Advances in technologies for 3D genomics research

doi:10.1007/s11427-019-1704-2

Review

. 2020 Jun;63(6):811-824.

doi: 10.1007/s11427-019-1704-2. Epub 2020 May 8.

Advances in technologies for 3D genomics research

Yan Zhang^{1

2}, Guoliang Li^{3

4}

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
² Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
³ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. guoliang.li@mail.hzau.edu.cn.
⁴ Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China. guoliang.li@mail.hzau.edu.cn.

PMID: 32394244
DOI: 10.1007/s11427-019-1704-2

Review

Advances in technologies for 3D genomics research

Yan Zhang et al. Sci China Life Sci. 2020 Jun.

. 2020 Jun;63(6):811-824.

doi: 10.1007/s11427-019-1704-2. Epub 2020 May 8.

Authors

Yan Zhang^{1

2}, Guoliang Li^{3

4}

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
² Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
³ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. guoliang.li@mail.hzau.edu.cn.
⁴ Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China. guoliang.li@mail.hzau.edu.cn.

PMID: 32394244
DOI: 10.1007/s11427-019-1704-2

Abstract

The spatial structure of the orderly organized chromatin in the nucleus has important roles in maintaining normal cell function and in regulation of gene expression, and the high-throughput Hi-C and ChIA-PET methods have been widely used in various biological studies for determining potential spatial genome structures and their functions. However, there are still great difficulties and challenges in three-dimensional (3D) genomics research. More efficient, economical, and unbiased approaches to studying 3D genomics need to be developed for more widespread and easier applications. Here, we review the most recent studies on new 3D genomics research technologies, such as improvements of the traditional Hi-C and ChIA-PET methods, new approaches based on non-proximal-ligation strategies, and imaging-based methods improved in recent years. Especially, we review the CRISPR-based methods for functional validations in 3D genomics, which could be the forthcoming directions. We hope this review can show some insights into the potential improvements for future 3D genomics.

Keywords: 3D genomics; CRISPR; ChIA-PET; FISH; Hi-C.

PubMed Disclaimer

Cited by

Molecular mechanisms of adaptive evolution in wild animals and plants.
Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Hu Y, et al. Sci China Life Sci. 2023 Mar;66(3):453-495. doi: 10.1007/s11427-022-2233-x. Epub 2023 Jan 13. Sci China Life Sci. 2023. PMID: 36648611 Free PMC article. Review.
The Genetics and Epigenetics of Ventricular Arrhythmias in Patients Without Structural Heart Disease.
Wang M, Tu X. Wang M, et al. Front Cardiovasc Med. 2022 Jun 15;9:891399. doi: 10.3389/fcvm.2022.891399. eCollection 2022. Front Cardiovasc Med. 2022. PMID: 35783865 Free PMC article. Review.
Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum.
Li CX, Liu L, Zhang T, Luo XM, Feng JX, Zhao S. Li CX, et al. Microbiol Spectr. 2022 Jun 29;10(3):e0212121. doi: 10.1128/spectrum.02121-21. Epub 2022 May 2. Microbiol Spectr. 2022. PMID: 35499317 Free PMC article.
Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure.
Bylino OV, Ibragimov AN, Pravednikova AE, Shidlovskii YV. Bylino OV, et al. Front Genet. 2021 Sep 20;12:733937. doi: 10.3389/fgene.2021.733937. eCollection 2021. Front Genet. 2021. PMID: 34616432 Free PMC article.
Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.
Gong H, Yang Y, Zhang S, Li M, Zhang X. Gong H, et al. Comput Struct Biotechnol J. 2021 Apr 8;19:2070-2083. doi: 10.1016/j.csbj.2021.04.016. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 33995903 Free PMC article. Review.

See all "Cited by" articles

References

1. Abbas, A., He, X., Niu, J., Zhou, B., Zhu, G., Ma, T., Song, J., Gao, J., Zhang, M.Q., and Zeng, J. (2019). Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Nat Commun 10, 2049. - PubMed - PMC - DOI
1. Barutcu, A.R., Lajoie, B.R., McCord, R.P., Tye, C.E., Hong, D., Messier, T. L., Browne, G., van Wijnen, A.J., Lian, J.B., Stein, J.L., et al. (2015). Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol 16, 214. - PubMed - PMC - DOI
1. Beagrie, R.A., Scialdone, A., Schueler, M., Kraemer, D.C.A., Chotalia, M., Xie, S.Q., Barbieri, M., de Santiago, I., Lavitas, L.M., Branco, M.R., et al. (2017). Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524. - PubMed - PMC - DOI
1. Bintu, B., Mateo, L.J., Su, J.H., Sinnott-Armstrong, N.A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A.N., and Zhuang, X. (2018). Superresolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783. - PubMed - PMC - DOI
1. Bonev, B., and Cavalli, G. (2016). Erratum: Organization and function of the 3D genome. Nat Rev Genet 17, 772. - PubMed - DOI

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions

LinkOut - more resources

Full Text Sources
- Springer

[1] Abbas, A., He, X., Niu, J., Zhou, B., Zhu, G., Ma, T., Song, J., Gao, J., Zhang, M.Q., and Zeng, J. (2019). Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Nat Commun 10, 2049. - PubMed - PMC - DOI

[2] Abbas, A., He, X., Niu, J., Zhou, B., Zhu, G., Ma, T., Song, J., Gao, J., Zhang, M.Q., and Zeng, J. (2019). Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Nat Commun 10, 2049. - PubMed - PMC - DOI

[3] Barutcu, A.R., Lajoie, B.R., McCord, R.P., Tye, C.E., Hong, D., Messier, T. L., Browne, G., van Wijnen, A.J., Lian, J.B., Stein, J.L., et al. (2015). Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol 16, 214. - PubMed - PMC - DOI

[4] Barutcu, A.R., Lajoie, B.R., McCord, R.P., Tye, C.E., Hong, D., Messier, T. L., Browne, G., van Wijnen, A.J., Lian, J.B., Stein, J.L., et al. (2015). Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol 16, 214. - PubMed - PMC - DOI

[5] Beagrie, R.A., Scialdone, A., Schueler, M., Kraemer, D.C.A., Chotalia, M., Xie, S.Q., Barbieri, M., de Santiago, I., Lavitas, L.M., Branco, M.R., et al. (2017). Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524. - PubMed - PMC - DOI

[6] Beagrie, R.A., Scialdone, A., Schueler, M., Kraemer, D.C.A., Chotalia, M., Xie, S.Q., Barbieri, M., de Santiago, I., Lavitas, L.M., Branco, M.R., et al. (2017). Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524. - PubMed - PMC - DOI

[7] Bintu, B., Mateo, L.J., Su, J.H., Sinnott-Armstrong, N.A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A.N., and Zhuang, X. (2018). Superresolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783. - PubMed - PMC - DOI

[8] Bintu, B., Mateo, L.J., Su, J.H., Sinnott-Armstrong, N.A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A.N., and Zhuang, X. (2018). Superresolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783. - PubMed - PMC - DOI

[9] Bonev, B., and Cavalli, G. (2016). Erratum: Organization and function of the 3D genome. Nat Rev Genet 17, 772. - PubMed - DOI

[10] Bonev, B., and Cavalli, G. (2016). Erratum: Organization and function of the 3D genome. Nat Rev Genet 17, 772. - PubMed - DOI

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Advances in technologies for 3D genomics research

Affiliations

Advances in technologies for 3D genomics research

Authors

Affiliations

Abstract

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources