694-702.

Hafner M, Max KE, Bandaru P, Morozov P, Gerstberger S, Brown M, Molina H, Tuschl T. Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. RNA. 2013 May;19(5):613-26. doi: 10.1261/rna.036491.112.

Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel DJ. Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. Genes Dev. 2013 Apr 15;27(8):928-40. doi: 10.1101/gad.216531.113.

Trompeter HI, Dreesen J, Hermann E, Iwaniuk KM, Hafner M, Renwick N, Tuschl T, Wernet P. MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood. BMC Genomics. 2013 Feb 19;14(1):111. doi: 10.1186/1471-2164-14-111.

Luo GZ, Hafner M, Shi Z, Brown M, Feng GH, Tuschl T, Wang XJ, Li X. Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression. BMC Genomics. 2012 Dec 26;13:727. doi: 10.1186/1471-2164-13-727.

Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T. FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature. 2012 Dec 20;492(7429):382-6. doi: 10.1038/nature11737.

Scheibe M, Butter F, Hafner M, Tuschl T, Mann M. Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Res.2012 Oct;40(19):9897-902. doi: 10.1093/nar/gks746.

Hafner M, Renwick N, Farazi TA, Mihailović A, Pena JT, Tuschl T. Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing. Methods. 2012 Oct;58(2):164-70. doi: 10.1016/j.ymeth.2012.07.030.

Hafner M, Lianoglou S, Tuschl T, Betel D. Genome-wide identification of miRNA targets by PAR-CLIP. Methods. 2012 Oct;58(2):94-105. doi: 10.1016/j.ymeth.2012.08.006.

Farazi TA, Brown M, Morozov P, Ten Hoeve JJ, Ben-Dov IZ, Hovestadt V, Hafner M, Renwick N, Mihailović A, Wessels LF, Tuschl T. Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing. Methods. 2012 Oct;58(2):171-87. doi: 10.1016/j.ymeth.2012.07.020.

Italiano A, Thomas R, Breen M, Zhang L, Crago AM, Singer S, Khanin R, Maki RG, Mihailovic A, Hafner M, Tuschl T, Antonescu CR. The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification. Genes Chromosomes Cancer. 2012 Jun;51(6):569-78. doi: 10.1002/gcc.21943.

Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T. Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip Rev RNA. 2012 Mar-Apr;3(2):159-77. doi: 10.1002/wrna.1103.

Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse HJ, Luftig MA, Tuschl T, Ohler U, Cullen BR. The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog. 2012 Jan;8(1):e1002484. doi: 10.1371/journal.ppat.1002484.

Hoell JI, Larsson E, Runge S, Nusbaum JD, Duggimpudi S, Farazi TA, Hafner M, Borkhardt A, Sander C, Tuschl T. RNA targets of wild-type and mutant FET family proteins. Nat Struct Mol Biol. 2011 Nov 13;18(12):1428-31. doi: 10.1038/nsmb.2163.

Hafner M, Ascano M Jr, Tuschl T. New insights in the mechanism of microRNA-mediated target repression. Nat Struct Mol Biol. 2011 Nov 4;18(11):1181-2. doi: 10.1038/nsmb.2170.

Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe. 2011 Nov 17;10(5):515-26. doi: 10.1016/j.chom.2011.09.012.

Lipchina I, Elkabetz Y, Hafner M, Sheridan R, Mihailovic A, Tuschl T, Sander C, Studer L, Betel D. Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes Dev. 2011 Oct 15;25(20):2173-86. doi: 10.1101/gad.17221311.

Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, Decarolis PL, Khanin R, O'Connor R, Mihailovic A, Taylor BS, Sheridan R, Gimble JM, Viale A, Crago A, Antonescu CR, Sander C, Tuschl T, Singer S. Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res. 2011 Sep 1;71(17):5659-69. doi: 10.1158/0008-5472.CAN-11-0890.

Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G, Tuschl T. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA. 2011 Sep;17(9):1697-712. doi: 10.1261/rna.2799511.

Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M Jr, Tuschl T, Ohler U, Keene JD. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell. 2011 Aug 5;43(3):327-39. doi: 10.1016/j.molcel.2011.06.007.

Wang H, Zhang X, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua NH, Wang XJ. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J. 2011 Jul;67(2):292-304. doi: 10.1111/j.1365-313X.2011.04594.x.

Farazi TA, Horlings HM, Ten Hoeve JJ, Mihailovic A, Halfwerk H, Morozov P, Brown M, Hafner M, Reyal F, van Kouwenhove M, Kreike B, Sie D, Hovestadt V, Wessels LF, van de Vijver MJ, Tuschl T. MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res. 2011 Jul 1;71(13):4443-53. doi: 10.1158/0008-5472.CAN-11-0608.

Bissels U, Wild S, Tomiuk S, Hafner M, Scheel H, Mihailovic A, Choi YH, Tuschl T, Bosio A. Combined characterization of microRNA and mRNA profiles delineates early differentiation pathways of CD133+ and CD34+ hematopoietic stem and progenitor cells. Stem Cells. 2011 May;29(5):847-57. doi: 10.1002/stem.627.

Trompeter HI, Abbad H, Iwaniuk KM, Hafner M, Renwick N, Tuschl T, Schira J, Müller HW, Wernet P. MicroRNAs MiR-17, MiR-20a, and MiR-106b act in concert to modulate E2F activity on cell cycle arrest during neuronal lineage differentiation of USSC. PLoS One. 2011 Jan 20;6(1):e16138. doi: 10.1371/journal.pone.0016138.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp. 2010 Jul 2;(41). pii: 2034. doi: 10.3791/2034.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010 Apr 2;141(1):129-41. doi: 10.1016/j.cell.2010.03.009.

Bissels U, Wild S, Tomiuk S, Holste A, Hafner M, Tuschl T, Bosio A. Absolute quantification of microRNAs by using a universal reference. RNA. 2009 Dec;15(12):2375-84. doi: 10.1261/rna.1754109.

Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A, Lim C, Holoch D, Berninger P, Zavolan M, Tuschl T. miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods. 2009 Feb;6(2):139-41. doi: 10.1038/nmeth.1294.

Yi R, Pasolli HA, Landthaler M, Hafner M, Ojo T, Sheridan R, Sander C, O'Carroll D, Stoffel M, Tuschl T, Fuchs E. DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):498-502. doi: 10.1073/pnas.0810766105.

Landthaler M, Gaidatzis D, Rothballer A, Chen PY, Soll SJ, Dinic L, Ojo T, Hafner M, Zavolan M, Tuschl T. Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA. 2008 Dec;14(12):2580-96. doi: 10.1261/rna.1351608.

Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods. 2008 Jan;44(1):3-12.

Hafner M, Vianini E, Albertoni B, Marchetti L, Grüne I, Gloeckner C, Famulok M. Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization. Nat Protoc. 2008;3(4):579-87. doi: 10.1038/nprot.2008.15.

Hafner M, Schmitz A, Grüne I, Srivatsan SG, Paul B, Kolanus W, Quast T, Kremmer E, Bauer I, Famulok M. Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance. Nature. 2006 Dec 14;444(7121):941-4.

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