Supplementary Figure 1: 34-nucleotide-long potential quadruplex sequences (PQSs) used for defining the L1-originated quadruplex sequence (LQS) family.
From: G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition
(a) Distribution of the Hamming distance of all 34-nt-long PQSs referenced against the most frequent PQS from L1 retrotransposons - LQSref. The peak with [0,5] borders, highlighted in red, defines the LQS family. The consensus sequence of the LQS family is illustrated via a sequence-logo plot. (b) Hierarchical clustering of all the 34-nt-long PQSs in the chromosome 1 with the Hamming distance applied as a similarity metrics. (c) Sub-trees depicting the region encompassing the LQS family (red box on panel b) together with some selected examples. (d) Genomic localization of repeat-associated PQSs and LQSs. It is noteworthy that almost all LQS sequences are found within the 3’-UTR of L1 elements. (e) Sequence composition of the LQS family of quadruplexes in different L1 subfamilies. Sequence-logo plots in e show the base frequencies at each LQS position in the retrotransposon remnants of a given subfamily. The analyzed subfamilies contain at least 5 conserved quadruplex sequences belonging to the LQS family.
