DataVXAdvanced SciencePaper
journal article·2022-10Open access

D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions

Yizhuo Che, Xiaofei Yang, Peng Jia, Tingjie Wang, Dan Xu, Tianxue Guo, Kai Ye

Advanced Science· Volume 9· Issue 30
Publisher pageOpen full text
Source abstract

Abstract

Abstract The execution of biological activities inside space‐limited cell nuclei requires sophisticated organization. Current studies on the 3D genome focus on chromatin interactions and local structures, e.g., topologically associating domains (TADs). In this study, two global physical properties: DNA density and distance to nuclear periphery (DisTP), are introduced and a 2D matrix, D2 plot, is constructed for mapping genetic and epigenetic markers. Distinct patterns of functional markers on the D2 plot, indicating its ability to compartmentalize functional genome regions, are observed. Furthermore, enrichments of transcription‐related markers are concatenated into a cross‐species transcriptional activation model, where the nucleus is divided into four areas: active, intermediate, repress and histone, and repress and repeat. Based on the trajectories of the genomic regions on D2 plot, the constantly active and newly activated genes are successfully identified during olfactory sensory neuron maturation. The analysis reveals that the D2 plot effectively categorizes functional regions and provides a universal and transcription‐related measurement for the 3D genome.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Genomics and Chromatin Dynamics · Plant Molecular Biology Research · Gene expression and cancer classification

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

School of Automation Science and Engineering Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 China

MOE Key Lab for Intelligent Networks and Networks Security Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 China

School of Computer Science and Technology Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 China

Key Laboratory of Biomedical Information Engineering of the Ministry of Education School of Life Sciences and Technology Xi'an Jiaotong University Xi'an Shaanxi 710049 China

School of Life Science and Technology Xi'an Jiaotong University Xi'an Shaanxi 710049 China

Faculty of Science Leiden University Leiden 2300 The Netherlands

Genome Institute The First Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi 710049 China

Funding

National Natural Science Foundation of China · Fundamental Research Funds for the Central Universities

References (39)

Show source-provided references
1. 10.1038/nrg.2016.11210.1038/nrg.2016.112 ↗
2. 10.1016/j.cell.2014.11.02110.1016/j.cell.2014.11.021 ↗
3. 10.1186/s13059-016-1003-310.1186/s13059-016-1003-3 ↗
4. 10.1093/nar/gkaa15910.1093/nar/gkaa159 ↗
5. 10.3389/fbinf.2021.74221610.3389/fbinf.2021.742216 ↗
6. 10.1038/nrg200810.1038/nrg2008 ↗
7. 10.1016/j.ceb.2016.02.01410.1016/j.ceb.2016.02.014 ↗
8. 10.1016/j.cell.2018.05.02410.1016/j.cell.2018.05.024 ↗
9. 10.1016/j.cell.2017.04.02210.1016/j.cell.2017.04.022 ↗
10. 10.1038/s41594-019-0205-210.1038/s41594-019-0205-2 ↗
11. 10.1038/s41587-020-0519-y10.1038/s41587-020-0519-y ↗
12. 10.1186/s13059-016-1146-210.1186/s13059-016-1146-2 ↗
13. 10.1016/j.molcel.2010.03.01610.1016/j.molcel.2010.03.016 ↗
14. 10.1101/gr.159400.11310.1101/gr.159400.113 ↗
15. 10.1126/science.aat564110.1126/science.aat5641 ↗
16. 10.1038/nature2142910.1038/nature21429 ↗
17. 10.1016/j.cell.2009.01.05210.1016/j.cell.2009.01.052 ↗
18. 10.1007/s00412-012-0389-210.1007/s00412-012-0389-2 ↗
19. 10.1093/abbs/gmaa13710.1093/abbs/gmaa137 ↗
20. 10.1016/j.cell.2019.01.02010.1016/j.cell.2019.01.020 ↗
21. 10.1038/s41580-019-0132-410.1038/s41580-019-0132-4 ↗
22. 10.1038/s41576-020-00303-x10.1038/s41576-020-00303-x ↗
23. 10.1038/cr.2011.2210.1038/cr.2011.22 ↗
24. 10.1038/s41588-021-00799-x10.1038/s41588-021-00799-x ↗
25. 10.1146/annurev-cellbio-101512-12231710.1146/annurev-cellbio-101512-122317 ↗
26. 10.1083/jcb.20170708210.1083/jcb.201707082 ↗
27. 10.7554/eLife.4927810.7554/eLife.49278 ↗
28. 10.1038/s41422-020-00466-610.1038/s41422-020-00466-6 ↗
29. 10.1038/s41586-019-1910-z10.1038/s41586-019-1910-z ↗
30. 10.1038/s41422-022-00676-010.1038/s41422-022-00676-0 ↗
31. 10.1016/j.tig.2019.11.00410.1016/j.tig.2019.11.004 ↗
32. 10.1016/j.cell.2020.12.03210.1016/j.cell.2020.12.032 ↗
33. 10.1126/science.aad245610.1126/science.aad2456 ↗
34. 10.1091/mbc.e10-06-050810.1091/mbc.e10-06-0508 ↗
35. 10.1093/nar/gkaa60910.1093/nar/gkaa609 ↗
36. 10.1093/nar/gkn92310.1093/nar/gkn923 ↗
37. 10.1038/s41586-020-2093-310.1038/s41586-020-2093-3 ↗
38. 10.1038/nature0990610.1038/nature09906 ↗
39. 10.1038/s41587-019-0150-y10.1038/s41587-019-0150-y ↗