Epigenetic gene regulation
From Purdue Genomics Database Facility
T. Kurata, C. Cheng, M. Obara, Y. Oguri, T. Nishiyama
tekurata@nibb.ac.jp, tomoakin@kenroku.kanazawa-u.ac.jp
The establishment and maintenance of epigenetic control over gene expression via chromatin and DNA modifications are critical for cell differentiation and development (Berger and Gaudin, 2003). Putative orthologues of the SET domain protein genes (ATXs and SDGs), which methylate the amino-terminal tail of histone H3 and maintain the active or repressive state of chromatin, were found in every lineage as well as in other histone modification enzyme genes, such as HDAs, HDTs, and HAG1. Land plant orthologues of each gene except HDA6 and 7 were found in every lineage, and lineage-specific expansions were observed for HDTs. DNA methylation is also associated with epigenetic modifications of chromatin (Chan et al., 2005), and land plant orthologues of DNA methyltransferase (METs, CMTs, and DRMs) and DNA glycosylase (DME1) genes were found in every lineage. All of the DNA methyltransferase genes expanded in the angiosperm lineage. Land plant orthologues of a methyl-binding domain protein gene (MBD11) was expanded in the P. patens lineage.
Chromatin assembly factors (CAFs) assemble new nucleosomes during DNA replication, and a CAF in A. thaliana is composed of three proteins (Kaya et al., 2001): NFB2/FAS1, NFB1/MUB3/FAS2, and MSI1; putative orthologues for each were found in all lineages. The nucleosome-DNA interaction is also affected by ATP-dependent chromatin remodelling factors (Varga-Weisz, 2001). Putative orthologues of the genes encoding the factors were found in all of the lineages except CHR10, CHR15/MOM, CHR37, and CHR41. Small RNAs function in genome stability, gene expression and the defence response (Bonnet et al., 2006; Brodersen and Voinnet, 2006). We found putative orthologues of DCLs, AGOs, HEN1, and RDRs involved in small RNA synthesis in all of the lineages, except for the lack of RDR6 in S. moellendorffii.
References
Berger, F., and Gaudin, V. (2003). Chromatin dynamics and Arabidopsis development. Chromosome Res. 11, 277-304.
Bonnet, E., Van de Peer, Y., and Rouze, P. (2006). The small RNA world of plants. New Phytol. 171, 451-468.
Brodersen, P., and Voinnet, O. (2006). The diversity of RNA silencing pathways in plants. Trends Genet. 22, 268-280.
Chan, S.W., Henderson, I.R., and Jacobsen, S.E. (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6, 351-360.
Kaya, H., Shibahara, K.I., Taoka, K.I., Iwabuchi, M., Stillman, B., and Araki, T. (2001). FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell 104, 131-142.
Varga-Weisz, P. (2001). ATP-dependent chromatin remodeling factors: nucleosome shufflers with many missions. Oncogene 20, 3076-3085.
Table of gene numbers
| Gene functions | Gene | Gene used as a query | The number of putative orthologs | |||
|---|---|---|---|---|---|---|
| Arabidopsis thaliana | Oryza sativa | Selaginalla moellendorffii (a) | Physcomitrella patens | |||
| Epigenetic gene regulation | ATX1/SDG27 and ATX2/SDG30 | ATX1 | 2 | 1 | 1 (3) | 3 |
| Epigenetic gene regulation | SDG3, 9, 11, 17, 19, 21 to 23, 32, and 33 | SDG3 | 12 | 12 | 6 (11) | 6 |
| Epigenetic gene regulation | HDT1 to 4 | HDT2 | 4 | 4 | 1 (2) | 3 |
| Epigenetic gene regulation | HDA6 and 7 | HDA6 | 2 | 1 | 0 | 0 |
| Epigenetic gene regulation | HDA19 | HDA19 | 1 | 3 | 1 (2) | 2 |
| Epigenetic gene regulation | HDA9 and 17 | HDA9 | 2 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | HAG1 | HAG1 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | MET1 to 4 | MET1 | 4 | 2 | 1 (2) | 1 |
| Epigenetic gene regulation | CMT1 to 3 | CMT3 | 3 | 3 | 1 (2) | 1 |
| Epigenetic gene regulation | DRM1 to 3 | DRM2 | 3 | 4 | 3 (6) | 2 |
| Epigenetic gene regulation | DME1 | DME1 | 4 | 4 | 1 (2) | 3 |
| Epigenetic gene regulation | MBD11 | MBD11 | 2 | 1 | 2 (4) | 7 |
| Epigenetic gene regulation | NFF2/NFB2/FAS1 | FAS1 | 1 | 2 | 1 (2) | 1 |
| Epigenetic gene regulation | NFB1/MUB3/FAS2 | FAS2 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | MSI2 and 3 | MSI1 | 2 | 1 | 0 | 0 |
| Epigenetic gene regulation | MSI4 | MSI4 | 2 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | MSI5 | MSI1 | 1 | 1 | 0 | 0 |
| Epigenetic gene regulation | CHR1/DDM1 | CHR1 | 1 | 2 | 1 (1) | 1 |
| Epigenetic gene regulation | CHR2 | CHR2 | 1 | 1 | 1 (1) | 2 |
| Epigenetic gene regulation | CHR3/SYD | SYD | 1 | 1 | 1 (1) | 1 |
| Epigenetic gene regulation | CHR4 | CHR4 | 1 | 1 | 1 (1) | 2 |
| Epigenetic gene regulation | CHR5 | CHR5 | 1 | 1 | 1 (1) | 2 |
| Epigenetic gene regulation | CHR6/GYM/PKL and CHR7 | CHR6 | 2 | 1 | 2 (3) | 2 |
| Epigenetic gene regulation | CHR8 | CHR8 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR9 | CHR9 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR10 | CHR10 | 1 | 1 | 0 | 1 |
| Epigenetic gene regulation | CHR11, 17 | CHR11 | 2 | 2 | 2 (4) | 2 |
| Epigenetic gene regulation | CHR12, 23 | CHR23 | 2 | 1 | 1 (1) | 1 |
| Epigenetic gene regulation | CHR13 | CHR13 | 1 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | CHR14 | CHR14 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR15/MOM | CHR15 | 1 | 1 | 1 (2) | 0 |
| Epigenetic gene regulation | CHR18 | CHR18 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR24 | CHR24 | 1 | 1 | 2 (4) | 2 |
| Epigenetic gene regulation | CHR25 | CHR25 | 1 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | CHR37 and 41 | CHR37 | 2 | 1 | 1 (2) | 0 |
| Epigenetic gene regulation | AtSWI3A and B | AtSWI3B | 2 | 2 | 1 (2) | 1 |
| Epigenetic gene regulation | AtSWI3C and D | AtSWI3C | 2 | 4 | 1 (2) | 3 |
| Epigenetic gene regulation | HIRA1 | HIRA1 | 1 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | RHL2 | RHL2 | 1 | 1 | 1 (2) | 1 |
| RISC complex | DCL1 | DCL4 | 1 | 1 | 1 (1) | 1 |
| RISC complex | DCL2 and 4 | DCL4 | 2 | 3 | 1 (2) | 1 |
| RISC complex | DCL3 | DCL4 | 1 | 2 | 2 (2) | 1 |
| RISC complex | AGO1 | AGO1 | 2 | 5 | 3(5) | 3 |
| RISC complex | AGO2, 3, and 7 | AGO7 | 3 | 3 | 1 (2) | 1 |
| RISC complex | AGO4, 6, 8, and 9 | AGO6 | 4 | 3 | 1 (2) | 3 |
| RISC complex | HEN1 | HEN1 | 2 | 1 | 1 (2) | 1 |
| RISC complex | RDR1 and 2 | RDR6 | 2 | 1 | 2 (4) | 1 |
| RISC complex | RDR3 to 5 | RDR4 | 3 | 2 | 1 (2) | 2 |
| RISC complex | RDR6 | RDR6 | 1 | 1 | 0 | 1 |
| RISC complex | HEN4 2) | HEN4 | 9 | 6 | 2 (3) | 1 |
