Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication.
Journal
Cell discovery
ISSN: 2056-5968
Titre abrégé: Cell Discov
Pays: England
ID NLM: 101661034
Informations de publication
Date de publication:
24 May 2021
24 May 2021
Historique:
received:
27
12
2020
accepted:
24
04
2021
entrez:
25
5
2021
pubmed:
26
5
2021
medline:
26
5
2021
Statut:
epublish
Résumé
Treatment options for COVID-19 remain limited, especially during the early or asymptomatic phase. Here, we report a novel SARS-CoV-2 viral replication mechanism mediated by interactions between ACE2 and the epigenetic eraser enzyme LSD1, and its interplay with the nuclear shuttling importin pathway. Recent studies have shown a critical role for the importin pathway in SARS-CoV-2 infection, and many RNA viruses hijack this axis to re-direct host cell transcription. LSD1 colocalized with ACE2 at the cell surface to maintain demethylated SARS-CoV-2 spike receptor-binding domain lysine 31 to promote virus-ACE2 interactions. Two newly developed peptide inhibitors competitively inhibited virus-ACE2 interactions, and demethylase access to significantly inhibit viral replication. Similar to some other predominantly plasma membrane proteins, ACE2 had a novel nuclear function: its cytoplasmic domain harbors a nuclear shuttling domain, which when demethylated by LSD1 promoted importin-α-dependent nuclear ACE2 entry following infection to regulate active transcription. A novel, cell permeable ACE2 peptide inhibitor prevented ACE2 nuclear entry, significantly inhibiting viral replication in SARS-CoV-2-infected cell lines, outperforming other LSD1 inhibitors. These data raise the prospect of post-exposure prophylaxis for SARS-CoV-2, either through repurposed LSD1 inhibitors or new, nuclear-specific ACE2 inhibitors.
Identifiants
pubmed: 34031383
doi: 10.1038/s41421-021-00279-w
pii: 10.1038/s41421-021-00279-w
pmc: PMC8143069
doi:
Types de publication
Journal Article
Langues
eng
Pagination
37Subventions
Organisme : Department of Health | National Health and Medical Research Council (NHMRC)
ID : APP1173880
Commentaires et corrections
Type : ErratumIn
Références
Ing, A. J., Cocks, C. & Green, J. P. COVID-19: in the footsteps of Ernest Shackleton. Thorax 75, 693–694 (2020).
doi: 10.1136/thoraxjnl-2020-215091
pubmed: 32461231
Long, Q. X. et al. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nat. Med. 26, 1200–1204 (2020).
doi: 10.1038/s41591-020-0965-6
pubmed: 32555424
Yang, R., Gui, X. & Xiong, Y. Comparison of clinical characteristics of patients with asymptomatic vs symptomatic coronavirus disease 2019 in Wuhan, China. JAMA Netw. Open 3, e2010182 (2020).
pubmed: 32459353
pmcid: 7254178
doi: 10.1001/jamanetworkopen.2020.10182
Beigel, J. H. et al. Remdesivir for the treatment of Covid-19—preliminary report. N. Engl. J. Med. 383, 1813–1826 (2020).
Grein, J. et al. Compassionate use of remdesivir for patients with severe Covid-19. N. Engl. J. Med. 382, 2327–2336 (2020).
pubmed: 32275812
doi: 10.1056/NEJMoa2007016
Paliani, U. & Cardona, A. COVID-19 and hydroxychloroquine: is the wonder drug failing? Eur. J. Intern. Med. 78, 1–3 (2020).
Furlow, B. COVACTA trial raises questions about tocilizumab’s benefit in COVID-19. Lancet Rheumatol. 2, e592 (2020).
pubmed: 32929415
pmcid: 7480990
doi: 10.1016/S2665-9913(20)30313-1
Investigators R.-C. et al. Interleukin-6 receptor antagonists in critically ill patients with covid-19. N. Engl. J. Med. 384, 1491–1502 (2021).
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280 (2020).
Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020).
pubmed: 32015507
pmcid: 7095418
doi: 10.1038/s41586-020-2012-7
Jiang, F. et al. Angiotensin-converting enzyme 2 and angiotensin 1-7: novel therapeutic targets. Nat. Rev. Cardiol. 11, 413–426 (2014).
pubmed: 24776703
pmcid: 7097196
doi: 10.1038/nrcardio.2014.59
Kuba, K., Imai, Y., Ohto-Nakanishi, T. & Penninger, J. M. Trilogy of ACE2: a peptidase in the renin-angiotensin system, a SARS receptor, and a partner for amino acid transporters. Pharm. Ther. 128, 119–128 (2010).
doi: 10.1016/j.pharmthera.2010.06.003
Alhenc-Gelas, F. & Drueke, T. B. Blockade of SARS-CoV-2 infection by recombinant soluble ACE2. Kidney Int. 97, 1091–1093 (2020).
pubmed: 32354636
pmcid: 7194930
doi: 10.1016/j.kint.2020.04.009
Batlle, D., Wysocki, J. & Satchell, K. Soluble angiotensin-converting enzyme 2: a potential approach for coronavirus infection therapy? Clin. Sci. 134, 543–545 (2020).
doi: 10.1042/CS20200163
Monteil, V. et al. Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell 181, 905–913 (2020).
Imai, Y. et al. Angiotensin-converting enzyme 2 protects from severe acute lung failure. Nature 436, 112–116 (2005).
pubmed: 16001071
pmcid: 7094998
doi: 10.1038/nature03712
Lumbers, E. R., Delforce, S. J., Pringle, K. G. & Smith, G. R. The lung, the heart, the novel coronavirus, and the renin-angiotensin system; the need for clinical trials. Front. Med. 7, 248 (2020).
doi: 10.3389/fmed.2020.00248
Caly, L., Wagstaff, K. M. & Jans, D. A. Nuclear trafficking of proteins from RNA viruses: potential target for antivirals? Antivir. Res. 95, 202–206 (2012).
pubmed: 22750233
doi: 10.1016/j.antiviral.2012.06.008
Jans, D. A., Martin, A. J. & Wagstaff, K. M. Inhibitors of nuclear transport. Curr. Opin. Cell Biol. 58, 50–60 (2019).
pubmed: 30826604
doi: 10.1016/j.ceb.2019.01.001
Rowland, R. R. et al. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells. J. Virol. 79, 11507–11512 (2005).
pubmed: 16103202
pmcid: 1193611
doi: 10.1128/JVI.79.17.11507-11512.2005
Timani, K. A. et al. Nuclear/nucleolar localization properties of C-terminal nucleocapsid protein of SARS coronavirus. Virus Res. 114, 23–34 (2005).
pubmed: 15992957
pmcid: 7114095
doi: 10.1016/j.virusres.2005.05.007
Wulan, W. N., Heydet, D., Walker, E. J., Gahan, M. E. & Ghildyal, R. Nucleocytoplasmic transport of nucleocapsid proteins of enveloped RNA viruses. Front. Microbiol. 6, 553 (2015).
pubmed: 26082769
pmcid: 4451415
doi: 10.3389/fmicb.2015.00553
Wurm, T. et al. Localization to the nucleolus is a common feature of coronavirus nucleoproteins, and the protein may disrupt host cell division. J. Virol. 75, 9345–9356 (2001).
pubmed: 11533198
pmcid: 114503
doi: 10.1128/JVI.75.19.9345-9356.2001
Hiscox, J. A. et al. The coronavirus infectious bronchitis virus nucleoprotein localizes to the nucleolus. J. Virol. 75, 506–512 (2001).
pubmed: 11119619
pmcid: 113943
doi: 10.1128/JVI.75.1.506-512.2001
Frieman, M. et al. Severe acute respiratory syndrome coronavirus ORF6 antagonizes STAT1 function by sequestering nuclear import factors on the rough endoplasmic reticulum/Golgi membrane. J. Virol. 81, 9812–9824 (2007).
pubmed: 17596301
pmcid: 2045396
doi: 10.1128/JVI.01012-07
Caly, L., Druce, J. D., Catton, M. G., Jans, D. A. & Wagstaff, K. M. The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antivir. Res. 178, 104787 (2020).
pubmed: 32251768
doi: 10.1016/j.antiviral.2020.104787
Huang, J. et al. p53 is regulated by the lysine demethylase LSD1. Nature 449, 105–108 (2007).
pubmed: 17805299
doi: 10.1038/nature06092
Wang, H. et al. SARS coronavirus entry into host cells through a novel clathrin-and caveolae-independent endocytic pathway. Cell Res. 18, 290–301 (2008).
pubmed: 18227861
doi: 10.1038/cr.2008.15
Yang, J. et al. Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes. Proc. Natl Acad. Sci. USA 107, 21499–21504 (2010).
pubmed: 21098664
pmcid: 3003019
doi: 10.1073/pnas.1016147107
Amente, S., Lania, L. & Majello, B. The histone LSD1 demethylase in stemness and cancer transcription programs. Biochim. Biophys. Acta 1829, 981–986 (2013).
pubmed: 23684752
doi: 10.1016/j.bbagrm.2013.05.002
Pedersen, M. T. & Helin, K. Histone demethylases in development and disease. Trends Cell Biol. 20, 662–671 (2010).
pubmed: 20863703
doi: 10.1016/j.tcb.2010.08.011
Hill, J. M. et al. Inhibition of LSD1 reduces herpesvirus infection, shedding, and recurrence by promoting epigenetic suppression of viral genomes. Sci. Transl. Med. 6, 265ra169 (2014).
pubmed: 25473037
pmcid: 4416407
doi: 10.1126/scitranslmed.3010643
Sakane, N. et al. Activation of HIV transcription by the viral Tat protein requires a demethylation step mediated by lysine-specific demethylase 1 (LSD1/KDM1). PLoS Pathog. 7, e1002184 (2011).
pubmed: 21876670
pmcid: 3158049
doi: 10.1371/journal.ppat.1002184
Sheng, W. et al. LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade. Cell 174, 549–563 e519 (2018).
pubmed: 29937226
pmcid: 6063761
doi: 10.1016/j.cell.2018.05.052
Wen, P. P. et al. Accurate in silico prediction of species-specific methylation sites based on information gain feature optimization. Bioinformatics 32, 3107–3115 (2016).
pubmed: 27354692
doi: 10.1093/bioinformatics/btw377
Satarker, S. & Nampoothiri, M. Structural proteins in severe acute respiratory syndrome coronavirus-2. Arch. Med. Res. 51, 482–491 (2020).
pubmed: 32493627
pmcid: 7247499
doi: 10.1016/j.arcmed.2020.05.012
Shang, J. et al. Structural basis of receptor recognition by SARS-CoV-2. Nature 581, 221–224 (2020).
pubmed: 32225175
pmcid: 7328981
doi: 10.1038/s41586-020-2179-y
Wan, Y., Shang, J., Graham, R., Baric, R. S. & Li, F. Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J. Virol. 2020 94, 7 (2020).
Hofmann, K. TMbase-A database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374, 166 (1993).
Chu, H. et al. Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study. Lancet Microbe 1, e14–e23 (2020).
pubmed: 32835326
pmcid: 7173822
doi: 10.1016/S2666-5247(20)30004-5
Vareille, M., Kieninger, E., Edwards, M. R. & Regamey, N. The airway epithelium: soldier in the fight against respiratory viruses. Clin. Microbiol. Rev. 24, 210–229 (2011).
pubmed: 21233513
pmcid: 3021210
doi: 10.1128/CMR.00014-10
Delgado, O. et al. Multipotent capacity of immortalized human bronchial epithelial cells. PLoS ONE 6, e22023 (2011).
pubmed: 21760947
pmcid: 3131301
doi: 10.1371/journal.pone.0022023
Leung, C., Wadsworth, S. J., Yang, S. J. & Dorscheid, D. R. Structural and functional variations in human bronchial epithelial cells cultured in air-liquid interface using different growth media. Am. J. Physiol. Lung Cell Mol. Physiol. 318, L1063–L1073 (2020).
pubmed: 32208929
doi: 10.1152/ajplung.00190.2019
Ravindra, N. G. et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biol. 19, e3001143 (2021).
Lukassen, S. et al. SARS‐CoV‐2 receptor ACE 2 and TMPRSS 2 are primarily expressed in bronchial transient secretory cells. EMBO J. 39, e105114 (2020).
pubmed: 32246845
pmcid: 7232010
doi: 10.15252/embj.2020105114
Schmidt, D. M. & McCafferty, D. G. trans-2-Phenylcyclopropylamine is a mechanism-based inactivator of the histone demethylase LSD1. Biochemistry 46, 4408–4416 (2007).
pubmed: 17367163
doi: 10.1021/bi0618621
Harancher, M. R., Packard, J. E., Cowan, S. P., DeLuca, N. A. & Dembowski, J. A. Antiviral properties of the LSD1 inhibitor SP-2509. J. Virol. 94, e00974–20 (2020).
Sehrawat, A. et al. LSD1 activates a lethal prostate cancer gene network independently of its demethylase function. Proc. Natl Acad. Sci. USA 115, E4179–E4188 (2018).
pubmed: 29581250
pmcid: 5939079
doi: 10.1073/pnas.1719168115
Tan, A. H. Y. et al. Lysine-specific histone demethylase 1A regulates macrophage polarization and checkpoint molecules in the tumor microenvironment of triple-negative breast cancer. Front. Immunol. 10, 1351 (2019).
pubmed: 31249575
pmcid: 6582666
doi: 10.3389/fimmu.2019.01351
Boulding, T. et al. LSD1 activation promotes inducible EMT programs and modulates the tumour microenvironment in breast cancer. Sci. Rep. 8, 73 (2018).
pubmed: 29311580
pmcid: 5758711
doi: 10.1038/s41598-017-17913-x
Han, M. et al. Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity. Med. Microbiol. Immunol. 209, 1–12 (2020).
Tan, L. et al. Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study. Signal Trans. Target Ther. 5, 1–3 (2020).
Urra, J., Cabrera, C., Porras, L. & Ródenas, I. Selective CD8 cell reduction by SARS-CoV-2 is associated with a worse prognosis and systemic inflammation in COVID-19 patients. Clin. Immunol. 217, 108486 (2020).
Zheng, M. et al. Functional exhaustion of antiviral lymphocytes in COVID-19 patients. Cell Mol. Immunol. 17, 533–535 (2020).
pubmed: 32203188
pmcid: 7091858
doi: 10.1038/s41423-020-0402-2
Nicin, L. et al. Cell type-specific expression of the putative SARS-CoV-2 receptor ACE2 in human hearts. Eur. Heart J. 41, 1804–1806 (2020).
pubmed: 32293672
doi: 10.1093/eurheartj/ehaa311
Stegbauer, J. et al. Role of the renin-angiotensin system in autoimmune inflammation of the central nervous system. Proc. Natl Acad. Sci. USA 106, 14942–14947 (2009).
pubmed: 19706425
pmcid: 2736426
doi: 10.1073/pnas.0903602106
World Health Organization. Clinical management of severe acute respiratory infection when novel coronavirus (2019-nCoV) infection is suspected: interim guidance. https://apps.who.int/iris/handle/10665/330893 .
Chu, H. et al. Middle East respiratory syndrome coronavirus efficiently infects human primary T lymphocytes and activates the extrinsic and intrinsic apoptosis pathways. J. Infect. Dis. 213, 904–914 (2016).
pubmed: 26203058
doi: 10.1093/infdis/jiv380
Nguyen, Ba. A. N., Pogoutse, A., Provart, N. & Moses, A. M. NLStradamus: a simple Hidden Markov model for nuclear localization signal prediction. BMC Bioinform. 10, 202 (2009).
doi: 10.1186/1471-2105-10-202
Jalkanen, S. & Salmi, M. Cell surface monoamine oxidases: enzymes in search of a function. EMBO J. 20, 3893–3901 (2001).
pubmed: 11483492
pmcid: 149172
doi: 10.1093/emboj/20.15.3893
Salmi, M. & Jalkanen, S. Cell-surface enzymes in control of leukocyte trafficking. Nat. Rev. Immunol. 5, 760–771 (2005).
pubmed: 16200079
doi: 10.1038/nri1705
Zhang, Q. et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 370, eabd4570 (2020).
Tu, W. J. et al. Targeting nuclear LSD1 to reprogram cancer cells and reinvigorate exhausted T cells via a novel LSD1-EOMES switch. Front. Immunol. 11, 1228 (2020).
pubmed: 32612611
pmcid: 7309504
doi: 10.3389/fimmu.2020.01228
Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036–1045 e1039 (2020).
pubmed: 32416070
pmcid: 7227586
doi: 10.1016/j.cell.2020.04.026
Hadjadj, J. et al. Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients. Science 369, 718–724 (2020).
Pedersen, S. F. & Ho, Y. -C. SARS-CoV-2: a storm is raging. J. Clin. Invest. 130, 2202–2205 (2020).
Kohler, C. A. et al. Peripheral alterations in cytokine and chemokine levels after antidepressant drug treatment for major depressive disorder: systematic review and meta-analysis. Mol. Neurobiol. 55, 4195–4206 (2018).
pubmed: 28612257
Strawbridge, R. et al. Inflammation and clinical response to treatment in depression: a meta-analysis. Eur. Neuropsychopharmacol. 25, 1532–1543 (2015).
pubmed: 26169573
doi: 10.1016/j.euroneuro.2015.06.007
Bouhaddou, M. et al. The global phosphorylation landscape of SARS-CoV-2 infection. Cell 182, 685–712 (2020).
pubmed: 32645325
pmcid: 7321036
doi: 10.1016/j.cell.2020.06.034
Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 459, 1–13 (2020).
Kuba, K. et al. A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat. Med. 11, 875–879 (2005).
pubmed: 16007097
pmcid: 7095783
doi: 10.1038/nm1267
Zhang, H., Penninger, J. M., Li, Y., Zhong, N. & Slutsky, A. S. Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med. 46, 586–590 (2020).
pubmed: 32125455
pmcid: 7079879
doi: 10.1007/s00134-020-05985-9
Wang, D. et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA 323, 1061–1069 (2020).
pubmed: 32031570
pmcid: 7042881
doi: 10.1001/jama.2020.1585
Goronzy, J. J., Fang, F., Cavanagh, M. M., Qi, Q. & Weyand, C. M. Naive T cell maintenance and function in human aging. J. Immunol. 194, 4073–4080 (2015).
pubmed: 25888703
doi: 10.4049/jimmunol.1500046
Donoghue, M. et al. A novel angiotensin-converting enzyme-related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9. Circ. Res. 87, E1–E9 (2000).
pubmed: 10969042
doi: 10.1161/01.RES.87.5.e1
Tipnis, S. R. et al. A human homolog of angiotensin-converting enzyme cloning and functional expression as a captopril-insensitive carboxypeptidase. J. Biol. Chem. 275, 33238–33243 (2000).
pubmed: 10924499
doi: 10.1074/jbc.M002615200
Gao, Y. et al. Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy. Nat. Cell Biol. 22, 1064–1075 (2020).
pubmed: 32839551
pmcid: 7484128
doi: 10.1038/s41556-020-0562-4
Lin, S.-Y. et al. Nuclear localization of EGF receptor and its potential new role as a transcription factor. Nat. Cell Biol. 3, 802–808 (2001).
pubmed: 11533659
doi: 10.1038/ncb0901-802
Gwathmey, T. M., Alzayadneh, E. M., Pendergrass, K. D. & Chappell, M. C. Novel roles of nuclear angiotensin receptors and signaling mechanisms. Am. J. Physiol. Regul. Integr. Comp. Physiol. 302, R518–R530 (2012).
pubmed: 22170620
doi: 10.1152/ajpregu.00525.2011
Simpson, J. et al. Respiratory syncytial virus infection promotes necroptosis and HMGB1 release by airway epithelial cells. Am. J. Respir. Crit. Care Med. 201, 1358–1371 (2020).
pubmed: 32105156
doi: 10.1164/rccm.201906-1149OC
La Linn, M., Bellett, A., Parsons, P. & Suhrbier, A. Complete removal of mycoplasma from viral preparations using solvent extraction. J. Virol. Methods 52, 51–54 (1995).
doi: 10.1016/0166-0934(94)00136-5
pubmed: 7539444
Na Pombejra, S., Salemi, M., Phinney, B. S. & Gelli, A. The metalloprotease, Mpr1, engages AnnexinA2 to promote the transcytosis of fungal cells across the blood-brain barrier. Front. Cell Infect. Microbiol. 7, 296 (2017).
pubmed: 28713781
pmcid: 5492700
doi: 10.3389/fcimb.2017.00296
Ozono, S. et al. SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nat. Commun. 12, 848 (2021).
pubmed: 33558493
pmcid: 7870668
doi: 10.1038/s41467-021-21118-2
Singh, S. et al. SATPdb: a database of structurally annotated therapeutic peptides. Nucleic Acids Res. 44, D1119–D1126 (2016).
pubmed: 26527728
doi: 10.1093/nar/gkv1114
Ensenat-Waser, R. et al. Direct visualization by confocal fluorescent microscopy of the permeation of myristoylated peptides through the cell membrane. IUBMB Life 54, 33–36 (2002).
pubmed: 12387573
doi: 10.1080/15216540213823
Sutcliffe, E. L. et al. Chromatin-associated protein kinase C-theta regulates an inducible gene expression program and microRNAs in human T lymphocytes. Mol. Cell 41, 704–719 (2011).
pubmed: 21419345
doi: 10.1016/j.molcel.2011.02.030
Wu, F. et al. Nuclear-biased DUSP6 expression is associated with cancer spreading including brain metastasis in triple-negative breast cancer. Int. J. Mol. Sci. 20, 3080 (2019).
Zafar, A. et al. Chromatinized protein kinase C-theta directly regulates inducible genes in epithelial to mesenchymal transition and breast cancer stem cells. Mol. Cell Biol. 34, 2961–2980 (2014).
pubmed: 24891615
pmcid: 4135602
doi: 10.1128/MCB.01693-13
Marfori, M. et al. Molecular basis for specificity of nuclear import and prediction of nuclear localization. Biochim. Biophys. Acta 1813, 1562–1577 (2011).
pubmed: 20977914
doi: 10.1016/j.bbamcr.2010.10.013
Teh, T., Tiganis, T. & Kobe, B. Crystallization of importin alpha, the nuclear-import receptor. Acta Crystallogr. D 55, 561–563 (1999).
pubmed: 10089379
doi: 10.1107/S0907444998012943
Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).
pubmed: 15915565
doi: 10.1016/j.pep.2005.01.016
Aragao, D. et al. MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron. J. Synchrotron Radiat. 25, 885–891 (2018).
pubmed: 29714201
pmcid: 5929359
doi: 10.1107/S1600577518003120
Battye, T. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr D 67, 271–281 (2011).
pubmed: 21460445
pmcid: 3069742
doi: 10.1107/S0907444910048675
Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006).
pubmed: 16369096
doi: 10.1107/S0907444905036693
McCoy, A. J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D 63, 32–41 (2007).
pubmed: 17164524
doi: 10.1107/S0907444906045975
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
doi: 10.1107/S0907444904019158
pubmed: 15572765
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
pubmed: 20124702
pmcid: 2815670
doi: 10.1107/S0907444909052925
Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012).
pubmed: 22505256
pmcid: 3322595
doi: 10.1107/S0907444912001308
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
doi: 10.14806/ej.17.1.200
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
doi: 10.1093/bioinformatics/bts635
pubmed: 23104886
DeLuca, D. S. et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28, 1530–1532 (2012).
pubmed: 22539670
pmcid: 3356847
doi: 10.1093/bioinformatics/bts196
Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 12, 323 (2011).
doi: 10.1186/1471-2105-12-323
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
pubmed: 19910308
doi: 10.1093/bioinformatics/btp616
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
pubmed: 25605792
pmcid: 4402510
doi: 10.1093/nar/gkv007
Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
pubmed: 22455463
pmcid: 3339379
doi: 10.1089/omi.2011.0118
Yu, G. & He, Q. Y. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Mol. Biosyst. 12, 477–479 (2016).
pubmed: 26661513
doi: 10.1039/C5MB00663E
Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).
pubmed: 27207943
doi: 10.1093/bioinformatics/btw313
Larsson, J. eulerr: Area-Proportional Euler and Venn Diagrams with Ellipses. R package version 5.1.0, https://cran.r-project.org/package=eulerr (2019).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 2723002
doi: 10.1093/bioinformatics/btp352