RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

Our work sheds light on the metabolism of RNA transcripts derived from genomic Alu repeats. Since it is unclear whether Alu elements are transcribed mainly by RNA polymerase II or III, we conducted a transcription shutoff experiment and metabolic RNA labeling. We find that Alu transcripts are as stable as mRNAs and originate in part from RNA polymerase II. Furthermore, we use the de Bruijn graph of all Alu sequences to discover sequence features that match transcription factor binding motifs. Differential expression analysis with DESeq2 of various RNA types (Alu transcripts, canonical transcripts, tRNA, mtRNA) under RNA polymerase II inhibition by alpha-amanitin using paired-end TT-seq. Alpha-amanitin and water control with two replicates each, labeled and total fraction.