Alu expression in human cell lines and their retrotranspositional potential

Table 2 Alu subfamily distribution of Alu elements bound by RNA polymerase III factors

Alu	% Total	# of disease	% Alu	% Alu loci	Pol III	# Pol III
subfamily^a	full Alus (530,850)	cases due to ade novo insertion	transcripts^d	bound by pol III	bound Alu enrichment	bound Alu with ERP
		(%)^c		factors^e		≥0.10
S + J	84.5	0 (0)	66	88.4	1.0	2
Y	15.5	13 (23)	33	9.8	0.6	0
Ya5	0.63	24 (44)	0.8	1.2	2.0	0
Yb8	0.42	18 (33)	0.5	0.6	1.5	1

^aIncludes all subfamily variants: for example, AluYa5, AluYa5a2, AluYa8 are classified as Ya5; ^bnumber of Alu elements meeting full length criteria (Details in supplemental data); ^csubfamily distribution of the 55 de novo Alu elements reported to cause a disease [2, 15]; ^danalysis was performed on transcripts isolated from the Ntera2 (teratocarcinoma) cell line [11]; ^eanalyses were performed on the cumulative data obtained from studies on IMR-90 (normal untransformed Tert-immortalized lung fibroblast) [13], HeLa (cervical adenocarcinoma), Jurkat (T-cell leukemia), HEK 293 T (T antigen-transformed kidney) [12] and K562 (myelogenous leukemia) cells [14] (raw data and detailed analysis for each cell line included in Additional file 1: Table S3); ^frepresents the increase in Alu loci bound by RNA polymerase III factors relative to copy number (that is, %AluY bound/%AluY copies in the genome, detailed analysis in Additional file 1: Table S3); ^gnumber of Alu loci bound by RNA polymerase III factors with estimated retrotransposition potential (ERP) scores of ≥0.10. An ‘ideal’ Alu will have ERP score of 1.00.