Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe.
Epigenetics
Fluorescent proteins
Genetically encoded sensor
H3K9me3
Histone modification
Machine learning
Journal
Cellular and molecular life sciences : CMLS
ISSN: 1420-9071
Titre abrégé: Cell Mol Life Sci
Pays: Switzerland
ID NLM: 9705402
Informations de publication
Date de publication:
02 Sep 2024
02 Sep 2024
Historique:
received:
20
03
2024
accepted:
10
07
2024
revised:
11
06
2024
medline:
2
9
2024
pubmed:
2
9
2024
entrez:
2
9
2024
Statut:
epublish
Résumé
Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods of analysis of epigenetic modifications such as mass-spectrometry and chromatin immuno-precipitation, work with fixed cells only. Here we present a genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, a histone modification associated with inactive chromatin. This probe, based on the chromodomain of MPP8, allows for visualization of H3K9me3 epigenetic landscapes in single living cells. We used this probe to track changes in H3K9me3 landscapes during the differentiation of induced pluripotent stem cells (iPSCs) into induced neurons. Our findings revealed two major waves of global H3K9me3 reorganization during 4-day differentiation, namely on the first and third days, whereas nearly no changes occurred on the second and fourth days. The proposed method LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscapes), which combines genetically encoded epigenetic probes and machine learning approaches, enables classification of multiparametric epigenetic signatures of single cells during stem cell differentiation and potentially in other biological models.
Identifiants
pubmed: 39222083
doi: 10.1007/s00018-024-05359-0
pii: 10.1007/s00018-024-05359-0
doi:
Substances chimiques
Histones
0
Fluorescent Dyes
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
381Subventions
Organisme : Russian Science Foundation
ID : 22-14-00141
Informations de copyright
© 2024. The Author(s).
Références
Nicetto D, Zaret KS (2019) Role of H3K9me3 heterochromatin in cell identity establishment and maintenance. Curr Opin Genet Dev 55:1–10
pubmed: 31103921
pmcid: 6759373
doi: 10.1016/j.gde.2019.04.013
Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680
pubmed: 19736561
pmcid: 3191340
doi: 10.1038/nrg2641
Hayashi-Takanaka Y, Yamagata K, Wakayama T et al (2011) Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling. Nucleic Acids Res 39:6475–6488
pubmed: 21576221
pmcid: 3159477
doi: 10.1093/nar/gkr343
Stasevich TJ, Hayashi-Takanaka Y, Sato Y et al (2014) Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516:272–275
pubmed: 25252976
doi: 10.1038/nature13714
Sato Y, Mukai M, Ueda J et al (2013) Genetically encoded system to track histone modification in vivo. Sci Rep 3:2436
pubmed: 23942372
pmcid: 3743053
doi: 10.1038/srep02436
Karemaker ID, Vermeulen M (2018) Single-cell DNA methylation profiling: technologies and biological applications. Trends Biotechnol 36:952–965
pubmed: 29724495
doi: 10.1016/j.tibtech.2018.04.002
Zhu C, Preissl S, Ren B (2020) Single-cell multimodal omics: the power of many. Nat Methods 17:11–14
pubmed: 31907462
doi: 10.1038/s41592-019-0691-5
Yun M, Wu J, Workman JL, Li B (2011) Readers of histone modifications. Cell Res 21:564–578
pubmed: 21423274
pmcid: 3131977
doi: 10.1038/cr.2011.42
Kungulovski G, Kycia I, Tamas R et al (2014) Application of histone modification-specific interaction domains as an alternative to antibodies. Genome Res 24:1842–1853
pubmed: 25301795
pmcid: 4216925
doi: 10.1101/gr.170985.113
Mauser R, Kungulovski G, Keup C et al (2017) Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. Epigenetics Chromatin 10:45
pubmed: 28946896
pmcid: 5613355
doi: 10.1186/s13072-017-0153-1
Delachat AM-F, Guidotti N, Bachmann AL et al (2018) Engineered multivalent sensors to detect coexisting histone modifications in living stem cells. Cell Chem Biol 25:51-56.e6
pubmed: 29174541
doi: 10.1016/j.chembiol.2017.10.008
Sánchez OF, Mendonca A, Min A et al (2019) Monitoring histone methylation (H3K9me3) changes in live cells. ACS Omega 4:13250–13259
pubmed: 31460452
pmcid: 6705211
doi: 10.1021/acsomega.9b01413
Villaseñor R, Pfaendler R, Ambrosi C et al (2020) ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 38:728–736
pubmed: 32123383
pmcid: 7289633
doi: 10.1038/s41587-020-0434-2
Takahashi K, Tanabe K, Ohnuki M et al (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:861–872
pubmed: 18035408
doi: 10.1016/j.cell.2007.11.019
Ho S-M, Topol A, Brennand KJ (2015) From “directed differentiation” to “neuronal induction”: modeling neuropsychiatric disease. Biomark Insights 10:31–41
pubmed: 26045654
pmcid: 4444490
Chambers SM, Fasano CA, Papapetrou EP et al (2009) Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol 27:275–280
pubmed: 19252484
pmcid: 2756723
doi: 10.1038/nbt.1529
Hulme AJ, Maksour S, St-Clair Glover M et al (2022) Making neurons, made easy: The use of Neurogenin-2 in neuronal differentiation. Stem Cell Reports 17:14–34
pubmed: 34971564
doi: 10.1016/j.stemcr.2021.11.015
Thoma EC, Wischmeyer E, Offen N et al (2012) Ectopic expression of neurogenin 2 alone is sufficient to induce differentiation of embryonic stem cells into mature neurons. PLoS ONE 7:e38651
pubmed: 22719915
pmcid: 3374837
doi: 10.1371/journal.pone.0038651
Zhang Y, Pak C, Han Y et al (2013) Rapid single-step induction of functional neurons from human pluripotent stem cells. Neuron 78:785–798
pubmed: 23764284
pmcid: 3751803
doi: 10.1016/j.neuron.2013.05.029
Busskamp V, Lewis NE, Guye P et al (2014) Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol 10:760
pubmed: 25403753
pmcid: 4299601
doi: 10.15252/msb.20145508
Bermingham NA, Hassan BA, Price SD et al (1999) Math1: an essential gene for the generation of inner ear hair cells. Science 284:1837–1841
pubmed: 10364557
doi: 10.1126/science.284.5421.1837
Sagal J, Zhan X, Xu J et al (2014) Proneural transcription factor Atoh1 drives highly efficient differentiation of human pluripotent stem cells into dopaminergic neurons. Stem Cells Transl Med 3:888–898
pubmed: 24904172
pmcid: 4116248
doi: 10.5966/sctm.2013-0213
Ng AHM, Khoshakhlagh P, Rojo Arias JE et al (2021) A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol 39:510–519
pubmed: 33257861
doi: 10.1038/s41587-020-0742-6
Farhy C, Hariharan S, Ylanko J et al (2019) Improving drug discovery using image-based multiparametric analysis of the epigenetic landscape. Elife. https://doi.org/10.7554/eLife.49683
doi: 10.7554/eLife.49683
pubmed: 31637999
pmcid: 6908434
Smith AS, Ankam S, Farhy C et al (2022) High-content analysis and Kinetic Image Cytometry identify toxicity and epigenetic effects of HIV antiretrovirals on human iPSC-neurons and primary neural precursor cells. J Pharmacol Toxicol Methods 114:107157
pubmed: 35143957
pmcid: 9103414
doi: 10.1016/j.vascn.2022.107157
Zhao H, Lin LF, Hahn J et al (2022) Single-cell image-based analysis reveals chromatin changes during the acquisition of tamoxifen drug resistance. Life. https://doi.org/10.3390/life12030438
doi: 10.3390/life12030438
pubmed: 36675957
pmcid: 9863881
Chang Y, Horton JR, Bedford MT et al (2011) Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding. J Mol Biol 408:807–814
pubmed: 21419134
pmcid: 3081990
doi: 10.1016/j.jmb.2011.03.018
Rawłuszko-Wieczorek AA, Knodel F, Tamas R et al (2018) Identification of protein lysine methylation readers with a yeast three-hybrid approach. Epigenetics Chromatin 11:4
pubmed: 29370823
pmcid: 5784651
doi: 10.1186/s13072-018-0175-3
Tchasovnikarova IA, Timms RT, Matheson NJ et al (2015) GENE SILENCING. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells. Science 348:1481–1485
pubmed: 26022416
pmcid: 4487827
doi: 10.1126/science.aaa7227
Liu N, Lee CH, Swigut T et al (2018) Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553:228–232
pubmed: 29211708
doi: 10.1038/nature25179
Müller I, Moroni AS, Shlyueva D et al (2021) MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells. Nat Commun 12:3034
pubmed: 34031396
pmcid: 8144423
doi: 10.1038/s41467-021-23308-4
Shaner NC, Lambert GG, Chammas A et al (2013) A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat Methods 10:407–409
pubmed: 23524392
pmcid: 3811051
doi: 10.1038/nmeth.2413
Kokura K, Sun L, Bedford MT, Fang J (2010) Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion. EMBO J 29:3673–3687
pubmed: 20871592
pmcid: 2982762
doi: 10.1038/emboj.2010.239
Bock I, Kudithipudi S, Tamas R et al (2011) Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails. BMC Biochem 12:48
pubmed: 21884582
pmcid: 3176149
doi: 10.1186/1471-2091-12-48
Zhao W, Ji X, Zhang F et al (2012) Embryonic stem cell markers. Molecules 17:6196–6236
pubmed: 22634835
pmcid: 6268870
doi: 10.3390/molecules17066196
Lemmens M, Perner J, Potgeter L et al (2023) Identification of marker genes to monitor residual iPSCs in iPSC-derived products. Cytotherapy 25:59–67
pubmed: 36319564
doi: 10.1016/j.jcyt.2022.09.010
Wang M, Da Y, Tian Y (2023) Fluorescent proteins and genetically encoded biosensors. Chem Soc Rev 52:1189–1214
pubmed: 36722390
doi: 10.1039/D2CS00419D
Lu K, Vu CQ, Matsuda T, Nagai T (2019) Fluorescent protein-based indicators for functional super-resolution imaging of biomolecular activities in living cells. Int J Mol Sci. https://doi.org/10.3390/ijms20225784
doi: 10.3390/ijms20225784
pubmed: 31906246
pmcid: 6982186
Stepanov AI, Besedovskaia ZV, Moshareva MA et al (2022) Studying chromatin epigenetics with fluorescence microscopy. Int J Mol Sci. https://doi.org/10.3390/ijms23168988
doi: 10.3390/ijms23168988
pubmed: 36555748
pmcid: 9786835
Stepanov AI, Zhurlova PA, Shuvaeva AA et al (2023) Optogenetics for sensors: On-demand fluorescent labeling of histone epigenetics. Biochem Biophys Res Commun 687:149174
pubmed: 37939505
doi: 10.1016/j.bbrc.2023.149174
Meanor JN, Keung AJ, Rao BM (2022) Modified histone peptides linked to magnetic beads reduce binding specificity. Int J Mol Sci. https://doi.org/10.3390/ijms23031691
doi: 10.3390/ijms23031691
pubmed: 35163614
pmcid: 8836101
Becker JS, Nicetto D, Zaret KS (2016) H3K9me3-dependent heterochromatin: barrier to cell fate changes. Trends Genet 32:29–41
pubmed: 26675384
doi: 10.1016/j.tig.2015.11.001
Soufi A, Donahue G, Zaret KS (2012) Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151:994–1004
pubmed: 23159369
pmcid: 3508134
doi: 10.1016/j.cell.2012.09.045
Werner S, Engler C, Weber E et al (2012) Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioeng Bugs 3:38–43
pubmed: 22126803
Kim D, Paggi JM, Park C et al (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37:907–915
pubmed: 31375807
pmcid: 7605509
doi: 10.1038/s41587-019-0201-4
Pertea M, Pertea GM, Antonescu CM et al (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295
pubmed: 25690850
pmcid: 4643835
doi: 10.1038/nbt.3122
Ritchie ME, Phipson B, Wu D et al (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43:e47
pubmed: 25605792
pmcid: 4402510
doi: 10.1093/nar/gkv007
(2013) Mahotas: Open source software for scriptable computer vision. J Open Res Softw 1:e3
Pedregosa F, Varoquaux G, Gramfort A et al (2011) Scikit-learn: machine learning in Python. J Mach Learn Res 12:2825–2830