The local density of H3K9me3 dictates the stability of HP1α condensates-mediated genomic interactions

a.
School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
b.
Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
c.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China

Funds: This work was funded by the National Natural Science Foundation of China (No. 31970591 to H. Ma), the Shanghai Pujiang Program (19PJ1408000 to H. Ma) and the Shanghai Science and Technology Innovation Action Plan (21JC1404800 to H. Ma). We thank Luke Lavis (Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA) for the HaloTag JF-549. U2OS Genomic DNA was a gift from Xingxu Huang. We thank Pengwei Zhang and Shuangli Zhang for their help with cell sorting. DeltaVision Ultra microscopy was provided by the Shanghai Institute for Advanced Immunochemical Studied (SIAIS) at Shanghaitech University.

摘要

- /
- /
- /
- /
Abstract: The human genome can be demarcated into domains based on distinct epigenetic states. The trimethylation of histone H3 lysine 9 (H3K9me3) is essential for the formation of constitutive heterochromatin nanodomains. However, the extent to which genomic regions require specific densities or degrees of H3K9me3 for stable interactions remains unclear. Here we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions. We select three loci (IDR3, TCF3, and PR1) with distinct levels of H3K9me3 to examine the genomic interactions and association with endogenous HP1α condensates. Our results demonstrate a positive correlation between the levels of H3K9me3 at the loci and their association with HP1α condensates. By dual-color labeling and long-term tracking of IDR3 and PR1 loci, we find a periodical association between the two ranging from one to three hours. Epigenetic perturbation-induced Genome organization (EpiGo)-KRAB introduces ∼20 kilobases of H3K9me3 at the TCF3 locus, which is sufficient to establish a stable association between TCF3 and HP1α condensates. In addition, EpiGo-mediated H3K9me3 also leads to stable genomic interaction between IDR3 and TCF3. Briefly, these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1α condensates.
- H3K9me3 /
- HP1α /
- chromatin dynamics /
- genomic interaction /
- epigenetic perturbation

HTML全文

参考文献(28)

[1]	Beliveau, B.J., Boettiger, A.N., Nir, G., Bintu, B., Yin, P., Zhuang, X., Wu, C.T., 2017. In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT. Methods Mol Biol 1663, 231-252.
[2]	Belton, J.M., McCord, R.P., Gibcus, J.H., Naumova, N., Zhan, Y., Dekker, J., 2012. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58, 268-276.
[3]	Bernstein, B.E., Meissner, A., Lander, E.S., 2007. The mammalian epigenome. Cell 128, 669-681.
[4]	Bickmore, W.A., 2013. The spatial organization of the human genome. Annu Rev Genomics Hum Genet 14, 67-84.
[5]	de Laat, W., Duboule, D., 2013. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502, 499-506.
[6]	Dekker, J., Belmont, A.S., Guttman, M., Leshyk, V.O., Lis, J.T., Lomvardas, S., Mirny, L.A., O'Shea, C.C., Park, P.J., Ren, B., et al., 2017. The 4D nucleome project. Nature 549, 219-226.
[7]	Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., Ren, B., 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380.
[8]	Falk, M., Feodorova, Y., Naumova, N., Imakaev, M., Lajoie, B.R., Leonhardt, H., Joffe, B., Dekker, J., Fudenberg, G., Solovei, I., et al., 2019. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 570, 395-399.
[9]	Feng, Y., Wang, Y., Wang, X., He, X., Yang, C., Naseri, A., Pederson, T., Zheng, J., Zhang, S., Xiao, X., et al., 2020. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Genome Biol 21, 296.
[10]	Fortin, J.P., Hansen, K.D., 2015. Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol 16, 180.
[11]	Gibcus, J.H., Dekker, J., 2013. The hierarchy of the 3D genome. Mol Cell 49, 773-782.
[12]	Kornberg, R.D., Lorch, Y., 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294.
[13]	Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.
[14]	Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., et al., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293.
[15]	Ma, H., Tu, L.C., Naseri, A., Chung, Y.C., Grunwald, D., Zhang, S., Pederson, T., 2018. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods 15, 928-931.
[16]	Ma, H., Tu, L.C., Naseri, A., Huisman, M., Zhang, S., Grunwald, D., Pederson, T., 2016. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34, 528-530.
[17]	Mosch, K., Franz, H., Soeroes, S., Singh, P.B., Fischle, W., 2011. HP1 recruits activity-dependent neuroprotective protein to H3K9me3 marked pericentromeric heterochromatin for silencing of major satellite repeats. PLoS ONE 6, e15894.
[18]	Nuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N., Mirny, L.A., 2018. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc. Natl. Acad. Sci. U. S. A. 115, E6697-E6706.
[19]	Ramirez, F., Ryan, D.P., Gruning, B., Bhardwaj, V., Kilpert, F., Richter, A.S., Heyne, S., Dundar, F., Manke, T., 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44(W1), W160-W165.
[20]	Rao, S.S., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A.L., Machol, I., Omer, A.D., Lander, E.S., et al., 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680.
[21]	Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., Cavalli, G., 2012. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472.
[22]	Spracklin, G., Pradhan, S., 2020. Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin. Nucleic Acids Res 48, e16.
[23]	Strom, A.R., Emelyanov, A.V., Mir, M., Fyodorov, D.V., Darzacq, X., Karpen, G.H., 2017. Phase separation drives heterochromatin domain formation. Nature 547, 241-245.
[24]	Szabo, Q., Bantignies, F., Cavalli, G., 2019. Principles of genome folding into topologically associating domains. Sci Adv 5, eaaw1668.
[25]	Tarasov, A., Vilella, A.J., Cuppen, E., Nijman, I.J., Prins, P., 2015. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31, 2032-2034.
[26]	Wang, L., Gao, Y., Zheng, X., Liu, C., Dong, S., Li, R., Zhang, G., Wei, Y., Qu, H., Li, Y., et al., 2019. Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism. Mol Cell 76, 646-659.
[27]	Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., et al., 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137.
[28]	Zheng, H., Xie, W., 2019. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol 20, 535-550.