How to Cite

Zhang, T., Marand, A., Jiang, J.M. (2015) PlantDHS: a database for DNase I hypersensitive sites in plants. Nucleic Acids Res. 44: D1148-D1153


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Nucleosome positioning and histone modification

Data Source

Arabidopsis tissues: 14 day old seedlings (leaf) and 14 day old closed buds (flower) for DNase-seq data and RNA-seq data:

Zhang, W.L., Zhang, T., Wu, Y.F., and Jiang, J.M. (2012) Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24: 2719-2731.

Rice tissues: 14 day old seedlings (leaf) and 14 day old callus  for DNase-seq data and RNA-seq data. Rice histone modification data:

Zhang, W.L., Wu, Y.F., Schnable, J.C., Zeng, Z.X., Freeling, M., Crawford, G.E., and Jiang, J.M. (2012) High-resolution mapping of open chromatin in the rice genome. Genome Res. 22: 151-162.

He, G.M., Zhu, X.P., Elling, A.A., Chen, L.B., Wang, X.F., Guo, L., Liang, M.Z., He, H., Zhang, H.Y., Chen, F.F., Qi, Y.J., Chen, R.S., and Deng, X.W. (2010). Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids. Plant Cell 22, 17-33.

Arabidopsis 14 day old seedlings (leaf) and closed buds (flower) and Rice 14 day old seedlings (leaf) nucleosome occupancy and positioning data:

Zhang, T., Zhang, W.L., and Jiang, J.M. (2015) Genome-wide nucleosome occupancy and positioning and their impact on gene expression and evolution in plants. Plant Physiol. 168: 1406-1416.

Arabidopsis histone modification data:

Bo, Z., Zhang, W.L., Zhang, T., Liu, B., Jiang, J.M. (2015) Genome-wide prediction and validation of intergenic enhancers in Arabidopsis thaliana using open chromatin signature. Plant Cell 27: 2415-2426

Arabidopsis transcription factor binding site data:

Heyndrickx, K.S., Van de Velde, J., Wang, C., Weigel, D., and Vandepoele, K. (2014). A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell 26, 3894-3910.


Version 0.3.2

Release Date: 2016/02/22 add ChIP-seq Bigwig files in Download page.

Version 0.3.1

Release Date: 2015/10/22 add Bigwig and nucleosome gff files in Download page.

Version 0.3

Release Date: 2015/09/15 add histone modification ChIP-seq data track in Jbrowse.

Version 0.2

Release Date: 2015/07/08 add Nucleosome positioning/occupancy data track in Jbrowse

Version 0.1

Release Date: 2015/06/02 data update

Version 0.01

Release Date: 2015/05/22