Nuclease-resistant histone mRNA stem–loop fragments were prominent in SLBP HITS-CLIP data. (A) Autoradiograph of P32-labeled crosslinked ribonucleoprotein complexes that were isolated during SLBP HITS-CLIP library preparation. Both the experiment and negative controls are on the same gel and are the same exposure, but several intervening lanes were removed. (B) The probability density plots show the sequencing read fragment length distribution of reads that contain a stem–loop motif. (C) Distribution of reads that either contain or do not contain the histone SL in the SLBP HITS-CLIP data. (D) The bar graph shows the number of reads per million (RPM) containing a SL motif sequence for each of the HITS-CLIP libraries that we generated. GFP libraries did not contain an appreciable number of SL-containing reads. (E) Reads that contain SL motifs were mapped to the genome, and the number of reads per million (RPM) is shown for each genomic locus that was detected in each of our HITS-CLIP libraries. Shown are the 95 SL sequences that had at least one read in the HITS-CLIP data. The reads that fall into histone HGNC gene models are shown in black and those not in HGNC gene models are in red. The SL-containing reads primarily mapped to histone genes (shown in color bar).
