Additional file 1: Figure S1. of A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples

Bioanalyzer profile of the fragment size distribution for the intact SEQC-A and SEQC-B samples. The curve for SEQC-A is shown in red and the curve for SEQC-B in blue. The two peaks represent the intact 18S and 28S ribosomal RNA profiles. Figure S2. Bioanalyzer profile of the fragment size distribution for the degraded SEQC-A and SEQC-B samples. The curve for SEQC-A is shown in red and the curve for SEQC-B in blue. The peaks for the 18S and 28S ribosomal RNAs are now following a unimodal distribution with a much wider peak around a fragment size of 850 nt, reflecting the level of degradation. Figure S3. Bioanalyzer profile of the fragment size distribution for the highly-degraded SEQC-A and SEQC-B samples. The curve for SEQC-A is shown in red and the curve for SEQC-B in blue. The peaks for the 18S and 28S ribosomal RNAs are now following a unimodal distribution with a much wider peak around a fragment size of 150–200 nt, reflecting a high level of degradation. Figure S4. Bargraph of the alignment statistics for the SEQC-B sample and all three protocols. Each bar represents the averaged values across the three technical replicates per condition. The percentage of total aligned reads is represented by the height of the bar, and the percentage of reads aligning to exons is in red, introns in blue, and intergenic regions in green. Figure S5. Venn diagram of the protein coding genes detected by each of the three protocols. Venn diagram of the protein coding genes detected by each of the three protocols on degraded samples at the input amounts 10 ng for RNA Access and 100 ng for Ribo-Zero and TruSeq. A gene is considered “expressed” if it has a FPKM value of at least 0.3 in one of the three technical replicates of at least one of the two samples (SEQC-A or SEQC-B). Table S1. Simplified Ensembl gene type mapping. The original Ensembl (v76) gene type category is contained in the left column and the simplified category is contained in the right column. (PDF 661 kb

YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers

<div><p>YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or <i>YAP1</i> amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting.</p></div

Additional file 3: of MiR-210 promotes sensory hair cell formation in the organ of corti

Table of miRNA raw counts. Raw counts from sequencing of each of the small miRNA libraries. The number of sequences that correspond to each miRNA is listed. (XLSM 60 kb

YAP1/TEAD1 associate with active enhancers.

<p>(A) Genomic distribution of YAP1/TEAD1 peaks. Promoter class defined as 2kb upstream of gene TSS. (B) Distance of YAP1/TEAD1 peaks and H3K27ac regions to closest gene TSS. (C) Genomic views of H3K27ac, YAP1 and TEAD1 ChIP enrichment at gene promoters of known target genes. (D) YAP1, TEAD1 and H3K27ac ChIP enrichment at all YAP1 peak regions centered on peak summit. (E) Luciferase reporter assay of six YAP1/TEAD1 distal enhancer binding sites containing single or double TEAD motifs in cells treated with YAP1 or TEADs siRNA compared to control siRNA. Data are representative of at least three independent experiments. Error bars indicate the standard deviation of triplicate qPCR data.</p

Primers used for RT-qPCR.

<p>Primers used for RT-qPCR.</p

Luciferase reporters (Fig 2I).

<p>Luciferase reporters (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005465#pgen.1005465.g002" target="_blank">Fig 2I</a>).</p

siRNAs (Fig 3A).

<p>siRNAs (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005465#pgen.1005465.g003" target="_blank">Fig 3A</a>).</p

Primers used for ChIP-qPCR.

<p>Primers used for ChIP-qPCR.</p

Cell adhesion.

<p>Effect of different doses of rosiglitazone (0.01, 0.1, 1, 10, 50 µM), AS601245 (0.01, 0.1, 1, 10, 50 µM) and combined treatment on CaCo-2, HT-28 and SW480 on cell adhesion to HUVECs. Cells were treated or not with the drugs for 24 hours, harvested and incubated for 1 hour on HUVEC monolayers. Data are expressed as percentage of adhesion inhibition versus untreated control cells. The control value of adhesion was about 55±6 cells per microscope field (n  = 6) for all cell lines. The values is the mean ± SD, of 3 separated experiments. Variance analysis: *<i>p</i><0.05, **<i>p</i><0.01 vs control; # p<0.05 vs rosiglitazone; ## p<0.01 vs rosiglitazone; § <0.01 vs both compounds.</p

YAP1 binding sites largely overlap in cancer cell lines from distinct lineages.

<p>(A) Correlation between SF268 and NCI-H2052 YAP1 ChIP-seq samples. (B) Genomic views of YAP1 shared, SF268-, NCI-H2052 and IMR90-specific regions. (C) Correlation between SF268 and IMR90 YAP1 ChIP-seq samples. (D) H3K27ac ChIP enrichment at YAP1 peak regions (centered on peak summit) that are shared, SF268-specific or IMR90-specific.</p