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Table 1 DNA methylation alterations of TEs and protein-encoding genes in the S0 generation of etoposide-treated plants relative to the controls, detected by methylation-sensitive gel-blotting in various rice genotypes

From: Changes in DNA methylation and transgenerational mobilization of a transposable element (mPing) by the Topoisomerase II inhibitor, Etoposide, in rice

Probe GenBank Accession No.a DNA methylation changes in Etoposide-treated rice plants (S0)
Nipponbare 93-11 Matsumae RZ1 RZ2 RZ35
10 mg/L
(H/M)b
20 mg/L
(H/M)
10 mg/L
(H/M)
20 mg/L
(H/M)
10 mg/L
(H/M)
20 mg/L
(H/M)
10 mg/L
(H/M)
20 mg/L
(H/M)
10 mg/L
(H/M)
20 mg/L
(H/M)
10 mg/L
(H/M)
20 mg/L
(H/M)
Transposable elements (TEs)             
Tos17 AC087545 n/- n/- n/n n/n n/n n/n n/n n/n n/- n/n n/- n/n
Osr2 AL442110 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
Osr23 AP002843 n/+ n/+ n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
Osr35 AC068924 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
Osr36 AP001551 n/- n/- n/n n/n n/n n/n n/+ n/+ n/n n/n n/n n/n
Ping-specific AB087616 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
Pong-specific BK000586 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
mPing AP005628 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
Protein-encoding genes             
Homeobox gene AB007627 n/- n/- n/n n/n n/n n/n n/- n/n n/n n/n n/n n/n
Binding X88798 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
CAL-2 AK069341 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
CAL-11 X81393 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
Elongation factor D12821 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
OsCDPK protein AY144497 n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n n/n
CDPK-related protein kinase AP004380 n/n n/n n/n n/n n/n n/n +/+ +/+ n/n n/n n/n n/n
Variation frequency(%)c 26.67 26.67 0 0 0 0 20 13.33 6.67 0 6.67 0
  1. a Determined by BlastN at NCBI.
  2. b Digestions by HpaII (H) and MspI (M) were separated by a slash “/”; n: no change in cytosine methylation; +: increase in cytosine methylation; -: decrease in cytosine methylation; HpaII is related to the methylation alteration at CG sites, MspI is related to the methylation alteration at CHG sites.
  3. c Defined as the number of probes showing alterations/the total number of analyzed probes.