Keywords: decoding modules, single-cell transcriptomics, transcriptomic analysis, DNA methylation

Latest 28 Papers

Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency

Authors: Renema, J., Luckicheva, S., Verwaerde, I., Aesaert, S., Coussens, G., De Block, J., Grones, C., Eekhout, T., De Rybel, B., Brew-Appiah, R. A. T., Bagley, C. A., Hoengenaert, L., Vandepoele, K., Pauwels, L.

Date: 2025-06-23 · Version: 1

DOI: 10.1101/2025.06.22.659756

Model Organism: Zea mays

somatic embryogenesis transcription factors Zea mays single-cell transcriptomics gene regulatory network

Constitutive expression of full-length or partial of SOC1 genes for yield enhancement in tomato

Authors: Danial, G. H., Jaikham, J., Song, G.-q.

Date: 2025-06-06 · Version: 1

DOI: 10.1101/2025.06.03.657751

Model Organism: Solanum lycopersicum

SOC1 tomato fruit yield heterologous gene expression branching transcriptomic analysis

Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana

Authors: Zhong, Z., Bailey, M., Kim, Y.-I., Pesaran-Afsharyan, N., Parker, B., Arathoon, L., Li, X., Rundle, C. A., Behrens, A., Nedialkova, D. D., Slavov, G., Hassani-Pak, K., Lilley, K. S., Theodoulou, F. L., Mott, R.

Date: 2025-03-31 · Version: 2

DOI: 10.1101/2025.01.08.631880

Model Organism: Arabidopsis thaliana

Arabidopsis thaliana codon usage gene expression DNA methylation ribosome profiling

Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

Authors: Tremblay, B. J.-M., Adeel, S. A., Saechao, M., Dong, Y., Andrianasolo, E., Steele, J. M., Traa, A., Yogadasan, N., Waduwara-Jayabahu, I., Katzenback, B. A., Hell, R., Wirtz, M., Moffatt, B. A.

Date: 2025-03-13 · Version: 1

DOI: 10.1101/2025.03.09.642221

Model Organism: General

sulfur metabolism methylthioadenosine nucleosidase methionine/S‑adenosylmethionine biosynthesis DNA methylation reproductive development

Arabidopsis REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes.

Authors: Wu, Z., Xue, Y., Wang, S., Shih, Y.-H., Zhong, Z., Feng, S., Draper, J., Lu, A., Sha, J., Li, L., Wohlschlegel, J., Wu, K., Jacobsen, S. E.

Date: 2025-02-23 · Version: 1

DOI: 10.1101/2025.02.21.639493

Model Organism: Arabidopsis thaliana

DNA methylation 24‑nt siRNA REM transcription factors RNA polymerase IV Arabidopsis

Transcription factors instruct DNA methylation patterns in plant reproductive tissues

Authors: Xu, G., Chen, Y., Wang, F., Li, E., Law, J.

Date: 2025-02-23 · Version: 1

DOI: 10.1101/2025.02.21.639562

Model Organism: Arabidopsis thaliana

DNA methylation RNA‑directed DNA methylation (RdDM)REPRODUCTIVE MERISTEM transcription factors sex‑specific epigenetic regulation Arabidopsis thaliana

The dynamics of ACR and DNA methylation impact asymmetric subgenome dominance in allotriploid Brassica species

Authors: dai, c., Dou, S., quan, c.

Date: 2025-02-20 · Version: 1

DOI: 10.1101/2025.02.16.638486

Model Organism: Brassica napus

polyploidy subgenome dominance accessible chromatin regions DNA methylation Brassica allotriploids

Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with different susceptibilities to Ralstonia solanacearum

Authors: Franco Ortega, S., James, S. R., Gilbert, L., Hogg, K., Stevens, H., Daff, J., Friman, V. P., Harper, A. L.

Date: 2025-02-17 · Version: 1

DOI: 10.1101/2025.02.12.637948

Model Organism: Solanum dulcamara

Ralstonia solanacearum resistance Solanum dulcamara genome pattern recognition receptors auxin transport genes DNA methylation

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