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JoVE Journal Genetics
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Genetics

Published: March 17, 2023 doi: 10.3791/64817
Automatic Translation
*1, *2, 1, 2, 2, 1
1Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 2KAUST Environmental Epigenetics Program (KEEP), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
* These authors contributed equally

Materials

Name Company Catalog Number Comments
1 kb Plus DNA Ladder Invitrogen 10787018
100% Ethanol
15 mL falcon tubes
16% Formaldehyde Solution (w/v), Methanol-free Thermo scientific 28906
5 mL tube
5PRIME Phase Lock tubes Quantabio 2302820 Phase lock gel - light
AGANI needle 25 G Terumo AN*2516R1
Agarose
Bovine Serum Albumin Sigma-Aldrich A7030
Bowtie open source, available from https://bowtie-bio.sourceforge.net/index.shtml
Branson sonifier 250 Branson Sonicator 
Centrifuge  Eppendorf 5430 R With rotors for 15 mL and 1.5 mL tubes
ChIP-grade antibody (here polyclonal H3K4me3 antibody) Diagenode C15410003
Complete EDTA-free Protease Inhibitor Cocktail Roche 11873580001 2 tablets/mL water for 100x stock
Cover glass vwr 48393 194
Disposable Spatula vwr 80081-188
DNA purification kit (here QIAGEN QIAquick PCR purification kit) QIAGEN 28104
Dounce tissue grinder Wheaton tight pestle
Dulbecco's Phosphate Buffered Saline (DPBS) 1x gibco 14190-094
Dynabeads Protein G Thermo Fisher Scientific 10004D
EDTA Sigma-Aldrich 3609
EGTA Sigma-Aldrich 324626
Electrophoresis system
Ethidium bromide
FASTQC v0.11.9 software
Gel Doc EZ Documentation System Bio-Rad 1708270 Gel imaging system
Glycine Sigma-Aldrich 50046
Injekt-F Tuberculin syringe 1 mL B. Braun 9166017V
Linear acrylamide (5 mg/mL) Invitrogen AM9520
Low-retention 1.5 mL tube
Magnetic separation rack for 1.5 mL tubes
Microscope
Microscope slide
Model-based Analysis of ChIP-Seq (MACS) open source
Mortar and pestle, porcelain
NanoDrop 2000c spectrophotometer Thermo scientific  ND-2000C
N-lauroylsarcosine Sigma-Aldrich 61739
Nuclease-free water
Pasteur pipette
Phenol:Chloroform:Isoamyl Alcohol Mixture (25:24:1) Sigma-Aldrich 77617
Proteinase K (20 mg/mL) Ambion AM2546
Purple Loading Dye 6x New England BioLabs B7024S
Qubit 2.0 Fluorometer Invitrogen
RNase Cocktail Enzyme Mix Invitrogen AM2286 RNase A = 500 U/mL, RNase T1 = 20000 U/mL
Sodium acetate Sigma-Aldrich S2889
Sodium chloride Sigma-Aldrich S9888
Sodium deoxycholate Sigma-Aldrich 30970
SYBR Safe DNA Gel Stain Invitrogen S33102
TAE buffer
Thermomixer Eppendorf 5384000012
Tris base Sigma-Aldrich 10708976001
Triton X-100 solution Sigma-Aldrich 93443
Trypan Blue Stain (0.4%) Gibco 15250-061 Danger: may cause cancer. Suspected of damaging fertility or the unborn child
Tube rotator SB3 Stuart
UltraPure SDS Solution, 10% Invitrogen 15553027
Vacuum pump

DOWNLOAD MATERIALS LIST

References

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  2. Cziesielski, M. J., Schmidt-Roach, S., Aranda, M. The past, present, and future of coral heat stress studies. Ecology and Evolution. 9 (17), 10055-10066 (2019).
  3. Eirin-Lopez, J., Putnam, H. Marine environmental epigenetics. Annual Review of Marine Science. 11, 335-368 (2021).
  4. Rädecker, N. Using Aiptasia as a model to study metabolic interactions in cnidarian-Symbiodinium symbioses. Frontiers in Physiology. 9 (214), (2018).
  5. Baumgarten, S. The genome of Aiptasia, a sea anemone model for coral symbiosis. PNAS. 112 (38), 11893-11898 (2015).
  6. Strahl, B. D., Allis, C. D. The language of covalent histone modifications. Nature. 403 (6765), 41-45 (2000).
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  9. Schwaiger, M. An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes. Nature Ecology & Evolution. 6 (12), 1921-1939 (2022).
  10. Ozment, E., et al. Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity. Elife. 10, e74336 (2021).
  11. Baumgarten, S., et al. Evidence for miRNA-mediated modulation of the host transcriptome in cnidarian-dinoflagellate symbiosis. Molecular Ecology. 27 (2), 403-418 (2018).
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  15. Weizman, E., Levy, O. The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia. Communications Biology. 2, 282 (2019).
  16. Liew, Y. J. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Science Advances. 4 (6), eaar8028 (2018).
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  18. Liew, Y. J., et al. Identification of microRNAs in the coral Stylophora pistillata. PLoS One. 9 (3), e91101 (2014).
  19. Huang, C., et al. Identification of long non-coding RNAs in two anthozoan species and their possible implications for coral bleaching. Scientific Reports. 7, 5333 (2017).
  20. Rodriguez-Casariego, J. A., et al. Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis. Ecology and Evolution. 8 (23), 12193-12207 (2018).
  21. Bodega, B., et al. A cytosolic Ezh1 isoform modulates a PRC2-Ezh1 epigenetic adaptive response in postmitotic cells. Nature Structural & Molecular Biology. 24 (5), 444-452 (2017).
  22. Jordán-Pla, A., Visa, N. Considerations on experimental design and data analysis of chromatin immunoprecipitation experiments. Chromatin Immunoprecipitation., edited by Visa, N., Jordán-Pla, A. Visa, N., Jordán-Pla, A. , Humana Press. Totowa, NJ. 9-28 (2017).
  23. ENCODE. Ren Lab ENCODE Tissue Fixation and Sonication Protocol for MicroChIP. , Stanford University. Available from: https://www.encodeproject.org/documents/ (2023).
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  34. Marinov, G. K., Lynch, M. Diversity and divergence of dinoflagellate histone proteins. G3 Genes, Genomes, Genetics. 6 (2), 397-422 (2016).
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Cite this Article

Dix, M. F., Liu, P., Cui, G., Della… More

Dix, M. F., Liu, P., Cui, G., Della Valle, F., Orlando, V., Aranda, M. Chromatin Immunoprecipitation in the Cnidarian Model System Exaiptasia diaphana. J. Vis. Exp. (193), e64817, doi:10.3791/64817 (2023).

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