Figure 1. Transcriptional interference induced by human retroelements. L1 and Alu positioned in the nucleosomal structure located in the intron of the hypothetical gene fragment act not only as “speed bumps” for RNA pol II, but also interfere with the host gene transcription by causing intron retention, forcing exonization and cryptic polyadenylation in their upstream region (characteristic structures 2 and 4 are shown at bottom). Also, in some instances, intron retention and exonization could include part of the retroelement (structures 3 and 5, respectively) and prematurely terminated transcripts may or may not contain poly(A) tail (structures 2 and 4). The observed TI effects depend on the L1 SP-ASP and Alu transcriptional activity, TF binding and the presence or absence of cryptic splice sites and polyadenylation signals upstream to or within the retroelements. TI effect may be also influenced by the nucleosome occupation in the L1 or Alu region. For the sake of simplicity, only two nucleosomes aligned to the 5′ region of the L1 and Alu are shown. Exons 1–3 are shown as colored boxes and their preferential location in nucleosomal regions is marked with small nucleosomes. Red arrow refers to the position, where TI effects occur. For each RNA pol II complex direction of transcription is shown with arrow.