Clover-Shaped Fold Predictions

<div><p>(A) Gene structure, EvoFold predictions, and cDNAs around the end of the gene <i>ZNF207</i>. The 3′UTR and the intron of an alternative splice variant harbor high-scoring clover-shaped fold predictions.</p><p>(B) Annotated segment of eight-way alignment spanning the 3′UTR fold (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020033#pcbi-0020033-g003" target="_blank">Figure 3</a>B for legend).</p><p>(C) Depictions of 3′UTR fold (left) and intronic fold (right).</p><p>(D) Annotated alignment of human primary sequences of 3′UTR and intronic folds. The alignment is annotated with the secondary structures of the folds and substitution differences in corresponding pairs are color-coded (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020033#pcbi-0020033-g003" target="_blank">Figure 3</a>B for color legend).</p></div

Breakdown of Types of RNA Folds Detected in the Human Genome Based on True Positive Estimates

<div><p>See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020033#s4" target="_blank">Materials and Methods</a>, Validation section.</p><p>Folds are classified according to (A) size (number of pairing bases), (B) location in the genome, and (C) shape. The relative abundance of each class of folds is indicated. For (B), also shown is the genomic span of the conserved segments relative to their genomic location, for comparison.</p></div

5′UTR miRNA-Like Hairpin and Coding Hairpin in Gene <i>(DGCR8)</i> Involved in miRNA Processing

<div><p>(A) Gene structure and EvoFold predictions are shown around the first exon of <i>DGCR8</i>.</p><p>(B) Annotated segment of the eight-way alignment spanning the long, miRNA-like 5′UTR-hairpin (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020033#pcbi-0020033-g003" target="_blank">Figure 3</a>B for legend).</p><p>(C) Depiction of folds.</p></div

Candidate Substrate for A-to-I Editing

<div><p>(A) Gene structure, EvoFold predictions, cDNAs, conservation, and eight-way alignment are shown at the start of the second exon of the <i>UBE1C</i> gene. The predicted hairpin is shown in parenthesis format and can be seen to overlap the intron–exon boundary. The red box highlights a position where the genomic sequence contains an A and a cDNA contains a G. The orange bar and label “4” indicate that up to four extra bases are present in this loop location in the indicated species.</p><p>(B) Depiction of hairpin (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020033#pcbi-0020033-g003" target="_blank">Figure 3</a>B for color legend) with indication of the potential site of ADAR editing (A-to-I).</p><p>(C) Which would lead to a lysine to arginine amino acid change.</p></div

Outline of EvoFold Prediction Method

<div><p>(A) Schematic representation of human genome and conserved elements. The conserved elements define the input alignments.</p><p>(B) Segment of eight-way genomic alignment.</p><p>(C) The SCFG of the fRNA model defines a distribution over all possible secondary-structure annotations. One of the many possible secondary structures is shown in parenthesis format. Substitutions in pairing regions of the alignment are color-coded relative to human: compensatory double substitutions are green, and compatible single substitutions are blue.</p><p>(D) Color-coded fold corresponding to the secondary-structure annotation of the alignment.</p><p>(E) Two phylogenetic models are used to evaluate the possible secondary-structure annotations: unpaired columns are evaluated using a single-nucleotide phylogenetic model. Paired columns are combined and evaluated using a di-nucleotide phylogenetic model. Horizontal branch lengths reflect the expected number of substitutions.</p></div

Additional file 3: Figure S1. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

Overlap of off-target detection for the EMX1 and VEGFA guides tested by different assays. Off-targets are only shown if they were detected by at least a single study and with a frequency of 0.1 %. See Additional file 1: Tables S1 and Additional file 4: Table S2 for the modification frequencies and additional details on the off-targets for the guides EMX1 and VEGFA, respectively. Additional file 4: Table S2 also includes the data by Hsu et al. [7], who quantified cleavage at putative off-target loci predicted by the CRISPR Design website ( http://crispr.mit.edu/ ) with targeted deep sequencing, Tsai et al. [3], who isolated double-strand breaks with modified oligonucleotides followed by sequencing, Frock et al. [28], who detected translocations, and Kim et al. [33] and Kim et al. [27], who performed whole-genome sequencing to find CRISPR-induced modifications. For details on the different studies, see Additional file 1: Table S1. (PDF 17 kb

Ilex serrata Thunb.

原著和名: ウメモドキ科名: モチノキ科 = Aquifoliaceae採集地: 愛知県 豊橋市 岩崎町 (三河 豊橋市 岩崎)採集日: 1968/10/20採集者: 萩庭丈壽整理番号: JH042317国立科学博物館整理番号: TNS-VS-99231

Mentha viridis L.

原著和名: ミドリハクカ科名: シソ科 = Labiatae採集地: 千葉県 千葉市 千葉大学 (下総 千葉市 千葉大学)採集日: 1967/8/13採集者: 萩庭丈壽整理番号: JH042898国立科学博物館整理番号: TNS-VS-99289

Acanthopanax trichodon Franch. et Savat.

原著和名: ミヤマウコギ科名: ウコギ科 = Araliaceae採集地: 千葉県 清澄山 (上総〜安房 清澄山)採集日: 1961/6/18採集者: 萩庭丈壽整理番号: JH042319国立科学博物館整理番号: TNS-VS-99231

Comparison of Substitution Rates in HAR1–HAR5

<p>For each HAR element, the estimated substitution rate is indicated by a circle for the human lineage and by a triangle for the chimp lineage. As a benchmark, background human-chimp substitution rates estimated from 4d sites in ENCODE regions [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020168#pgen-0020168-b039" target="_blank">39</a>] are marked with vertical lines, solid red for the genome-wide neutral rate, and dotted blue for the neutral rate in final chromosome bands. The chimp rates in all five elements fall well below the human rates, which exceed the background rates by as much as an order of magnitude. H, human; C, chimp.</p