. 2009 Jun 27;16(4):195–211. doi: 10.1093/dnares/dsp011

Table 1.

Primer sets used for determination of HERV LTRs methylation

Sequence amplified	Primer sequence for HERV LTRs methylation analyzes^a			Length (bp)	Hyb. temp. (°C)
MaLR[LTR]–ERVWE1[5′LTR]	PCR1	U1	5′(-208)-AATTCATTCAACATCCATTC	1036	45
	PCR1	L1	5′(+828)-GGTttAATATTAtTtAttAtTTTGGA	1036	45
	Nested PCR	U2	5′(-177)-CTCTtaCCTTCCTATACTCTCTaaA	507	51
	Nested PCR	L2	5′(+330)-AGAGTGtAGTTGtAAGATTTAATAGAGT	507	51
ERVWE1[env-3′LTR]	PCR1	U1	5′(-232)-aCTaTAAAACTACAAATaaAaCCCA	984	50.9
	PCR1	L1	5′(+752)-TGtAtttTtATGGTTGTGTTAtTT	984	50.9
	Nested PCR	U2	5′(-222)-TACAAATaaAaCCCAAaATaCA	553	59.3
	Nested PCR	L2	5′(+331)-AGAGTGtAGTTGtAAGATTTAATAGAGT	553	59.3
HW_4[5′ LTR]	PCR1	U1	5′(-128)-CCAACATCACTAACACAACC	550	55
	PCR1	L1	5′(+422)-GGGAGTtAGtAAGGGGTtTG	550	55
	Nested PCR	U2	5′(-113)-CAACCTaTTAaACAAAaCTaAATT	428	43.9
	Nested PCR	L2	5′(+315)-AGATTTAATAGAGTGAAAAtAGAGtTt	428	43.9
HW_12[solo LTR]	PCR1	U1	5′(-13)-aCCCACATCCAATTaAaAa	810	45
	PCR1	L1	5′(+799)-GATGAATGTGTTAtAGGGGTt	810	45
	Nested PCR	U2	5′(+3)-AaAaACAaaACTAaCTaaATTTCC	313	46.2
	Nested PCR	L2	5′(+315)-AGATTTAATAGAGTGAAAAtAGAGtTt	313	46.2
ERVFRDE1[5′ LTR]	PCR1	U1	5′(-36)-CAaTTCTATCAaaAaaCCATT	677	54.7
	PCR1	L1	5′(+641)-GGGGTAGGTTAGTAAGtAGGA	677	54.7
	Nested PCR	U2	5′(-20)-CCATTAaaTTAAaCTaaTTCTaTTAa	568	50.9
	Nested PCR	L2	5′(+548)-GTtTTAttAtTAGGGAAGGTAGA	568	50.9
ERV3[5′ LTR]	PCR1	U1	5′(-25)-GTTATAtTttTATAGGtAGTGTATATG	764	53.8
	PCR1	L1	5′(+739)-aaTCATaaaAaAaCCAATCTCC	764	53.8
	Nested PCR	U2	5′(-19)-tTttTAtAGGtAGTGTATATGAGGt	644	57.8
	Nested PCR	L2	5′(+625)-TaTAaTCTCCCCTCCTaaCT	644	57.8

^aNucleotides in bold and lowercase letters represent changes in primers relative to the genomic sequence due to bisulfite treatment, as follows: t is C and a is G in the untreated sequence. The position relative to the LTR start is given in parentheses.