IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-34183-y.html
   My bibliography  Save this article

FRET-FISH probes chromatin compaction at individual genomic loci in single cells

Author

Listed:
  • Ana Mota

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory)

  • Szymon Berezicki

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory)

  • Erik Wernersson

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory)

  • Luuk Harbers

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory)

  • Xiaoze Li-Wang

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory)

  • Katarina Gradin

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory)

  • Christiane Peuckert

    (Stockholm University, The Department of Molecular Biosciences, The Wenner-Gren Institute)

  • Nicola Crosetto

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory
    Human Technopole)

  • Magda Bienko

    (Tumor and Cell Biology, Karolinska Institutet
    Science for Life Laboratory
    Human Technopole)

Abstract

Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.

Suggested Citation

  • Ana Mota & Szymon Berezicki & Erik Wernersson & Luuk Harbers & Xiaoze Li-Wang & Katarina Gradin & Christiane Peuckert & Nicola Crosetto & Magda Bienko, 2022. "FRET-FISH probes chromatin compaction at individual genomic loci in single cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34183-y
    DOI: 10.1038/s41467-022-34183-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-34183-y
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-34183-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Eleni Gelali & Gabriele Girelli & Masahiro Matsumoto & Erik Wernersson & Joaquin Custodio & Ana Mota & Maud Schweitzer & Katalin Ferenc & Xinge Li & Reza Mirzazadeh & Federico Agostini & John P. Schel, 2019. "iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    2. Yodai Takei & Jina Yun & Shiwei Zheng & Noah Ollikainen & Nico Pierson & Jonathan White & Sheel Shah & Julian Thomassie & Shengbao Suo & Chee-Huat Linus Eng & Mitchell Guttman & Guo-Cheng Yuan & Long , 2021. "Integrated spatial genomics reveals global architecture of single nuclei," Nature, Nature, vol. 590(7845), pages 344-350, February.
    3. Alistair N. Boettiger & Bogdan Bintu & Jeffrey R. Moffitt & Siyuan Wang & Brian J. Beliveau & Geoffrey Fudenberg & Maxim Imakaev & Leonid A. Mirny & Chao-ting Wu & Xiaowei Zhuang, 2016. "Super-resolution imaging reveals distinct chromatin folding for different epigenetic states," Nature, Nature, vol. 529(7586), pages 418-422, January.
    4. Sinan Kilic & Suren Felekyan & Olga Doroshenko & Iuliia Boichenko & Mykola Dimura & Hayk Vardanyan & Louise C. Bryan & Gaurav Arya & Claus A. M. Seidel & Beat Fierz, 2018. "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Robin Aguilar & Conor K. Camplisson & Qiaoyi Lin & Karen H. Miga & William S. Noble & Brian J. Beliveau, 2024. "Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Kosuke Tomimatsu & Takeru Fujii & Ryoma Bise & Kazufumi Hosoda & Yosuke Taniguchi & Hiroshi Ochiai & Hiroaki Ohishi & Kanta Ando & Ryoma Minami & Kaori Tanaka & Taro Tachibana & Seiichi Mori & Akihito, 2024. "Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Halima H. Schede & Pradeep Natarajan & Arup K. Chakraborty & Krishna Shrinivas, 2023. "A model for organization and regulation of nuclear condensates by gene activity," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    4. Ting Peng & Yingping Hou & Haowei Meng & Yong Cao & Xiaotian Wang & Lumeng Jia & Qing Chen & Yang Zheng & Yujie Sun & Hebing Chen & Tingting Li & Cheng Li, 2023. "Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    5. Lindsay Lee & Hongyu Yu & Bojing Blair Jia & Adam Jussila & Chenxu Zhu & Jiawen Chen & Liangqi Xie & Antonina Hafner & Shreya Mishra & Duan Dennis Wang & Caterina Strambio-De-Castillia & Alistair Boet, 2023. "SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    6. Jinhyun Kim & Sungsik Kim & Huiran Yeom & Seo Woo Song & Kyoungseob Shin & Sangwook Bae & Han Suk Ryu & Ji Young Kim & Ahyoun Choi & Sumin Lee & Taehoon Ryu & Yeongjae Choi & Hamin Kim & Okju Kim & Yu, 2023. "Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Takeo Kubota & Kazuki Mochizuki, 2016. "Epigenetic Effect of Environmental Factors on Autism Spectrum Disorders," IJERPH, MDPI, vol. 13(5), pages 1-12, May.
    8. Gerard Llimos & Vincent Gardeux & Ute Koch & Judith F. Kribelbauer & Antonina Hafner & Daniel Alpern & Joern Pezoldt & Maria Litovchenko & Julie Russeil & Riccardo Dainese & Riccardo Moia & Abdurraouf, 2022. "A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    9. Xinyu Hu & Bob van Sluijs & Óscar García-Blay & Yury Stepanov & Koen Rietrae & Wilhelm T. S. Huck & Maike M. K. Hansen, 2024. "ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    10. Markus Götz & Anders Barth & Søren S.-R. Bohr & Richard Börner & Jixin Chen & Thorben Cordes & Dorothy A. Erie & Christian Gebhardt & Mélodie C. A. S. Hadzic & George L. Hamilton & Nikos S. Hatzakis &, 2022. "A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    11. Harsh Nagpal & Ahmad Ali-Ahmad & Yasuhiro Hirano & Wei Cai & Mario Halic & Tatsuo Fukagawa & Nikolina Sekulić & Beat Fierz, 2023. "CENP-A and CENP-B collaborate to create an open centromeric chromatin state," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    12. Michal Polonsky & Louisa M. S. Gerhardt & Jina Yun & Kari Koppitch & Katsuya Lex Colón & Henry Amrhein & Barbara Wold & Shiwei Zheng & Guo-Cheng Yuan & Matt Thomson & Long Cai & Andrew P. McMahon, 2024. "Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    13. Jinxin Phaedo Chen & Constantin Diekmann & Honggui Wu & Chong Chen & Giulia Chiara & Enrico Berrino & Konstantinos L. Georgiadis & Britta A. M. Bouwman & Mohit Virdi & Luuk Harbers & Sara Erika Bellom, 2024. "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Bohan Li & Feng Bao & Yimin Hou & Fengji Li & Hongjue Li & Yue Deng & Qionghai Dai, 2024. "Tissue characterization at an enhanced resolution across spatial omics platforms with deep generative model," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    15. Allison P. Siegenfeld & Shelby A. Roseman & Heejin Roh & Nicholas Z. Lue & Corin C. Wagen & Eric Zhou & Sarah E. Johnstone & Martin J. Aryee & Brian B. Liau, 2022. "Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    16. Surya K Ghosh & Daniel Jost, 2018. "How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-26, May.
    17. Markus Götz & Olivier Messina & Sergio Espinola & Jean-Bernard Fiche & Marcelo Nollmann, 2022. "Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    18. Mattia Conte & Ehsan Irani & Andrea M. Chiariello & Alex Abraham & Simona Bianco & Andrea Esposito & Mario Nicodemi, 2022. "Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    19. Milad Mokhtaridoost & Jordan J. Chalmers & Marzieh Soleimanpoor & Brandon J. McMurray & Daniella F. Lato & Son C. Nguyen & Viktoria Musienko & Joshua O. Nash & Sergio Espeso-Gil & Sameen Ahmed & Kate , 2024. "Inter-chromosomal contacts demarcate genome topology along a spatial gradient," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    20. Khalil Joron & Juliane Oliveira Viegas & Liam Haas-Neill & Sariel Bier & Paz Drori & Shani Dvir & Patrick Siang Lin Lim & Sarah Rauscher & Eran Meshorer & Eitan Lerner, 2023. "Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34183-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.