University of Dundee

2020

Al Mamun M, Albergante L, Blow J, Newman T. 2020. 3 tera-basepairs as a fundamental limit for robust DNA replication. Physical Biology. 17(4):Article 046002. https://doi.org/10.1088/1478-3975/ab8c2f

Alabert C, Loos C, Voelker-Albert M, Graziano S, Forné I, Reveron-Gomez N, Schuh L, Hasenauer J, Marr C, Imhof A, Groth A. 2020. Domain Model Explains Propagation Dynamics and Stability of Histone H3K27 and H3K36 Methylation Landscapes. Cell Reports. 30(4):1223-1234.e8.  https://doi.org/10.1016/j.celrep.2019.12.060

Bage M, Cowling VH and Pisliokov A (2020)  Identification of novel RNA Polymerase II CTD interaction sites on the mRNA Capping Enzyme.   bioRxiv 2020.02.25.964700;  https://doi.org/10.1101/2020.02.25.964700 (and in revision)

Branigan E, Penedo JC, Hay R. 2020. Ubiquitin transfer by a RING E3 ligase occurs from a closed E2~ubiquitin conformation. Nature Communications. 11:Article 2846. https://doi.org/10.1038/s41467-020-16666-y

Bustamante HA, Cereceda K, González AE, Valenzuela GE, Cheuquemilla Y, Hernández S, Arias-Muñoz E, Cerda-Troncoso C, Bandau S, Soza A, Kausel G, Kerr B, Mardones GA, Cancino J, Hay RT, Rojas-Fernandez A, Burgos PV. 2020. The Proteasomal Deubiquitinating Enzyme PSMD14 Regulates Macroautophagy by Controlling Golgi-to-ER Retrograde Transport. Cells. 9(3):1-24. https://doi.org/10.3390/cells9030777

Chen X, Raimi O, Ferenbach A, van Aalten D. 2020. A missense mutation in a patient with developmental delay that affects AGX1 activity and structure. FEBS Letters. https://doi.org/10.1002/1873-3468.13968

Culjkovic-Kraljacic B, Skrabanek L, Revuelta MV, Gasiorek J, Cowling VH, Cerchietti L, Borden KLB. 2020. The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts. Proceedings of the National Academy of Sciences of the United States of America. 117(43):26773-26783. https://doi.org/10.1073/pnas.2002360117

Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. 2020. Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nature Communications. 11:Article 1572. https://doi.org/10.1038/s41467-020-15098-y

Eykelenboom JK, Tanaka TU. 2020. Zooming in on Chromosome Dynamics. Cell Cycle. 19(12):1422-1432. https://doi.org/10.1080/15384101.2020.1757242

Fernandez-Alonso R, Bustos F, Budzyk M, Kumar P, Helbig AO, Hukelmann J, Lamond AI, Lanner F, Zhou H, Petsalaki E, Findlay GM. 2020. Phosphoproteomics identifies a bimodal EPHA2 receptor switch that promotes embryonic stem cell differentiation. Nature Communications. 11:Article 1357. https://doi.org/10.1038/s41467-020-15173-4

Flaus A, Downs JA, Owen-Hughes T.  2020,  Histones isoforms and the onchohistone code.  Current Opinion in Genetics and Development.  67.  61-66. https://10.1016/j.gde.2020.11.03

Fu C, van Aalten DMF. 2020. Native detection of protein O-GlcNAcylation by gel electrophoresis. Analyst. 145(21):6826-6830. https://doi.org/10.1039/C9AN02506E

Galloway A, Atrih A, Grzela R, Darzynkiewicz E, Ferguson MAJ, Cowling VH. 2020. CAP-MAP: cap analysis protocol with minimal analyte processing, a rapid and sensitive approach to analysing mRNA cap structures. Open Biology. 10(2):Article 190306. https://doi.org/10.1098/rsob.190306

Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker G-J, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Le Dévédec SE, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, Roudot P, Schuster M, Sergeant G, Strömblad S, Swedlow JR, van Erp M, Van Troys M, Zaritsky A, Sansone S-A, Martens L. 2020. Community standards for open cell migration data. GigaScience. 9(5):1-11. https://doi.org/10.1093/gigascience/giaa041

Gorelik A, van Aalten D. 2020. Tools for functional dissection of site-specific O-GlcNAcylation. RSC Chemical Biology. https://doi.org/10.1039/d0cb00052c

Griesser E, Wyatt H, Ten Have S, Stierstorfer B, Lenter M, Lamond AI. 2020. Quantitative profiling of the human substantia nigra proteome from laser-capture microdissected FFPE tissue. Molecular & Cellular Proteomics. 19(5):839-851. https://doi.org/10.1074/mcp.RA119.001889

Hegarat N, Crncec A, Suarez Peredoa Rodriguez MF, Iturra FE, Gu Y, Busby O, Lang PF, Barr AR, Bakal C, Kanemaki MT, Lamond AI, Novak B, Ly T, Hochegger H. 2020. Cyclin A triggers Mitosis either via the Greatwall kinase pathway or Cyclin B. EMBO Journal. 39(11):1-23. https://doi.org/10.15252/embj.2020104419

Ibrahim AFM, Shen L, Tatham MH, Dickerson D, Prescott AR, Abidi N, Xirodimas DP, Hay RT. 2020. Antibody RING-Mediated Destruction of Endogenous Proteins. Molecular Cell. 79(1):155-166. https://doi.org/10.1016/j.molcel.2020.04.032

Kasprzyk R, Fido M, Mamot A, Wanat P, Smietanski M, Kopcial M, Cowling VH, Kowalska J, Jemielity J. 2020. Direct High-Throughput Screening Assay for mRNA Cap Guanine-N7 Methyltransferase Activity. Chemistry: a European Journal. https://doi.org/10.1002/chem.202001036

Knatko EV, Tatham MH, Zhang Y, Castro C, Higgins M, Dayalan Naidu S, Leonardi C, de la Vega L, Honda T, Griffin JL, Hay RT, Dinkova-Kostova AT. 2020. Downregulation of Keap1 confers features of a fasted metabolic state. iScience. 23(10):Article 101638. https://doi.org/10.1016/j.isci.2020.101638

Llabrés S, Tsenkov MI, MacGowan S, Barton G, Zachariae U. 2020. Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain. Journal of Structural Biology. 209(1):1-8. https://doi.org/10.1016/j.jsb.2019.107405

Lockhart D, Stanley M, Raimi O, Robinson D, Boldovjakova D, Squair D, Ferenbach A, Fang W, van Aalten D. 2020. Targeting a critical step in fungal hexosamine biosynthesis. Journal of Biological Chemistry. 295(26):8678-8691. https://doi.org/10.1074/jbc.RA120.012985

MacGowan S, Madeira F, Britto-Borges T, Warowny M, Drozdetskiy A, Procter J, Barton G. 2020. The Dundee Resource for Sequence Analysis and Structure Prediction. Protein Science. 29(1):277-297. https://doi.org/10.1002/pro.3783

Man Suen K, Braukmann F, Butler R, Bensaddek D, Akay A, Lin C-C, Milonaitytė D, Doshi N, Sapetschnig A, Lamond A, Ladbury JE, Miska EA. 2020. DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans. Nature Communications. 11(1):Article 4242. https://doi.org/10.1038/s41467-020-18089-1

Mathur S, Fletcher AJ, Branigan E, Hay RT, Virdee S. 2020. Photocrosslinking Activity-Based Probes for Ubiquitin RING E3 Ligases. Cell Chemical Biology. 27(1):74-82.e6. https://doi.org/10.1016/j.chembiol.2019.11.013

McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R, HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. 2020. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nature Methods. 17(4):414-421. https://doi.org/10.1038/s41592-020-0766-3

Meier B, Volkova NV, Gerstung M, Gartner A. 2020. Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis. DNA Repair. 95:Article 102957. https://doi.org/10.1016/j.dnarep.2020.102957

Mirauta BA, Seaton DD, Bensaddek D, Brenes Murillo A, Bonder MJ, Kilpinen H, HipSci Consortium, Stegle O, Lamond AI. 2020. Population-scale proteome variation in human induced pluripotent stem cells. eLife. 9:Article e57390. https://doi.org/10.7554/eLife.57390

Muha V, Fenckova M, Ferenbach A, Catinozzi M, Eidhof I, Storkebaum E, Schenck A, van Aalten D. 2020. O-GlcNAcase contributes to cognitive function in Drosophila. Journal of Biological Chemistry. 295(26):8636-8646. https://doi.org/10.1074/jbc.RA119.010312

Murphy P, Xu Y, Rouse SL, Jaffray EG, Plechanovova A, Matthews SJ, Penedo JC, Hay R. 2020. Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer. Nature Communications. 11:Article 3807. https://doi.org/10.1038/s41467-020-17647-x

Parker MT, Knop K, Simpson GG. 2020. Making a mark: The role of RNA modifications in plant biology. Biochemist. 42(4):26-30. https://doi.org/10.1042/BIO20200046

Parker MT, Knop K, Sherwood AV, Schurch NJ, Mackinnon K, Gould PD, Hall AJW, Barton GJ, Simpson GG. 2020. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife. 9:1-35. https://doi.org/10.7554/eLife.49658

Pravata V, Omelkova M, Stavridis M, Desbiens CM, Stephen HM, Lefeber DJ, Gécz J, Gundogdu M, Õunap K, Joss S, Schwartz CE, Wells L, van Aalten D. 2020. An intellectual disability syndrome with single nucleotide variants in O-GlcNAc Transferase. European Journal of Human Genetics. 28:706-714. https://doi.org/10.1038/s41431-020-0589-9

Princz A, Pelisch F, Tavernarakis N. 2020. SUMO promotes longevity and maintains mitochondrial homeostasis during ageing in Caenorhabditis elegans. Scientific Reports. 10:Article 15513. https://doi.org/10.1038/s41598-020-72637-9

Raimi O, Hurtado-Guerrero R, Borodkin V, Ferenbach A, Urbaniak M, Ferguson M, van Aalten D. 2020. A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor. RSC Chemical Biology. (1):13-25. https://doi.org/10.1039/c9cb00017h

Song J, Freeman ADJ, Knebel A, Gartner A, Lilley DMJ. 2020. Human ANKLE1 is a nuclease specific for branched DNA. Journal of Molecular Biology. 432(21):5825-5834. https://doi.org/10.1016/j.jmb.2020.08.022

Stubbe M, Mai J, Paulus C, Stubbe HC, Berscheminski J, Karimi M, Hofmann S, Weber E, Hadian K, Hay R, Groitl P, Nevels M, Dobner T, Schreiner S. 2020. Viral DNA Binding Protein SUMOylation Promotes PML Nuclear Body Localization Next to Viral Replication Centers. MBio. 11(2):1-21. https://doi.org/10.1128/mBio.00049-20

Sundaramoorthy R, Owen-Hughes T. 2020. Chromatin remodelling comes into focus. F1000Research. 9:Article 1011. https://doi.org/10.12688/f1000research.21933.1

Taylor SJP, Pelisch F. 2020. Chromosome segregation during female meiosis in C. elegans: A tale of pushing and pulling. Journal of Cell Biology. 219(12):Article e202011035. https://doi.org/10.1083/jcb.202011035

Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Vöhringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. 2020. Mutational signatures are jointly shaped by DNA damage and repair. Nature Communications. 11:1-15. https://doi.org/10.1038/s41467-020-15912-7

Zdańkowski P, Trusiak M, McGloin D, Swedlow JR. 2020. Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging. ACS Nano. 14(1):394-405. https://doi.org/10.1021/acsnano.9b05891