Cited by 1Advanced Fluorescence Microscopy TechniquesCRISPR and Genetic EngineeringPluripotent Stem Cells Research

The DOI matches its Crossref record; its reference list is not available.

Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies

Open access

Published version of a preprint

Abstract

Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG2 1-10 ) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG2 11 ). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.7554/elife.92819.3

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

No citation lists for this paper

No citation lists for this paper yet — checked again daily.

References 92 · Cited by 1

Research works printed but not linked: 93

  1. Aban, 2021, Downregulation of E-cadherin in pluripotent stem cells triggers partial EMT, Scientific Reports, 11, 10.1038/s41598-021-81735-1 · DOI
  2. Adriaans, 2019, PLK1 plays dual roles in centralspindlin regulation during cytokinesis, The Journal of Cell Biology, 218, 1250, 10.1083/jcb.201805036 · DOI
  3. Beaudet, 2017, Active ran regulates anillin function during cytokinesis, Molecular Biology of the Cell, 28, 3517, 10.1091/mbc.E17-04-0253 · DOI
  4. Bhargava, 2022, Development of an efficient single-cell cloning and expansion strategy for genome edited induced pluripotent stem cells, Molecular Biology Reports, 49, 7887, 10.1007/s11033-022-07621-9 · DOI
  5. Bukhari, 2019, Endogenous fluorescence tagging by crispr, Trends in Cell Biology, 29, 912, 10.1016/j.tcb.2019.08.004 · DOI
  6. Burgio, 2020, Anticipating and identifying collateral damage in genome editing, Trends in Genetics, 36, 905, 10.1016/j.tig.2020.09.011 · DOI
  7. Cabrera, 2022, The sound of silence: transgene silencing in mammalian cell engineering, Cell Systems, 13, 950, 10.1016/j.cels.2022.11.005 · DOI
  8. Chaigne, 2020, Abscission couples cell division to embryonic stem cell fate, Developmental Cell, 55, 195, 10.1016/j.devcel.2020.09.001 · DOI
  9. Chaigne, 2021, Three-dimensional geometry controls division symmetry in stem cell colonies, Journal of Cell Science, 134, 10.1242/jcs.255018 · DOI
  10. Chalfie, 1994, Green fluorescent protein as a marker for gene expression, Science, 263, 802, 10.1126/science.8303295 · DOI · Paper page
  11. Chen, 2018, Improving single-cell cloning workflow for gene editing in human pluripotent stem cells, Stem Cell Research, 31, 186, 10.1016/j.scr.2018.08.003 · DOI
  12. Cho, 2022, opencell: endogenous tagging for the cartography of human cellular organization, Science, 375, 10.1126/science.abi6983 · DOI · Paper page
  13. Chu, 2015, Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells, Nature Biotechnology, 33, 543, 10.1038/nbt.3198 · DOI · Paper page
  14. Clavel, 2016, Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution, Acta Crystallographica. Section D, Structural Biology, 72, 1298, 10.1107/S2059798316018623 · DOI
  15. Clement, 2019, CRISPResso2 provides accurate and rapid genome editing sequence analysis, Nature Biotechnology, 37, 224, 10.1038/s41587-019-0032-3 · DOI
  16. CMCI. 2023. Colony_Screening. Software Heritage. swh:1:rev:fbc789cf6587fce9b36db0c9111a9ab6c5e35d79. https://archive.softwareheritage.org/swh:1:dir:f6522771e1ed91168fa70763e84208fa03367301;origin=https://github.com/CMCI/colony_screening;visit=swh:1:snp:de6f83ea0b52cc18ab5d4ff6ae980e37a62fcfcd;anchor=swh:1:rev:fbc789cf6587fce9b36db0c9111a9ab6c5e35d79.
  17. Concordet, 2018, CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens, Nucleic Acids Research, 46, W242, 10.1093/nar/gky354 · DOI
  18. Cumin, 2022, Glycosphingolipids are mediators of cancer plasticity through independent signaling pathways, Cell Reports, 40, 10.1016/j.celrep.2022.111181 · DOI
  19. Dambournet, 2018, Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiation, The Journal of Cell Biology, 217, 3301, 10.1083/jcb.201710084 · DOI
  20. Doench, 2016, Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9, Nature Biotechnology, 34, 184, 10.1038/nbt.3437 · DOI · Paper page
  21. Doyon, 2011, Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells, Nature Cell Biology, 13, 331, 10.1038/ncb2175 · DOI
  22. Drubin, 2017, Stem cells: the new “model organism.”, Molecular Biology of the Cell, 28, 1409, 10.1091/mbc.E17-03-0183 · DOI · Paper page
  23. Feng, 2017, Improved split fluorescent proteins for endogenous protein labeling, Nature Communications, 8, 10.1038/s41467-017-00494-8 · DOI
  24. Feng, 2019, Bright split red fluorescent proteins for the visualization of endogenous proteins and synapses, Communications Biology, 2, 10.1038/s42003-019-0589-x · DOI
  25. Gibson, 2013, The transience of transient overexpression, Nature Methods, 10, 715, 10.1038/nmeth.2534 · DOI
  26. Grancharova, 2021, A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes, Scientific Reports, 11, 10.1038/s41598-021-94732-1 · DOI · Paper page
  27. Green, 2012, Cytokinesis in animal cells, Annual Review of Cell and Developmental Biology, 28, 29, 10.1146/annurev-cellbio-101011-155718 · DOI
  28. Guo, 2010, The beta isotypes of tubulin in neuronal differentiation, Cytoskeleton, 67, 431, 10.1002/cm.20455 · DOI
  29. Hesse, 2012, Direct visualization of cell division using high-resolution imaging of M-phase of the cell cycle, Nature Communications, 3, 10.1038/ncomms2089 · DOI
  30. Hong, 2019, Neural lineage differentiation from pluripotent stem cells to mimic human brain tissues, Frontiers in Bioengineering and Biotechnology, 7, 10.3389/fbioe.2019.00400 · DOI
  31. Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nature Biotechnology, 31, 827, 10.1038/nbt.2647 · DOI · Paper page
  32. Huh, 2003, Global analysis of protein localization in budding yeast, Nature, 425, 686, 10.1038/nature02026 · DOI · Paper page
  33. Husser, 2021, CRISPR-Cas tools to study gene function in cytokinesis, Journal of Cell Science, 134, 10.1242/jcs.254409 · DOI
  34. Husser, 2022, Cytokinetic diversity in mammalian cells is revealed by the characterization of endogenous anillin, Ect2 and RhoA, Open Biology, 12, 10.1098/rsob.220247 · DOI
  35. Iwasaki, 2022, Multi-omics approach reveals posttranscriptionally regulated genes are essential for human pluripotent stem cells, iScience, 25, 10.1016/j.isci.2022.104289 · DOI
  36. Kamiyama, 2016, Versatile protein tagging in cells with split fluorescent protein, Nature Communications, 7, 10.1038/ncomms11046 · DOI
  37. Karst, 2021, High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing, Nature Methods, 18, 165, 10.1038/s41592-020-01041-y · DOI
  38. Khaliullin, 2018, A positive-feedback-based mechanism for constriction rate acceleration during cytokinesis in Caenorhabditis elegans, eLife, 7, 10.7554/eLife.36073 · DOI
  39. Kim, 2014, Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins, Genome Research, 24, 1012, 10.1101/gr.171322.113 · DOI · Paper page
  40. Koh, 2022, Seeing is believing: tools to study the role of Rho GTPases during cytokinesis, Small GTPases, 13, 211, 10.1080/21541248.2021.1957384 · DOI
  41. Köker, 2018, Characterization of split fluorescent protein variants and quantitative analyses of their self-assembly process, Scientific Reports, 8, 10.1038/s41598-018-23625-7 · DOI
  42. Kotýnková, 2016, Plasma membrane association but not midzone recruitment of rhogef ect2 is essential for cytokinesis, Cell Reports, 17, 2672, 10.1016/j.celrep.2016.11.029 · DOI
  43. Kuang, 2019, Evaluation of commonly used ectoderm markers in iPSC trilineage differentiation, Stem Cell Research, 37, 10.1016/j.scr.2019.101434 · DOI
  44. Lee, 2015, A highly characterized yeast toolkit for modular, multipart assembly, ACS Synthetic Biology, 4, 975, 10.1021/sb500366v · DOI
  45. Leite, 2020, Equatorial non-muscle myosin ii and plastin cooperate to align and compact f-actin bundles in the cytokinetic ring, Frontiers in Cell and Developmental Biology, 8, 10.3389/fcell.2020.573393 · DOI
  46. Leonetti, 2016, A scalable strategy for high-throughput GFP tagging of endogenous human proteins, PNAS, 113, E3501, 10.1073/pnas.1606731113 · DOI
  47. Li, 2018, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, 34, 3094, 10.1093/bioinformatics/bty191 · DOI · Paper page
  48. Liang, 2015, Rapid and highly efficient mammalian cell engineering via cas9 protein transfection, Journal of Biotechnology, 208, 44, 10.1016/j.jbiotec.2015.04.024 · DOI · Paper page
  49. Luo, 2014, Stable enhanced green fluorescent protein expression after differentiation and transplantation of reporter human induced pluripotent stem cells generated by AAVS1 transcription activator-like effector nucleases, Stem Cells Translational Medicine, 3, 821, 10.5966/sctm.2013-0212 · DOI
  50. Mahdessian, 2021, Spatiotemporal dissection of the cell cycle with single-cell proteogenomics, Nature, 590, 649, 10.1038/s41586-021-03232-9 · DOI
  51. Mahen, 2014, Comparative assessment of fluorescent transgene methods for quantitative imaging in human cells, Molecular Biology of the Cell, 25, 3610, 10.1091/mbc.E14-06-1091 · DOI
  52. Mahlandt, 2021, Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor, Journal of Cell Science, 134, 10.1242/jcs.258823 · DOI
  53. Maruyama, 2015, Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining, Nature Biotechnology, 33, 538, 10.1038/nbt.3190 · DOI · Paper page
  54. Maurer, 2008, Contrasting expression of keratins in mouse and human embryonic stem cells, PLOS ONE, 3, 10.1371/journal.pone.0003451 · DOI
  55. Maurissen, 2020, Synergistic gene editing in human iPS cells via cell cycle and DNA repair modulation, Nature Communications, 11, 10.1038/s41467-020-16643-5 · DOI
  56. Oceguera-Yanez, 2016, Engineering the AAVS1 locus for consistent and scalable transgene expression in human iPSCs and their differentiated derivatives, Methods, 101, 43, 10.1016/j.ymeth.2015.12.012 · DOI
  57. Oceguera-Yanez, 2022, Differentiation of pluripotent stem cells for modeling human skin development and potential applications, Frontiers in Cell and Developmental Biology, 10, 10.3389/fcell.2022.1030339 · DOI
  58. O’Hagan, 2021, Efficient generation of endogenous protein reporters for mouse development, Development, 148, 10.1242/dev.197418 · DOI
  59. Osório, 2019, Crosslinking activity of non-muscle myosin II is not sufficient for embryonic cytokinesis in C. elegans, Development, 146, 10.1242/dev.179150 · DOI
  60. Ozugergin, 2022, Diverse mechanisms regulate contractile ring assembly for cytokinesis in the two-cell Caenorhabditis elegans embryo, Journal of Cell Science, 135, 10.1242/jcs.258921 · DOI
  61. Ozugergin, 2022, Diversity is the spice of life: an overview of how cytokinesis regulation varies with cell type, Frontiers in Cell and Developmental Biology, 10, 10.3389/fcell.2022.1007614 · DOI
  62. Paim, 2022, Cell size and polarization determine cytokinesis furrow ingression dynamics in mouse embryos, PNAS, 119, 10.1073/pnas.2119381119 · DOI
  63. Piekny, 2008, Anillin is a scaffold protein that links RhoA, actin, and myosin during cytokinesis, Current Biology, 18, 30, 10.1016/j.cub.2007.11.068 · DOI · Paper page
  64. Piekny, 2010, The myriad roles of anillin during cytokinesis, Seminars in Cell & Developmental Biology, 21, 881, 10.1016/j.semcdb.2010.08.002 · DOI
  65. Pollard, 2019, Molecular mechanism of cytokinesis, Annual Review of Biochemistry, 88, 661, 10.1146/annurev-biochem-062917-012530 · DOI
  66. Reymann, 2016, Cortical flow aligns actin filaments to form a furrow, eLife, 5, 10.7554/eLife.17807 · DOI
  67. Roberts, 2017, Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization, Molecular Biology of the Cell, 28, 2854, 10.1091/mbc.E17-03-0209 · DOI · Paper page
  68. Roberts, 2019, Fluorescent gene tagging of transcriptionally silent genes in hipscs, Stem Cell Reports, 12, 1145, 10.1016/j.stemcr.2019.03.001 · DOI
  69. Rodrigues, 2015, Kinetochore-localized PP1-Sds22 couples chromosome segregation to polar relaxation, Nature, 524, 489, 10.1038/nature14496 · DOI
  70. Schimmel, 2023, Modulating mutational outcomes and improving precise gene editing at CRISPR-Cas9-induced breaks by chemical inhibition of end-joining pathways, Cell Reports, 42, 10.1016/j.celrep.2023.112019 · DOI
  71. Shi, 2017, Induced pluripotent stem cell technology: a decade of progress, Nature Reviews. Drug Discovery, 16, 115, 10.1038/nrd.2016.245 · DOI · Paper page
  72. Singh, 2019, An efficient protocol for single-cell cloning human pluripotent stem cells, Frontiers in Cell and Developmental Biology, 7, 10.3389/fcell.2019.00011 · DOI
  73. Skryabin, 2020, Pervasive head-to-tail insertions of DNA templates mask desired CRISPR-Cas9-mediated genome editing events, Science Advances, 6, 10.1126/sciadv.aax2941 · DOI
  74. Sobral, 2021, Plastin and spectrin cooperate to stabilize the actomyosin cortex during cytokinesis, Current Biology, 31, 5415, 10.1016/j.cub.2021.09.055 · DOI
  75. Spira, 2017, Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments, eLife, 6, 10.7554/eLife.30867 · DOI
  76. Strebinger, 2019, Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions, Molecular Systems Biology, 15, 10.15252/msb.20199002 · DOI
  77. Su, 2011, Targeting of the RhoGEF Ect2 to the equatorial membrane controls cleavage furrow formation during cytokinesis, Developmental Cell, 21, 1104, 10.1016/j.devcel.2011.11.003 · DOI
  78. Takahashi, 2007, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell, 131, 861, 10.1016/j.cell.2007.11.019 · DOI · Paper page
  79. Tamura, 2021, Multiplexed labeling of cellular proteins with split fluorescent protein tags, Communications Biology, 4, 10.1038/s42003-021-01780-4 · DOI
  80. Thorvaldsdóttir, 2013, Integrative genomics viewer (igv): high-performance genomics data visualization and exploration, Briefings in Bioinformatics, 14, 178, 10.1093/bib/bbs017 · DOI · Paper page
  81. Tristan, 2023, Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail, Nature Protocols, 18, 58, 10.1038/s41596-022-00753-z · DOI
  82. Turaç, 2013, Combined flow cytometric analysis of surface and intracellular antigens reveals surface molecule markers of human neuropoiesis, PLOS ONE, 8, 10.1371/journal.pone.0068519 · DOI
  83. van Oostende Triplet, 2014, Anillin interacts with microtubules and is part of the astral pathway that defines cortical domains, Journal of Cell Science, 127, 3699, 10.1242/jcs.147504 · DOI
  84. Verma, 2017, Crispr/cas-mediated knockin in human pluripotent stem cells, Methods in Molecular Biology, 1513, 119, 10.1007/978-1-4939-6539-7_9 · DOI
  85. Wang, 2014, Genetic screens in human cells using the CRISPR-Cas9 system, Science, 343, 80, 10.1126/science.1246981 · DOI · Paper page
  86. Watanabe, 2007, A ROCK inhibitor permits survival of dissociated human embryonic stem cells, Nature Biotechnology, 25, 681, 10.1038/nbt1310 · DOI · Paper page
  87. Weigert, 2018, Content-aware image restoration: pushing the limits of fluorescence microscopy, Nature Methods, 15, 1090, 10.1038/s41592-018-0216-7 · DOI
  88. Whitford, 2022, Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer, Scientific Reports, 12, 10.1038/s41598-022-12613-7 · DOI
  89. Ye, 2012, Primer-blast: a tool to design target-specific primers for polymerase chain reaction, BMC Bioinformatics, 13, 10.1186/1471-2105-13-134 · DOI
  90. Yonemura, 2004, Rho localization in cells and tissues, Experimental Cell Research, 295, 300, 10.1016/j.yexcr.2004.01.005 · DOI
  91. Yüce, 2005, An ECT2-centralspindlin complex regulates the localization and function of RhoA, The Journal of Cell Biology, 170, 571, 10.1083/jcb.200501097 · DOI
  92. Zhou, 2020, Improved yellow-green split fluorescent proteins for protein labeling and signal amplification, PLOS ONE, 15, 10.1371/journal.pone.0242592 · DOI
  93. Iwasaki M, Takahashi K, Okubo C. 2022. Post-transcriptionally regulated genes are essential for pluripotent stem cell survival. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199820. GSE199820.

Metadata

Authors
Husser, M. C., Pham, N. P., Law, C., Araujo, F. R., Martin, V. J., & Piekny, A.
Affiliations
  • Concordia University (US)
  • Concordia University (CA)
Venue
eLife
Published
2024-04-23
Volume
12
ISSN
2050-084X (ISSN-L)
OpenAlex
W4395082447
Cited by
1
References
92
Citations by year
2025: 1
FWCI
0.19
Type
journal article
Language
en
Open access
Locations
eLife (publishedVersion, cc-by)
Funders
  • Fonds de recherche du Québec – Nature et technologies (Doctoral Training Scholarship B2X)
  • Concordia University (SynBioApps scholarship)
  • National Research Council Canada (Disruptive Technology Solutions for Cell and Gene Therapy Challenge)
  • Natural Sciences and Engineering Research Council of Canada (Discovery Grant, RGPIN-2023-04805)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
Keywords
endogenous tagging, human induced pluripotent stem cells, live-cell imaging, homology-directed repair, protein structure visualization, cytokinesis, HEK293 cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review