Selected Publications

Macromolecular Structure Group

Peer-Reviewed Publications

  1. Qiu C, Wine RN, Campbell ZT, Hall TMT. 2022. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res. 50(1):536-548. doi: 10.1093/nar/gkab1220. [ AbstractQiu C, Wine RN, Campbell ZT, Hall TMT. 2022. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res. 50(1):536-548. doi: 10.1093/nar/gkab1220. ]
  2. McCann KL, Kavari SL, Burkholder AB, Phillips BT, Hall TMT. H/ACA snoRNA levels are regulated during stem cell differentiation.Nucleic Acids Res2020 doi: 10.1093/nar/gkaa612 [Online 25 July 2020]. [ AbstractMcCann KL, Kavari SL, Burkholder AB, Phillips BT, Hall TMT. H/ACA snoRNA levels are regulated during stem cell differentiation. Nucleic Acids Res 2020 doi: 10.1093/nar/gkaa612 [Online 25 July 2020]. ]
  3. Teramoto T, Kaitany KJ, Kakuta Y, Kimura M, Fierke CA, Hall TMT. Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA.Nucleic Acids Res2020 doi: 10.1093/nar/gkaa627 [Online 28 July 2020]. [ AbstractTeramoto T, Kaitany KJ, Kakuta Y, Kimura M, Fierke CA, Hall TMT. Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA. Nucleic Acids Res 2020 doi: 10.1093/nar/gkaa627 [Online 28 July 2020]. ]
  4. Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Hall TM. Nop9 recognizes structured and single-stranded RNA elements of pre-ribosomal RNA.RNA2020 doi: 10.1261/rna.075416.120 [Online 5 May 2020]. [ AbstractZhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Hall TM. Nop9 recognizes structured and single-stranded RNA elements of pre-ribosomal RNA. RNA 2020 doi: 10.1261/rna.075416.120 [Online 5 May 2020]. ]
  5. Phillips BT, Williams JG, Atchley DT, Adams AL, Johnson KL, Hall TMT. Mass spectrometric identification of candidate RNA-binding proteins associated with Transition Nuclear Protein mRNA in the mouse testis.Sci Rep2019 9(1):13618. [ AbstractPhillips BT, Williams JG, Atchley DT, Adams AL, Johnson KL, Hall TMT. Mass spectrometric identification of candidate RNA-binding proteins associated with Transition Nuclear Protein mRNA in the mouse testis. Sci Rep 2019 9(1):13618. ]
  6. Qiu C, Bhat VD, Rajeev S, Zhang C, Lasley AE, Wine RN, Campbell ZT, Hall TMT. A Crystal Structure of a Collaborative RNA Regulatory Complex Reveals Mechanisms to Refine Target Specificity.eLife2019 doi: 10.7554/eLife.48968 [Online 8 August 2019]. [ AbstractQiu C, Bhat VD, Rajeev S, Zhang C, Lasley AE, Wine RN, Campbell ZT, Hall TMT. A Crystal Structure of a Collaborative RNA Regulatory Complex Reveals Mechanisms to Refine Target Specificity. eLife 2019 doi: 10.7554/eLife.48968 [Online 8 August 2019]. ]
  7. Qiu C, Goldstrohm AC, Hall TMT. Preparation of cooperative RNA recognition complexes for crystallographic structural studies.Methods in Enzymology2019 623():1-22. [ AbstractQiu C, Goldstrohm AC, Hall TMT. Preparation of cooperative RNA recognition complexes for crystallographic structural studies. Methods in Enzymology 2019 623():1-22. ]
  8. Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TMT. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.Nucleic Acids Research2019 doi: 10.1093/nar/gkz583 [Online 11 July 2019] [ AbstractQiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TMT. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Research 2019 doi: 10.1093/nar/gkz583 [Online 11 July 2019] ]
  9. Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo T-W, Hall TMT, Campbell ZT. Engineering a conserved RNA regulatory protein repurposes its biological functionin vivo.eLife2019 doi: 10.7554/eLife.43788 [Online 17 January 2019] [ AbstractBhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo T-W, Hall TMT, Campbell ZT. Engineering a conserved RNA regulatory protein repurposes its biological function in vivo. eLife 2019 doi: 10.7554/eLife.43788 [Online 17 January 2019] ]
  10. Arvola RM, Weidman CA, Hall TMT, Goldstrohm AC. Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins.RNA biology2017 14(11):1445-1456. [ AbstractArvola RM, Weidman CA, Hall TMT, Goldstrohm AC. Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins. RNA biology 2017 14(11):1445-1456. ]
  11. Skrajna A, Yang XC, Bucholc K, Zhang J, Hall TMT, Dadlez M, Marzluff WF, Dominski Z. U7 snRNP is recruited to histone pre-mRNA in a FLASH-dependent manner by two separate regions of the stem-loop binding proteinRNA2017 23:938-951. [ AbstractSkrajna A, Yang XC, Bucholc K, Zhang J, Hall TMT, Dadlez M, Marzluff WF, Dominski Z. U7 snRNP is recruited to histone pre-mRNA in a FLASH-dependent manner by two separate regions of the stem-loop binding protein RNA 2017 23:938-951. ]
  12. Tamayo JV, Teramoto T, Chatterjee S, Hall TMT, Gavis ER. TheDrosophilahnRNP F/H Homolog Glorund Uses Two Distinct RNA-binding Modes to Diversify Target RecognitionCell Reports2017 19:150-161. [ AbstractTamayo JV, Teramoto T, Chatterjee S, Hall TMT, Gavis ER. The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-binding Modes to Diversify Target Recognition Cell Reports 2017 19:150-161. ]
  13. Zhang J, Gonzalez LE, Hall TMT. Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate.Nucleic Acids Research2017 45:2829-2837. [ AbstractZhang J, Gonzalez LE, Hall TMT. Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate. Nucleic Acids Research 2017 45:2829-2837. ]
  14. Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TMT. Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA.Nature Communications2016 7():13085-. [ AbstractZhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TMT. Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA. Nature Communications 2016 7():13085-. ]
  15. McCann KL, Teramoto T, Zhang J, Hall TMT, Baserga SJ. The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome.eLife2016 ():-. [ AbstractMcCann KL, Teramoto T, Zhang J, Hall TMT, Baserga SJ. The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome. eLife 2016 ():-. ]
  16. Weidmann CA, Qiu C, Arvola RM, Lou TF, Killingsworth J, Campbell ZT, Hall TMT, Goldstrohm AC. Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio.eLife2016 Jul 1 [ AbstractWeidmann CA, Qiu C, Arvola RM, Lou TF, Killingsworth J, Campbell ZT, Hall TMT, Goldstrohm AC. Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio. eLife 2016 Jul 1 ]
  17. Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Hall TMT, Wickens M. RNA regulatory networks diversified through curvature of the PUF protein scaffold.Nature communications2015 6():8213-. [ AbstractWilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Hall TMT, Wickens M. RNA regulatory networks diversified through curvature of the PUF protein scaffold. Nature communications 2015 6():8213-. ]
  18. Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TM. A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization.Proceedings of the National Academy of Sciences of the United States of America2014 111(52):18554-18559. [ AbstractQiu C, McCann KL, Wine RN, Baserga SJ, Hall TM. A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization. Proceedings of the National Academy of Sciences of the United States of America 2014 111(52):18554-18559. ]
  19. Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM. Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation.Proceedings of the National Academy of Sciences of the United States of America2014 111(29):E2937-E2946. [ AbstractZhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM. Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation. Proceedings of the National Academy of Sciences of the United States of America 2014 111(29):E2937-E2946. ]
  20. Wang Y, Wang Z, Hall TMT. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism.The FEBS Journal2013 280(16):3755-3767. [ AbstractWang Y, Wang Z, Hall TMT. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism. The FEBS Journal 2013 280(16):3755-3767. ]
  21. Valley CT, Porter DF, Qiu C, Campbell ZT, Hall TMT, Wickens M. Patterns and plasticity in PUF RNA interactions enable recruitments of multiple PUF proteins through a single site.Proceedings of the National Academy of Sciences, USA2012 109:6054-6059. [ AbstractValley CT, Porter DF, Qiu C, Campbell ZT, Hall TMT, Wickens M. Patterns and plasticity in PUF RNA interactions enable recruitments of multiple PUF proteins through a single site. Proceedings of the National Academy of Sciences, USA 2012 109:6054-6059. ]
  22. Qiu C, Kershner A, Wang Y, Holley CP, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket.Journal of Biological Chemistry2012 287:6949-6957. [ AbstractQiu C, Kershner A, Wang Y, Holley CP, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket. Journal of Biological Chemistry 2012 287:6949-6957. ]
  23. Wang H, Falck JR, Hall TMT, Shears SB. Structural Basis for an Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding.Nature Chemical Biology2012 8:111–116. [ AbstractWang H, Falck JR, Hall TMT, Shears SB. Structural Basis for an Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding. Nature Chemical Biology 2012 8:111–116. ]
  24. Dong S, Wang Y, Cassidy-Amstutz C, Lu G, Bigler R, Jezyk MR, Li C, Hall TMT, Wang Z. A specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains.The Journal of Biological Chemistry2011 286(30):26732-26742. [ AbstractDong S, Wang Y, Cassidy-Amstutz C, Lu G, Bigler R, Jezyk MR, Li C, Hall TMT, Wang Z. A specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains. The Journal of Biological Chemistry 2011 286(30):26732-26742. ]
  25. Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Hall TMT, Zamore PD. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease.Molecular Cell2011 42(2):172-184. [ AbstractCenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Hall TMT, Zamore PD. Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease. Molecular Cell 2011 42(2):172-184. ]
  26. Lu G and Hall TMT. Alternate Modes of Cognate RNA Recognition by Human PUMILIO Proteins.Structure2011 19(3):361-367. [ AbstractLu G and Hall TMT. Alternate Modes of Cognate RNA Recognition by Human PUMILIO Proteins. Structure 2011 19(3):361-367. ]
  27. Koh YY, Wang Y, Qiu C, Opperman L, Gross L, Hall TMT, Wickens M. Stacking interactions in PUF-RNA complexesRNA2011 17:718-727. [ AbstractKoh YY, Wang Y, Qiu C, Opperman L, Gross L, Hall TMT, Wickens M. Stacking interactions in PUF-RNA complexes RNA 2011 17:718-727. ]
  28. Mueller GA, Miller MT, Derose EF, Ghosh M, London RE, Hall TMT. Solution structure of the Drosha double-stranded RNA-binding domain.Silence2010 1:2. [ AbstractMueller GA, Miller MT, Derose EF, Ghosh M, London RE, Hall TMT. Solution structure of the Drosha double-stranded RNA-binding domain. Silence 2010 1:2. ]
  29. Zhu D, Stumpf CR, Krahn JM, Wickens M, Hall TMT. A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.Proceedings of the National Academy of Sciences, USA2009 106(48):20192-20197. [ AbstractZhu D, Stumpf CR, Krahn JM, Wickens M, Hall TMT. A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs. Proceedings of the National Academy of Sciences, USA 2009 106(48):20192-20197. ]
  30. Wang Y, Opperman L, Wickens M, Hall TMT. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein.Proceedings of the National Academy of Sciences, USA2009 106(48):20186-20191. [ AbstractWang Y, Opperman L, Wickens M, Hall TMT. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein. Proceedings of the National Academy of Sciences, USA 2009 106(48):20186-20191. ]
  31. Wang Y, Cheong CG, Hall TMT, Wang Z. Engineering splicing factors with designed specificities.Nature Methods2009 6(11):825-830. [ AbstractWang Y, Cheong CG, Hall TMT, Wang Z. Engineering splicing factors with designed specificities. Nature Methods 2009 6(11):825-830. ]
  32. Miller MT, Higgin JJ, Hall TMT. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p.Nature Structural and Molecular Biology2008 15(4):397-402. [ AbstractMiller MT, Higgin JJ, Hall TMT. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. Nature Structural and Molecular Biology 2008 15(4):397-402. ]
  33. Cheong CG and Hall TMT. Engineering RNA Sequence Specificity of Pumilio Repeats.Proceedings of the National Academy of Sciences, USA2006 103:13635-13639. [ AbstractCheong CG and Hall TMT. Engineering RNA Sequence Specificity of Pumilio Repeats. Proceedings of the National Academy of Sciences, USA 2006 103:13635-13639. ]
  34. Longo A, Leonard CW, Bassi GS, Berndt D, Krahn JM, Hall TMT, Weeks KM. Mechanism for evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.Nature Structural and Molecular Biology2005 12:779-787. [ AbstractLongo A, Leonard CW, Bassi GS, Berndt D, Krahn JM, Hall TMT, Weeks KM. Mechanism for evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nature Structural and Molecular Biology 2005 12:779-787. ]
  35. Vargason JM, Szittya G, Burgyán J, Hall TMT. Size selective recognition of siRNA by an RNA silencing suppressor.Cell2003 115:799-811. [ AbstractVargason JM, Szittya G, Burgyán J, Hall TMT. Size selective recognition of siRNA by an RNA silencing suppressor. Cell 2003 115:799-811. ]
  36. Wang X, McLachlan J, Zamore PD, Hall TMT. Modular recognition of RNA by a human Pumilio-homology domain.Cell2002 110:501-512. [ AbstractWang X, McLachlan J, Zamore PD, Hall TMT. Modular recognition of RNA by a human Pumilio-homology domain. Cell 2002 110:501-512. ]
  37. Wang X, Zamore PD, Hall TMT. Crystal structure of a Pumilio homology domain.Molecular Cell2001 7:855-865. [ AbstractWang X, Zamore PD, Hall TMT. Crystal structure of a Pumilio homology domain. Molecular Cell 2001 7:855-865. ]
  38. Wang X and Hall TMT. Structural basis for recognition of AU-rich element RNA by the HuD protein.Nature Structural Biology2001 8:141-145. [ AbstractWang X and Hall TMT. Structural basis for recognition of AU-rich element RNA by the HuD protein. Nature Structural Biology 2001 8:141-145. ]
  39. Hall TMT, Porter JA, Young KE, Koonin EV, Beachy PA, Leahy DJ. Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins.Cell1997 91:85-97. [ AbstractHall TMT, Porter JA, Young KE, Koonin EV, Beachy PA, Leahy DJ. Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins. Cell 1997 91:85-97. ]
  40. Hall TMT, Porter JA, Beachy PA, Leahy DJ. A potential catalytic site revealed by the 1.7 Å crystal structure of the amino-terminal signaling domain of Sonic hedgehog.Nature1995 378:212-216. [ AbstractHall TMT, Porter JA, Beachy PA, Leahy DJ. A potential catalytic site revealed by the 1.7 Å crystal structure of the amino-terminal signaling domain of Sonic hedgehog. Nature 1995 378:212-216. ]

Review and Methods Articles

  1. Lou TF, Weidmann CA, Killingsworth J, Hall TMT, Goldstrohm AC, Campbell ZT. Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).Methods2017 118-119:171-181. [ AbstractLou TF, Weidmann CA, Killingsworth J, Hall TMT, Goldstrohm AC, Campbell ZT. Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS). Methods 2017 118-119:171-181. ]
  2. Hall TMT. De-coding and Re-coding RNA recognition by PUF and PPR repeat proteins.Current Opinion in Structural Biology2016 36:116-121. [ AbstractHall TMT. De-coding and Re-coding RNA recognition by PUF and PPR repeat proteins. Current Opinion in Structural Biology 2016 36:116-121. ]
  3. Hall TM. Expanding the RNA-recognition code of PUF proteins.Nature Structural & Molecular Biology2014 21(8):653-655. [ AbstractHall TM. Expanding the RNA-recognition code of PUF proteins. Nature Structural & Molecular Biology 2014 21(8):653-655. ]
  4. Wang Y, Wang Z, Hall TMT. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolismFEBS Journal2013 280:3755-67 [ AbstractWang Y, Wang Z, Hall TMT. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism FEBS Journal 2013 280:3755-67 ]
  5. Lu G, Dolgner SJ, Hall TMT. Understanding and engineering RNA sequence specificity of PUF proteins.Current Opinion in Structural Biology2009 19(1):110-115. [ AbstractLu G, Dolgner SJ, Hall TMT. Understanding and engineering RNA sequence specificity of PUF proteins. Current Opinion in Structural Biology 2009 19(1):110-115. ]
  6. Hall TMT. Structure and function of Argonaute proteins.Structure2005 13:1403-1408. [ AbstractHall TMT. Structure and function of Argonaute proteins. Structure 2005 13:1403-1408. ]
  7. Hall TMT. Multiple modes of recognition of RNA by zinc finger proteins.Current Opinion in Structural Biology2005 15:367-373. [ AbstractHall TMT. Multiple modes of recognition of RNA by zinc finger proteins. Current Opinion in Structural Biology 2005 15:367-373. ]
  8. Hall TMT. SAM breaks its stereotype.Nature Structural Biology2003 10:677-679. [ AbstractHall TMT. SAM breaks its stereotype. Nature Structural Biology 2003 10:677-679. ]
  9. Hall TMT. Poly(A) tail synthesis and regulation: Recent structural insights.Current Opinion in Structural Biology2002 12:82-88. [ AbstractHall TMT. Poly(A) tail synthesis and regulation: Recent structural insights. Current Opinion in Structural Biology 2002 12:82-88. ]