Screening and Reconstruction for Single-Molecular Localization Superresolution Images of Nuclear Pore Complexes

Mengdi Hou; Fen Hu; Jianyu Yang; Hao Dong; Leiting Pan

doi:10.3788/CJL231072

[1] Tai L H, Yin G L, Sun F et al. Cryo-electron microscopy reveals the structure of the nuclear pore complex[J]. Journal of Molecular Biology, 435, 168051(2023).

[2] Allegretti M, Zimmerli C E, Rantos V et al. In-cell architecture of the nuclear pore and snapshots of its turnover[J]. Nature, 586, 796-800(2020).

[3] Lin D H, Hoelz A. The structure of the nuclear pore complex (an update)[J]. Annual Review of Biochemistry, 88, 725-783(2019).

[4] Schreiner S M, Koo P K, Zhao Y et al. The tethering of chromatin to the nuclear envelope supports nuclear mechanics[J]. Nature Communications, 6, 7159(2015).

[5] Sakuma S, D’Angelo M A. The roles of the nuclear pore complex in cellular dysfunction, aging and disease[J]. Seminars in Cell & Developmental Biology, 68, 72-84(2017).

[6] Alber F, Dokudovskaya S, Veenhoff L M et al. The molecular architecture of the nuclear pore complex[J]. Nature, 450, 695-701(2007).

[7] Rout M P, Aitchison J D, Suprapto A et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism[J]. The Journal of Cell Biology, 148, 635-651(2000).

[8] Stoffler D, Goldie K N, Feja B et al. Calcium-mediated structural changes of native nuclear pore complexes monitored by time-lapse atomic force microscopy[J]. Journal of Molecular Biology, 287, 741-752(1999).

[9] Bley C J, Nie S, Mobbs G W et al. Architecture of the cytoplasmic face of the nuclear pore[J]. Science, 376, eabm9129(2022).

[10] Petrovic S, Samanta D, Perriches T et al. Architecture of the linker-scaffold in the nuclear pore[J]. Science, 376, eabm9798(2022).

[11] Mosalaganti S, Obarska-Kosinska A, Siggel M et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores[J]. Science, 376, eabm9506(2022).

[12] Fontana P, Dong Y, Pi X et al. Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold[J]. Science, 376, eabm9326(2022).

[13] Zhu X C, Huang G, Zeng C et al. Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex[J]. Science, 376, eabl8280(2022).

[14] Rust M J, Bates M, Zhuang X W. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)[J]. Nature Methods, 3, 793-796(2006).

[15] Betzig E, Patterson G H, Sougrat R et al. Imaging intracellular fluorescent proteins at nanometer resolution[J]. Science, 313, 1642-1645(2006).

[16] Jungmann R, Avendaño M S, Woehrstein J B et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT[J]. Nature Methods, 11, 313-318(2014).

[17] Kanchanawong P, Shtengel G, Pasapera A M et al. Nanoscale architecture of integrin-based cell adhesions[J]. Nature, 468, 580-584(2010).

[18] Hu F, Zhu D L, Dong H et al. Super-resolution microscopy reveals nanoscale architecture and regulation of podosome clusters in primary macrophages[J]. iScience, 25, 105514(2022).

[19] Cieslinski K, Wu Y L, Nechyporenko L et al. Nanoscale structural organization and stoichiometry of the budding yeast kinetochore[J]. Journal of Cell Biology, 222, 202209094(2023).

[20] Thevathasan J V, Kahnwald M, Cieśliński K et al. Nuclear pores as versatile reference standards for quantitative superresolution microscopy[J]. Nature Methods, 16, 1045-1053(2019).

[21] Szymborska A, de Marco A, Daigle N et al. Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging[J]. Science, 341, 655-658(2013).

[22] Salas D, le Gall A, Fiche J B et al. Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images[J]. Proceedings of the National Academy of Sciences of the United States of America, 114, 9273-9278(2017).

[23] Sieben C, Banterle N, Douglass K M et al. Multicolor single-particle reconstruction of protein complexes[J]. Nature Methods, 15, 777-780(2018).

[24] Curd A P, Leng J, Hughes R E et al. Nanoscale pattern extraction from relative positions of sparse 3D localizations[J]. Nano Letters, 21, 1213-1220(2021).

[25] Ester M, Kriegel H P, Sander J et al. A density-based algorithm for discovering clusters in large spatial databases with noise[C], 226-231(1996).

[26] Peng D H, Gui Z P, Wang D H et al. Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivity[J]. Nature Communications, 13, 5455(2022).

[27] Levet F, Hosy E, Kechkar A et al. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data[J]. Nature Methods, 12, 1065-1071(2015).

[28] Pratim M P. Probabilistic optically-selective single-molecule imaging based localization encoded (POSSIBLE) microscopy for ultra-superresolution imaging[J]. PLoS One, 15, e0242452(2020).

[29] Murtagh F, Contreras P. Algorithms for hierarchical clustering: an overview[J]. Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, 2, 86-97(2012).

[30] Pritchard H A T, Pires P W, Yamasaki E et al. Nanoscale remodeling of ryanodine receptor cluster size underlies cerebral microvascular dysfunction in Duchenne muscular dystrophy[J]. Proceedings of the National Academy of Sciences of the United States of America, 115, E9745-E9752(2018).

[31] Yan Q Y, Lu Y T, Zhou L L et al. Mechanistic insights into GLUT1 activation and clustering revealed by super-resolution imaging[J]. Proceedings of the National Academy of Sciences of the United States of America, 115, 7033-7038(2018).

[32] Pageon S V, Nicovich P R, Mollazade M et al. Clus-DoC: a combined cluster detection and colocalization analysis for single-molecule localization microscopy data[J]. Molecular Biology of the Cell, 27, 3627-3636(2016).

[33] Levet F, Julien G, Galland R et al. A tessellation-based colocalization analysis approach for single-molecule localization microscopy[J]. Nature Communications, 10, 2379(2019).

[34] Ejdrup A L, Lycas M D, Lorenzen N et al. A density-based enrichment measure for assessing colocalization in single-molecule localization microscopy data[J]. Nature Communications, 13, 4388(2022).

[35] Pan L T, Yan R, Li W et al. Super-resolution microscopy reveals the native ultrastructure of the erythrocyte cytoskeleton[J]. Cell Reports, 22, 1151-1158(2018).

[36] Yang J Y, Hu F, Xing F L et al. Clustering segmentation for single-molecule localization super-resolution image of membrane protein by combining multi-step DBSCAN and hierarchical clustering algorithm[J]. Chinese Journal of Lasers, 50, 0307106(2023).

[37] Walther T C, Alves A, Pickersgill H et al. The conserved Nup107-160 complex is critical for nuclear pore complex assembly[J]. Cell, 113, 195-206(2003).

[38] Hoogenboom B W, Hough L E, Lemke E A et al. Physics of the nuclear pore complex: theory, modeling and experiment[J]. Physics Reports, 921, 1-53(2021).