Fig. 2

Genomic, transcriptomic and functional projections of the HERV prototype repertoire. a HERV structure distribution. The 42 HERV groups corresponding to the “HERV_prototypes” repertoire are voluntarily depicted as 100% of the HERV-V3 chip. Solo LTR, 5’ LTR, 3’ LTR and proviral genes account for 100% of the HERV chip in the proportion described in Additional file 2: Table S1b. The transcriptome pie-chart is obtained from results detailed in Additional file 2: Table S1c. b LTR features. The descriptive table summarises the assignment of features. ^a,b,c,d Loss of information from HERV database to understandable functions. ^a Summary of Additional file 2: Table S1a, ^b Summary of Additional file 2: Table S1b, ^c Enumeration of LTRs whose function is attributable, i.e. defined as LTRs combining U3 and U5 adjacent structures on the genome and existing probesets onto the chip allowing discrimination between U3 and U5 expression signals, ^d Enumeration of LTRs whose function is attributed using both a 2^4.5 positive threshold and a fold change of 3 between U3 and U5 regions. More specifically, to retain sensitivity and robustness with regard to function assignation, we voluntarily selected a lower expression level cut-off of 2^4.5 for positive signal attribution. As such, the LTR was referred to as promoter (Pr), polyadenylation signal (pA), readthrough (RdT) or Silent. All other remaining LTRs were classified as undetermined. c Specialisation of LTR features. Number of LTRs from the “HERV_prototypes” repertoire according to all the combinations of functions observed in each of the 45 PBMC samples. Silent LTR, Pr: LTR referred to as a promoter, pA: LTR referred to as a polyadenylation signal, RdT: read-through. The combinations obtained could either contain one (e.g. Pr), two (e.g. Silent/Pr), three (e/g. Silent/pA/Pr), or four functions (Silent/pA/Pr/RdT). 987 LTRs were excluded from the analysis as classified at least once as undetermined