FANTOM5 CAGE profiles of human and mouse samples

Abstract

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

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“…In contrast to this hypothesis, SPPL2c mRNA was found in a variety of human tissues ; however, since the SPPL2c gene does not contain any introns, traces of genomic DNA co‐purified with RNA may well reflect a false‐positive detection of mRNA. This is supported by the FANTOM5 CAGE profiles of human and mouse samples, and the genotype‐tissue expression (GTEx) project, which detect SPPL2c mRNA almost exclusively in testis .…”

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“…Peaks were considered as described in Bowman et al (2016). FANTOM5 mouse permissive enhancers were downloaded from http://fantom.gsc.riken.jp/5/ (Noguchi et al, 2017). FANTOM5 mouse permissive enhancers were downloaded from http://fantom.gsc.riken.jp/5/ (Noguchi et al, 2017).…”

“…We next used the previously described approach of (Bowman et al, 2016) to combine our RNA-seq data and external published data to explore the diversity of promoter and enhancer landscapes of the two DEG sub-sets. To capture additionally the active enhancer regions in both subgroups, we included a further data set from the FANTOM5 consortium (Noguchi et al, 2017). However, the promotor landscape differed between CTL-and BKM-DEGs (Supporting Information Figure S7).…”

“…Promoters were defined as the −2 kb/+500 bp regions relative to the transcription start site (TSS) and enhancers as the + 50 kb/−50 kb regions relative to the TSS (excluding the promoter regions). FANTOM5 mouse permissive enhancers were downloaded from http://fantom.gsc.riken.jp/5/ (Noguchi et al, 2017). Peak calling, merging and annotation were performed using HOMER with default parameters (Heinz et al, 2010).…”

“…However, the promotor landscape differed between CTL-and BKM-DEGs (Supporting Information Figure S7). To capture additionally the active enhancer regions in both subgroups, we included a further data set from the FANTOM5 consortium (Noguchi et al, 2017). We also associated our CTL-and BKM-DEGs, respectively, with the FAN-TOM5 enhancer data set.…”