Publications

 

Research articles

Pervasive mislocalization of pathogenic coding variants underlying human disorders. Lacoste J*, Haghighi M*, Haider S, Lin ZY, Segal D, Reno C, Qian WW, Xiong X, Shafqat-Abbasi H, Ryder P, Senft R, Cimini B, Roth F, Calderwood M, Hill D, Vidal M, Yi S, Sahni N, Peng J, Gingras AC, Singh S, Carpenter A, Taipale M. Cell (in revision). bioRxiv.

Proteome-scale discovery of protein degradation and stabilization effectors. Poirson J, Cho H*, Dhillon A*, Haider S, Imrit AZ, Lam MHY, Alerasool N, Lacoste J, Mizan L, Wong C, Gingras AC , Schramek D, Taipale M. Nature (accepted). bioRxiv.

PP2A-based triple-strike therapy overcomes mitochondrial apoptosis resistance in brain cancer cells. Denisova OV, Merisaari J, Huhtaniemi R, Qiao X, Yetukuri L, Jumppanen M, Kaur A, Pääkkönen M, von Schantz-Fant С, Ohlmeyer M, Wennerberg K, Kauko O, Koch R, Aittokallio T, Taipale M, Westermarck J. Mol Oncol. 2023 Sep;17(9):1803-1820. Journal.

A universal deep-learning model for zinc finger design enables transcription factor reprogramming. Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, Giganti DO, Goldberg GW, Adams S, Spencer JM, Razavi R, Nim S, Zheng H, Gianco C, Clark FT, Strokach A, Hughes TR, Lionnet T, Taipale M, Kim PM, Noyes MB. Nature Biotechnology 2023 Aug;41(8): 1117-1129. Journal.

A central chaperone-like role for 14-3-3 proteins in human cells. Segal D, Maier S, Mastromarco GJ, Qian WW, Nabeel-Shah S, Lee H, Moore G, Lacoste J, Larsen B, Lin ZY, Selvabaskaran A, Liu K, Smibert C, Zhang Z, Greenblatt J, Peng J, Lee HO, Gingras AC, Taipale M. Molecular Cell 2023 Mar 16;83(6):974-993.e15. Journal.

A proteome-scale map of the SARS-CoV-2-human contactome. Kim DK, Weller B, Lin CW, Sheykhkarimli D, Knapp JJ, Dugied G, Zanzoni A, Pons C, Tofaute MJ, Maseko SB, Spirohn K, Laval F, Lambourne L, Kishore N, Rayhan A, Sauer M, Young V, Halder H, Marín-de la Rosa N, Pogoutse O, Strobel A, Schwehn P, Li R, Rothballer ST, Altmann M, Cassonnet P, Coté AG, Vergara LE, Hazelwood I, Liu BB, Nguyen M, Pandiarajan R, Dohai B, Rodriguez Coloma PA, Poirson J, Giuliana P, Willems L, Taipale M, Jacob Y, Hao T, Hill DE, Brun C, Twizere JC, Krappmann D, Heinig M, Falter C, Aloy P, Demeret C, Vidal M, Calderwood MA, Roth FP, Falter-Braun P. Nature Biotechnology 2023 Jan;41(1): 140-149. Journal. 

Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors. Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J. Heliyon. 2023 Jan;9(1):e12744. Journal.

Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4. Chana CK, Maisonneuve P, Posternak G, Grinberg NGA, Poirson J, Ona SM, Ceccarelli DF, Mader P, St-Cyr DJ, Pau V, Kurinov I, Tang X, Deng D, Cui W, Su W, Kuai L, Soll R, Tyers M, Röst HL, Batey RA, Taipale M, Gingras AC, Sicheri F.  J Med Chem. 2022 Oct 13;65(19):12725-12746. Journal.

Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells. Denisova OV, Merisaari J, Kaur A, Yetukuri L, Jumppanen M, von Schantz-Fant C, Ohlmeyer M, Wennerberg K, Aittokallio T, Taipale M, Westermarck J. Sci Rep. 2022 Aug 13;12(1):13796. Journal.

MRG Proteins Are Shared by Multiple Protein Complexes With Distinct Functions. Devoucoux M, Roques C, Lachance C, Lashgari A, Joly-Beauparlant C, Jacquet K, Alerasool N, Prudente A, Taipale M, Droit A, Lambert JP, Hussein SMI, Côté J. Molecular and Cellular Proteomics. 2022 Jul; 21(7): 100253. Journal.

Oncogenic ZMYND11-MBTD1 fusion protein anchors the NuA4/TIP60 histone acetyltransferase complex to the coding region of active genes. Devoucoux M, Fort V, Khelifi G, Xu J, Alerasool N, Galloy M, Wong N, Bourriquen G, Fradet-Turcotte A, Taipale M, Hope K, Hussein SMI, Côté J. Cell Reports. 2022 Jun 13; 39(11):110947. Journal.

Recurrent chromosomal translocations in sarcomas create a megacomplex that mislocalizes NuA4/TIP60 to Polycomb target loci. Sudarshan D, Avvakumov N, Lalonde ME, Alerasool N, Joly-Beauparlant C, Jacquet K, Mameri A, Lambert JP, Rousseau J, Lachance C, Paquet E, Herrmann L, Thonta Setty S, Loehr J, Bernardini MQ, Rouzbahman M, Gingras AC, Coulombe B, Droit A, Taipale M, Doyon Y, Côté J. Genes Dev. 2022 Jun 1;36(11-12):664-683. Journal.

HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state. Smith RS, Takagishi SR, Amici DR, Metz K, Gayatri S, Alasady MJ, Wu Y, Brockway S, Taiberg SL, Khalatyan N, Taipale M, Santagata S, Whitesell L, Lindquist S, Savas JN, Mendillo ML. 2022 Mar 18;8(11):eabj6526. Journal.

Identification and functional characterization of transcriptional activators in human cells. Alerasool N, Leng H, Lin ZY, Gingras AC, Taipale M. Molecular Cell 2022 Feb 3;82(3): 677-695.e7. Journal. bioRxiv

Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains. Piette BP, Alerasool N, Lin ZY, Lacoste J, Lam M, Qian W, Tran S, Larsen B, Campos E, Peng J, Gingras AC*, Taipale M*. Molecular Cell 2021 Jun 17;81(12):2549-2565.e8. Journal. 

An efficient KRAB domain for CRISPRi applications in human cells. Alerasool N, Segal D, Lee H, Taipale M. Nature Methods 2020 Nov;17(11):1093-1096. Journal.

Recognition of semaphorin proteins by P. sordellii Lethal Toxin reveals principles of receptor specificity in clostridial toxins. Lee H*, Beilhartz GL*, Kucharska I*, Raman S, Cui H, Lam MHY, Rubinstein JL, Schramek D, Julien JP*, Melnyk RA*, and Taipale M*. Cell 2020 Jul 23;182(2):345-356.e16. Journal. bioRxiv.

A conformational switch driven by phosphorylation regulates the activity of the evolutionarily conserved SNARE Ykt6. McGrath K, Agarwal S, Tonelli M, Dergai M, Gaeta AL, Shum AK, Lacoste J, Zhang Y, Wen W, Chung D, Wiersum G, Shevade A, Zaichick S, van Rossum DB, Shuvalova L, Savas JN, Kuchin S, Taipale M, Caldwell KA, Caldwell GA, Fasshauer D, Caraveo G. Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):e2016730118. Journal.

The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids. Hesketh GG, Papazotos F, Pawling J, Rajendran D, Knight JDR, Martinez S, Taipale M, Schramek D, Dennis JW, Gingras AC. Science 2020 Oct 16;370(6514):351-356. Journal.

In-cell identification and measurement of RNA-protein interactions. Graindorge A, Pinheiro I, Nawrocka A, Mallory AC, Tsvetkov P, Gil N, Carolis C, Buchholz F, Ulitsky I, Heard E, Taipale M, and Shkumatava A. Nature Communications 2019 Nov 22;10(1):5317. Journal. PubMed Central.

Functional characterization of a PROTAC directed against BRAF mutant V600E. Posternak G, Tang X, Maisonneuve P, Jin T, Lavoie H, Daou S, Orlicky S, Goullet de Rugy T, Caldwell L, Chan K, Aman A, Prakesch M, Poda G, Mader P, Wong C, Maier S, Kitaygorodsky J, Larsen B, Colwill K, Yin Z, Ceccarelli DF, Batey RA, Taipale M, Kurinov I, Uehling D, Wrana J, Durocher D, Gingras AC, Al-Awar R, Therrien M, Sicheri F. Nat Chem Biol. 2020 Aug 10. Journal.

A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions. Kim DK, Knapp JJ, Kuang D, Chawla A, Cassonnet P, Lee H, Sheykhkarimli D, Samavarchi-Tehrani P, Abdouni H, Rayhan A, Li R, Pogoutse O, Coyaud É, van der Werf S, Demeret C, Gingras AC, Taipale M, Raught B, Jacob Y, Roth FP. G3 (Bethesda). 2020 Sep 2;10(9):3399-3402. Journal.

Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome. Gayden T, Sepulveda FE, Khuong-Quang DA, Pratt J, Valera ET, Garrigue A, Kelso S, Sicheri F, Mikael LG, Hamel N, Bajic A, Dali R, Deshmukh S, Dervovic D, Schramek D, Guerin F, Taipale M, Nikbakht H, Majewski J, Moshous D, Charlebois J, Abish S, Bole-Feysot C, Nitschke P, Bader-Meunier B, Mitchell D, Thieblemont C, Battistella M, Gravel S, Nguyen VH, Conyers R, Diana JS, McCormack C, Prince HM, Besnard M, Blanche S, Ekert PG, Fraitag S, Foulkes WD, Fischer A, Neven B, Michonneau D, de Saint Basile G, and Jabado N. Nature Genetics 2018 Dec;50(12):1650-1657. Journal.

Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila. Urbanus ML, Quaile AT, Stogios PJ, Morar M, Rao C, Di Leo R, Evdokimova E, Lam M, Oatway C, Cuff ME, Osipiuk J, Michalska K, Nocek BP, Taipale M, Savchenko A, and Ensminger AW. Mol Syst Biol. 2016 Dec 16;12(12):893. Journal. PubMed Central.

 

Reviews and commentaries

Voices on technology: The molecular biologists’ ever-expanding toy box. McCord RP, Taipale M, Teichmann S, Vorhees R, Wan Y, Dekker C, Sanjana NE. Mol Cell. 2022 Jan 20;82(2):221-226. Journal.

Disruption of protein function by pathogenic mutations: common and uncommon mechanisms. Taipale M. Biochemistry and Cell Biology 2019 Feb;97(1):46-57. Journal.

Function, evolution, and structure of J-domain proteins. Kampinga HH, Andreasson C, Barducci A, Cheetham ME, Cyr D, Emanuelsson C, Genevaux P, Gestwicki JE, Goloubinoff P, Huerta-Cepas J, Kirstein J, Liberek K, Mayer MP, Nagata K, Nillegoda NB, Pulido P, Ramos C, De Los Rios P, Rospert S, Rosenzweig R, Sahi C, Taipale M, Tomiczek B, Ushioda R, Young JC, Zimmermann R, Zylicz A, Zylicz M, Craig EA, and Marszalek J. Cell Stress and Chaperones. 2019 Jan;24(1):7-15. Journal. PubMed Central.

Two protein/protein interaction assays in one go. Taipale M. Molecular Systems Biology 2018 Jul 18;14(7):e8485. Journal. PubMed Central.

Quantitative Profiling of Chaperone/Client Interactions with LUMIER Assay. Taipale M. Methods in Molecular Biology 2018;1709:47-58. Journal.

Papers from Mikko’s previous lives

Widespread macromolecular interaction perturbations in human genetic disorders.
Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M. Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S. Cell. 2014 Jul 17;158(2):434-448. doi: 10.1016/j.cell.2014.05.039.

Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells. Taipale M, Krykbaeva I, Whitesell L, Santagata S, Zhang J, Liu Q, Gray NS, Lindquist S. Nature Biotechnology 2013 Jul;31(7):630-7. doi: 10.1038/nbt.2620.

Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition. Taipale M, Krykbaeva I, Koeva M, Kayatekin C, Westover KD, Karras GI, Lindquist S. Cell. 2012 Aug 31;150(5):987-1001. doi: 10.1016/j.cell.2012.06.047.

An inter-species protein-protein interaction network across vast evolutionary distance. Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M. Molecular Systems Biology 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins. DeBartolo J, Taipale M, Keating AE. PLoS Comput Biol. 2014 Jun 26;10(6):e1003693. doi: 10.1371/journal.pcbi.1003693.

The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat CF, Sayad A, Sierra JR, Mattiazzi Usaj M, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, Lindquist S, Jurisica I, Stagljar I. Nat Methods. 2014 May;11(5):585-92. doi: 10.1038/nmeth.2895.

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.
Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC. Nat Methods. 2013 Dec;10(12):1239-45. doi: 10.1038/nmeth.2702.

DNA-binding specificities of human transcription factors. Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J. Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.

Widespread regulation of translation by elongation pausing in heat shock. Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, Burge CB. Mol Cell. 2013 Feb 7;49(3):439-52. doi: 10.1016/j.molcel.2012.11.028.

The aromatase gene CYP19A1: several genetic and functional lines of evidence supporting a role in reading, speech and language.
Anthoni H, Sucheston LE, Lewis BA, Tapia-Páez I, Fan X, Zucchelli M, Taipale M, Stein CM, Hokkanen ME, Castrén E, Pennington BF, Smith SD, Olson RK, Tomblin JB, Schulte-Körne G, Nöthen M, Schumacher J, Müller-Myhsok B, Hoffmann P, Gilger JW, Hynd GW, Nopola-Hemmi J, Leppanen PH, Lyytinen H, Schoumans J, Nordenskjöld M, Spencer J, Stanic D, Boon WC, Simpson E, Mäkelä S, Gustafsson JÅ, Peyrard-Janvid M, Iyengar S, Kere J.
Behav Genet. 2012 Jul;42(4):509-27. doi: 10.1007/s10519-012-9532-3.

Protein homeostasis and the phenotypic manifestation of genetic diversity: principles and mechanisms. Jarosz DF, Taipale M, Lindquist S. Annual Review of Genetics 2010;44:189-216. doi: 10.1146/annurev.genet.40.110405.090412.

HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Taipale M, Jarosz DF, Lindquist S. Nat Rev Mol Cell Biol. 2010 Jul;11(7):515-28. doi: 10.1038/nrm2918.

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J. EMBO Journal 2010 Jul 7;29(13):2147-60. doi: 10.1038/emboj.2010.106.

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J. Genome Research 2010 Jun;20(6):861-73. doi: 10.1101/gr.100552.109.

The histone acetyltransferase hMOF is frequently downregulated in primary breast carcinoma and medulloblastoma and constitutes a biomarker for clinical outcome in medulloblastoma. Pfister S, Rea S, Taipale M, Mendrzyk F, Straub B, Ittrich C, Thuerigen O, Sinn HP, Akhtar A, Lichter P. International Journal of Cancer 2008 Mar 15;122(6):1207-13. doi: 10.1002/ijc.23283.

Epigenetiikka, geeninsäätely ja syöpä. (Epigenetics, gene regulation and cancer.) Taipale M. Duodecim. 2006;122(21):2611-8.

Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. Mendjan S, Taipale M, Kind J, Holz H, Gebhardt P, Schelder M, Vermeulen M, Buscaino A, Duncan K, Mueller J, Wilm M, Stunnenberg HG, Saumweber H, Akhtar A. Molecular Cell 2006 Mar 17;21(6):811-23. doi: 10.1016/j.molcel.2006.02.007.

A general precursor ion-like scanning mode on quadrupole-TOF instruments compatible with chromatographic separation. Niggeweg R, Köcher T, Gentzel M, Buscaino A, Taipale M, Akhtar A, Wilm M. Proteomics. 2006 Jan;6(1):41-53. doi: 10.1002/pmic.200501332.

The axon guidance receptor gene ROBO1 is a candidate gene for developmental dyslexia. Hannula-Jouppi K, Kaminen-Ahola N, Taipale M, Eklund R, Nopola-Hemmi J, Kääriäinen H, Kere J. PLoS Genet. 2005 Oct;1(4):e50. doi: 10.1371/journal.pgen.0010050.

hMOF histone acetyltransferase is required for histone H4 lysine 16 acetylation in mammalian cells. Taipale M, Rea S, Richter K, Vilar A, Lichter P, Imhof A, Akhtar A. Molecular and Cellular Biology 2005 Aug;25(15):6798-810. doi: 10.1128/MCB.25.15.6798-6810.2005.

Chromatin mechanisms in Drosophila dosage compensation. Taipale M, Akhtar A. Prog Mol Subcell Biol. 2005;38:123-49. doi: 10.1007/3-540-27310-7_5.

A candidate gene for developmental dyslexia encodes a nuclear tetratricopeptide repeat domain protein dynamically regulated in brain. Taipale M, Kaminen N, Nopola-Hemmi J, Haltia T, Myllyluoma B, Lyytinen H, Muller K, Kaaranen M, Lindsberg PJ, Hannula-Jouppi K, Kere J. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11553-8. doi: 10.1073/pnas.1833911100.

MOF-regulated acetylation of MSL-3 in the Drosophila dosage compensation complex. Buscaino A, Köcher T, Kind JH, Holz H, Taipale M, Wagner K, Wilm M, Akhtar A. Molecular Cell. 2003 May;11(5):1265-77. doi: 10.1016/s1097-2765(03)00140-0.

A dominant gene for developmental dyslexia on chromosome 3. Nopola-Hemmi J, Myllyluoma B, Haltia T, Taipale M, Ollikainen V, Ahonen T, Voutilainen A, Kere J, Widén E. J Med Genet. 2001 Oct;38(10):658-64. doi: 10.1136/jmg.38.10.658.

Two translocations of chromosome 15q associated with dyslexia. Nopola-Hemmi J, Taipale M, Haltia T, Lehesjoki AE, Voutilainen A, Kere J. J Med Genet. 2000 Oct;37(10):771-5. doi: 10.1136/jmg.37.10.771.

Clustering of private mutations in the congenital chloride diarrhea/down-regulated in adenoma gene. Höglund P, Haila S, Gustavson KH, Taipale M, Hannula K, Popinska K, Holmberg C, Socha J, de la Chapelle A, Kere J. Human Mutation 1998;11(4):321-7. doi: 10.1002/(SICI)1098-1004(1998)11:4<321::AID-HUMU10>3.0.CO;2-A.