Bell, O., Tiwari, V.K., Thoma, N.H., Schubeler, D., 2011.Determinants and dynamics of genome accessibility.Nat. Rev. Genet.12(8), 554-564
|
Boyle, A.P., Davis, S., Shulha, H.P., Meltzer, P., Margulies, E.H., Weng, Z., Furey, T.S., Crawford, G.E., 2008.High-resolution mapping and characterization of open chromatin across the genome.Cell132(2), 311-322
|
Buenrostro, J.D., Wu, B., Chang, H.Y., Greenleaf, W.J., 2015.ATAC-seq: amethod for assaying chromatin accessibility genome-wide. Curr.Protoc.Mol. Biol.109, 21.29.21-21.29.29
|
Concia, L., Veluchamy, A., Ramirez-Prado, J.S., Martin-Ramirez, A., Huang, Y., Perez, M., Domenichini, S., Rodriguez Granados, N.Y., Kim, S., Blein, T., Duncan, S., Pichot, C., Manza-Mianza, D., Juery, C., Paux, E., Moore, G., Hirt, H., Bergounioux, C., Crespi, M., Mahfouz, M.M., Bendahmane, A., Liu, C., Hall, A., Raynaud, C., Latrasse, D., Benhamed, M., 2020. Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol. 21(1), 104
|
Giresi, P.G., Kim, J., McDaniell, R.M., Iyer, V.R., Lieb, J.D., 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17(6), 877-885
|
Kelly, T.K., Liu, Y., Lay, F.D., Liang, G., Berman, B.P., Jones, P.A., 2012. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.Genome Res. 22(12), 2497-2506
|
Klemm, S.L., Shipony, Z., Greenleaf, W.J., 2019.Chromatin accessibility and the regulatory epigenome.Nat. Rev. Genet.20(4), 207-220
|
Li, B., Carey, M., Workman, J.L., 2007.The role of chromatin during transcription.Cell128(4), 707-719
|
Liang, Z., Shen, L., Cui, X., Bao, S., Geng, Y., Yu, G., Liang, F., Xie, S., Lu, T., Gu, X., Yu, H., 2018. DNA N6-adenine methylation in Arabidopsis thaliana. Dev. Cell45(3), 406-416 e403
|
Liang, Z., Zhang, Q., Ji, C., Hu, G., Zhang, P., Wang, Y., Yang, L., Gu, X., 2021. Reorganization of the 3D chromatin architecture of rice genomes during heat stress.BMC Biol. 19(1), 53
|
Qiu, T., Shi, X., Wang, J., Li, Y., Qu, S., Cheng, Q., Cui, T., Sui, S., 2019. Deep learning: a rapid and efficient route to automatic metasurfacedesign. Adv. Sci.6(12), 1900128
|
Schones, D.E., Cui, K., Cuddapah, S., Roh, T.Y., Barski, A., Wang, Z., Wei, G., Zhao, K., 2008.Dynamic regulation of nucleosome positioning in the human genome.Cell132(5), 887-898
|
Shen, Y., Chen, L.L., Gao, J., 2021. CharPlant: ade novo open chromatin region prediction tool for plant genomes. Genom. Proteomics Bioinf
|
Thurman, R.E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M.T., Haugen, E., Sheffield, N.C., Stergachis, A.B., Wang, H., Vernot, B., Garg, K., John, S., Sandstrom, R., Bates, D., Boatman, L., Canfield, T.K., Diegel, M., Dunn, D., Ebersol, A.K., Frum, T., Giste, E., Johnson, A.K., Johnson, E.M., Kutyavin, T., Lajoie, B., Lee, B.K., Lee, K., London, D., Lotakis, D., Neph, S., Neri, F., Nguyen, E.D., Qu, H., Reynolds, A.P., Roach, V., Safi, A., Sanchez, M.E., Sanyal, A., Shafer, A., Simon, J.M., Song, L., Vong, S., Weaver, M., Yan, Y., Zhang, Z., Zhang, Z., Lenhard, B., Tewari, M., Dorschner, M.O., Hansen, R.S., Navas, P.A., Stamatoyannopoulos, G., Iyer, V.R., Lieb, J.D., Sunyaev, S.R., Akey, J.M., Sabo, P.J., Kaul, R., Furey, T.S., Dekker, J., Crawford, G.E., Stamatoyannopoulos, J.A., 2012. The accessible chromatin landscape of the human genome.Nature489(7414), 75-82
|
Tsompana, M., Buck, M.J., 2014.Chromatin accessibility: a window into the genome. Epigenet. Chromatin7, 33
|
Wang, Y., Zhang, P., Guo, W., Liu, H., Li, X., Zhang, Q., Du, Z., Hu, G., Han, X., Pu, L., Tian, J., Gu, X., 2021. A deep learning approach to automate whole-genome prediction of diverse epigenomic modifications in plants.New Phytol.232(2), 880-897
|
Zhang, Q., Liang, Z., Cui, X., Ji, C., Li, Y., Zhang, P., Liu, J., Riaz, A., Yao, P., Liu, M., Wang, Y., Lu, T., Yu, H., Yang, D., Zheng, H., Gu, X., 2018. N6-Methyladenine DNA methylation in japonica and indicarice genomes and its association with gene expression, plant development, and stress responses. Mol. Plant11(12), 1492-1508
|
Zhou, C., Wang, C., Liu, H., Zhou, Q., Liu, Q., Guo, Y., Peng, T., Song, J., Zhang, J., Chen, L., Zhao, Y., Zeng, Z., Zhou, D.X., 2018. Identification and analysis of adenine N6-methylation sites in the rice genome. Native Plants4(8), 554-563
|