Functionally related gene sets are regulated by similar contributions of translational control and mRNA abundance changes in different species.

<p>(A) The distribution of the translation component of regulation for transcripts differentially-expressed in RPF data (fdr = 0.1) in the four species. Shaded regions correspond to changes that are >75% translational (right) and <25% translational (left). Pairwise comparisons showed statistically significant differences in the distributions between each species pair (p<2.2e-16; Kolmogorov-Smirnov test). The percentage of transcripts falling in these two regions and in between are shown above. Stacked barplots represent the fractions of transcripts in each shaded category. (B) Density distributions of the translational component of regulation for genes in several functional categories in the four species.</p

Supplementary_Table_2_Curated_Spirulina_hits.txt

Table S2. Details of Spirulina spacers with identified metagenomic sources. Each record (separated by ***) contains BLASTx results for a metagenomic sequence or assembly identified as related to a known ORF, followed by BLASTn results depicting the best mapping of a Spirulina spacer to the metagenomic read or assembly. Other, weaker spacer matches to the same metagenomic target are also summarized. The only type III-B spacer match is indicated at the beginning of the relevant record

Phylogeny of the <i>elegans</i> supergroup and experimental overview.

<p>(A) Phylogenetic relationships of the four <i>Caenorhabditis</i> species used in this work, according to Kiontke <i>et al. </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003739#pgen.1003739-Kiontke1" target="_blank">[33]</a>. (B) Graphical overview of experimental procedure.</p

Changes in translation efficiency and mRNA abundance tend to act cooperatively.

<p>(A) Log(2) fold-changes for mRNA abundance are plotted against RPF fold-changes for <i>C. elegans</i>, with regions inferred to represent concordant and discordant changes in translation efficiency and mRNA abundance indicated. Transcripts called as significantly differentially-expressed in both RPF and mRNA-seq datasets (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003739#pgen-1003739-g002" target="_blank"><b>Fig. 2</b></a>) are shown in color; blue: concordant changes, gold: discordant changes. (B–D) Equivalent plots for the three additional species. (E) Counts of transcripts subject to concordant and discordant changes in the four species as well as the ratio (concordant:discordant) and significance. P-values: binomial test with the null hypothesis that concordant and discordant changes are equally likely (P_concordant = P_discordant = 0.5). Strongly discordant <i>C. elegans</i> transcripts are listed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003739#pgen.1003739.s013" target="_blank">Table S6</a>.</p

The transcriptome and translatome are substantially remodeled upon exiting diapause.

<p>(A–B) Expression mean versus log(2) fold change (MA) plots for <i>C. elegans</i> (A) mRNA and (B) RPF abundance changes resulting from feeding-induced diapause release. Colored points represent transcripts determined to be differentially expressed by a negative binomial test (fdr = 0.1) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003739#pgen.1003739-Anders1" target="_blank">[28]</a>. (C) Distributions of fold changes in mRNA (black) and RPF (red) abundances and translation efficiency (TE: the ratio of RPF:mRNA abundance; in blue). Shaded regions: >2-fold change; black (mRNA), red (RPF), or blue (TE) text indicates percentage of all transcripts showing >2-fold change in the indicated direction. We include the translation efficiency metric for reference, noting that this measure is dependent on the ratio of RPF to mRNA values and is thus not an independent metric of the other two values shown. Controls demonstrating that observed differences are not due to differences in variance of the data types are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003739#pgen.1003739.s007" target="_blank">Fig. S7</a>.</p

Additional file 2: Figure S2. of A streamlined tethered chromosome conformation capture protocol

Correlation between N2 DpnII experimental data and data from Crane et al. [22]. The 50KB chromatin contact matrix constructed using N2 young adults treated with DpnII restriction enzyme data (GSM2041038- SRR3105476) was compared with 50KB resolution chromatin contacts matrix constructed using the Crane et al. data (GSM1556154 - SRR1665087) from [22]. The total number of paired-ended 37X2 reads in our dataset was 88,466,514, while Crane et al. provide a total of 115,983,178 paired-ended 100X2 reads was. In order to build the chromatin contacts matrix we used the ICE pipeline [38] iterative mapping implementation from [ https://bitbucket.org/mirnylab/hiclib ], starting from 21nt up to 37nt in increments of 8. The number of detected Hi-C valid pairs in our dataset was 18,779,498 , consisting of 4,542,078 inter-chromosomal contacts and 14,237,420 intra-chromosomal contacts. In Crane’s dataset the number of valid Hi-C pairs was 59,200,047, consisting of 6,457,271 inter-chromosomal contacts and 52,742,776 intra-chromosomal contacts. Similarly to Additional file 1: Figure S1, any contacts between any location on chromosome I and region containing rRNA on chromosome I (the bin 15,050,000-end of chromosome I) are colored in green. Contacts between genomic loci in adjacent regions (up to 100KB apart are colored in purple). Versions of software used for analysis are as follows: Bowtie2-2.2.6 [39], and mirnylib/hiclib [ https://bitbucket.org/mirnylab/hiclib ] downloaded on December 1, 2015. Slight differences in aligned read counts from Tables 2 and 3 reflect updates in alignment software in the concerted package compared to the legacy versions used in Tables 2 and 3. (PDF 1132 kb

Additional file 3: Figure S3. of A streamlined tethered chromosome conformation capture protocol

Comparison between RTCC experimental data (this work; black lines), Hi-C data from Crane et al. (2015; magenta lines); and relative representation in anti-LEM2 ChIP-chip data [28]. The curves were obtained by running the ICE pipeline [38] on our N2 dataset (N2 DpnII GSM2041038- SRR3105476) and on Crane et al. dataset (GSM1556154 - SRR1665087), as implemented in [ https://bitbucket.org/mirnylab/hiclib ], downloaded on Dec 1, 2015. To obtain the first Eigen Vector values, representing compartments along the chromosome axis, we have followed the tutorial from [ https://bitbucket.org/mirnylab/hiclib ], using the binnedData class function doEig(numPCs = 1). To inspect the correlation to LEM-2 binding compartments we added LEM-2 binding data [28] (MA2C normalized log2 ratio of ChIP signal over control), lifted from the ce4 genome assembly to the ce10 assembly, and averaged in 50KB bins. (PDF 46 kb

Supplementary_Table_3_RNA_viruses.docx

Table S3. List of RNA phage genomes analyzed. CRISPR spacers from all published genomes were tested for similarity to RNA phage genomes listed here

Supplementary_Table_1_RT_cas_loci_details.xlsx

<b>Table S1. Comprehensive survey of RT-containing CRISPR-Cas loci. Genomic co-ordinates, Genbank IDs, and annotations are provided for genes in the vicinity of CRISPR-associated RTs.</b

Supplementary_Table_4_RT_loci_spacer_hits.xlsx

Table S4. Spacer matches for CRISPR arrays encoded in RT-Cas1 loci in NR database. CRISPR spacers from all RT-containing loci were tested for similarity to all non-redundant protein records. The few observed matches are listed here