Table 3 Potential functions in the 290 transcripts presenting extensively high methylation in all of the three organs of leaves, flowers and roots in Arabidopsis

Transporter

AT1G23900, AT1G06470, AT1G60070, AT1G79610, AT2G07671, AT2G07687, AT2G07698, AT2G07741, AT2G41700, AT3G08650, AT3G08960, AT3G17430, AT3G20560, AT3G20920, AT3G46830, AT4G00630, AT4G00800, AT4G38920, AT4G39850, AT5G27970, AT5G36940, AT5G53530, AT5G01990, AT3G55320, AT4G13750, AT1G16820, AT1G77140, AT5G05570, AT5G07770, AT2G21340, AT2G27460, AT1G74720, AT1G47550, AT5G66380, AT5G47490, AT5G08470, AT3G03720, AT5G61310, AT5G62600, AT5G11980, AT1G56290, AT2G20840, AT2G15240, AT4G39420, AT5G07980,

[15–21]

Defense or stress response

AT1G63770, AT1G64790, AT1G67090, AT1G80030, AT2G05580, AT2G27380, AT2G35510, AT2G42560, AT3G20290, AT3G22640, AT3G49600, AT4G01210, AT4G04920, AT4G08230, AT4G25520, AT4G33650, AT5G10450, AT5G11530, AT5G14030, AT5G14790, AT5G34850, AT5G35620, AT5G43460, AT5G63110, AT3G46920, AT1G10522, AT2G46240, AT1G58220, AT1G57870, AT1G01260, AT1G67890, AT4G31390, AT3G54610, AT1G74720, AT1G80010, AT1G31835, AT1G50730, AT4G05631

[18, 22–33]

Redox process

AT1G50430, AT1G67140, AT1G76150, AT2G27110, AT1G80560, AT2G07687, AT2G07727, AT2G38020, AT3G20560, AT2G48060, AT4G08280, AT4G23420, AT4G39850, AT5G42790, AT5G65750, AT4G01860, AT3G08950, AT3G01380, AT4G36080, AT2G43420, AT4G16310, AT5G21060, AT1G56000, AT4G17150, AT5G08470, AT4G16070, AT4G30993, AT3G20560

[18, 34–36]

Signal transduction

AT1G03060, AT1G43130, AT1G48090, AT1G51690, AT1G58250, AT3G46830, AT3G49600, AT4G38200, AT5G06260, AT5G28900, AT5G35180, AT5G49470, AT5G39760, AT2G15240, AT3G55850, AT1G13180, AT1G10522, AT1G67890, AT5G07770, AT5G06350, AT4G02970, AT1G58230, AT2G46700, AT3G18040, AT5G07770, AT1G74720

[19, 28, 33, 37–39]

Nucleic acid binding, DNA repair, DNA/RNA synthesis

AT1G02990, AT1G08840, AT1G12930, AT1G50840, AT2G20000, AT2G32000, AT1G17580, AT3G54280, AT1G20920, AT1G58060, AT2G19520, AT3G23780, AT3G48190, AT3G61240, AT4G09680, AT4G25880, AT5G05560, AT5G16630, AT5G22010, AT2G03070, AT3G23780, AT3G53500, AT1G07705, AT4G00060, AT4G16280, AT4G32200, AT1G33390, AT3G54460

[18, 40–43]

Regulation of transcription

AT1G07470, AT2G20330, AT2G35110, AT3G53500, AT4G04920, AT5G42770, AT5G49470, AT5G63260, AT1G07705, AT1G53541, AT5G39760, AT1G17450, AT1G10522, AT5G13240, AT1G58220, AT1G01260, AT5G08230, AT2G48110, AT1G33390, AT5G08550, AT2G36960, AT3G61740, AT3G10070, AT5G49430

[18, 30, 44]

DNA methylaytion, demethylation, and gene silencing

AT1G08060, AT1G54490, AT2G06210, AT3G01460, AT4G16280, AT3G07610, AT5G05570

[18, 45, 46]

Cell proliferation, circadian rhythm, or differentiation

AT1G17110, AT1G17580, AT1G22620, AT1G22770, AT1G67490, AT2G25730, AT2G26890, AT2G35110, AT3G07160, AT3G49600, AT5G06265, AT5G11030, AT5G12980, AT5G24740, AT5G40740, AT5G42770, AT5G51290, AT2G19390, AT1G55540, AT3G15120, AT5G10340, AT5G48120, AT1G77460, AT4G13750, AT3G27670, AT4G32200, AT4G04970, AT3G19630, AT4G18600, AT1G11060, AT4G02070, AT1G67140

[18, 21, 40, 47–51]

Protein phosphorylation or histone acetylation

AT1G13320, AT1G16710, AT1G49340, AT5G04510, AT5G18525, AT5G49470, AT3G46920, AT1G31860, AT1G57870, AT4G31390, AT2G46700, AT3G18040

[18, 52, 53]

Protein post translational process, for example, folding, ubiquitination

AT1G62330, AT3G06440, AT3G18520, AT3G56120, AT3G59410, AT4G33650, AT5G05920, AT5G06260, AT5G11530, AT5G51660, AT5G63110, AT1G79940, AT1G80030, AT1G73950, AT3G60350, AT5G07910, AT3G54610, AT1G80010, AT3G46220, AT3G20560, AT1G56290

[18, 54, 55]

RNA post-transcriptional processing

AT1G24050, AT1G24706, AT1G31870, AT1G32500, AT1G64572, AT3G11540, AT1G35470, AT1G73720, AT3G11960, AT3G19670,

[18, 56–59]

AT3G47890, AT3G53500, AT3G53500, AT5G51660, AT3G56825, AT3G57570, AT3G19515, AT3G19630, AT3G13290, AT5G10370, AT4G02970, AT5G62600, AT3G55220, AT3G10070

Proteolysis or protein synthesis

AT1G67120, AT1G67550, AT2G40930, AT4G26510, AT5G35620, AT5G58200, AT5G23110, AT1G28350, AT5G49030, AT5G27700, AT3G47060, AT2G07715, AT2G24640, AT2G25740

[18]

Protein located in mitochondria or chloroplast

AT1G09980, AT1G58350, AT1G68160, AT2G01008, AT2G07671, AT2G07708, AT2G07687, AT2G07727, AT2G11910, AT2G31141, AT2G33980, AT2G35750, AT2G07698, AT3G12590, AT3G41762, AT3G50380, AT4G00585, AT4G02770, AT4G31350, AT4G38120, AT4G39690, AT5G08060, AT5G15320, AT5G15750, AT5G26850, AT5G59613, AT1G07705, AT3G58010, AT3G63052, AT1G30910, AT3G08950, AT3G47060, AT2G07715, AT1G10522, AT3G06310, AT1G31860, AT5G53740, AT1G49700, AT4G31390, AT2G21340, AT3G43540, AT2G25660, AT5G66380, AT1G45332, AT5G61310, AT5G15700, AT3G18040, AT3G56120, AT4G01210, AT4G00630, AT4G13730, AT4G38920, AT5G53530, AT1G63770

[17, 18, 28, 29, 60–63]

Transposable element gene

AT3G28945, AT4G06477, AT4G08114, AT4G08115, AT5G35935, AT3G42806, AT4G16870, AT4G08112

Pseudogenes

AT2G07709, AT2G07711,AT2G07717, AT2G07733, AT2G07811, AT2G07747, AT2G35743

sn (o) RNA or other ncRNA

AT1G15405, AT1G08115, AT3G56705, AT5G09585, AT5G61455,

AT3G55485, AT2G01020, AT1G16635, AT2G01010, AT2G43375, AT3G56825, AT2G46192, AT5G06165, AT1G61275, AT4G39363, AT3G41979, AT1G12013

RNA post-transcriptional processing

AT1G24050, AT1G24706, AT1G31870, AT1G32500, AT1G64572, AT3G11540, AT1G35470, AT1G73720, AT3G11960, AT3G19670,

[18, 56–59]

AT3G47890, AT3G53500, AT3G53500, AT5G51660, AT3G56825, AT3G57570, AT3G19515, AT3G19630, AT3G13290, AT5G10370, AT4G02970, AT5G62600, AT3G55220, AT3G10070