A) Expression, in CD34+ cells of PMF patients and controls, of miRNAs and moRNAs produced from the same hairpin, considering the hairpins expressing most abundant moRNAs; the boxplot in panel (B) shows the distribution of Pearson correlation values calculated pairwise between expression profiles of moRNAs and miRNAs produced from the same hairpin arm, considering all moRNAs detected in CD34+ cells.

<p>A) Expression, in CD34+ cells of PMF patients and controls, of miRNAs and moRNAs produced from the same hairpin, considering the hairpins expressing most abundant moRNAs; the boxplot in panel (B) shows the distribution of Pearson correlation values calculated pairwise between expression profiles of moRNAs and miRNAs produced from the same hairpin arm, considering all moRNAs detected in CD34+ cells.</p

List of most abundant moRNAs in considered CD34+ samples, which are expressed over the third quartile of all sRNAs expression.

<p>For each moRNA, the table reports expression (per sample group normalized read count), position and sequence.</p

Putative targets of 3’-moR-128-2 variants in the “Regulatory RNA” pathway.

<p>Putative targets of 3’-moR-128-2 variants in the “Regulatory RNA” pathway.</p

Differential expression of 3’-moR-128-2 in PMF (n = 3) vs CTR (3) cells.

<p>A) moR expression in PMF and CTR CD34+ according to RNA-seq data. B) RT-PCR expression (RQ) in CD34+ cells from independent cohort of normal controls (n = 8) and of PMF (20) samples. C) RT-PCR expression (RQ) in granulocytes from independent cohort of normal controls (n = 10) and of PMF (50) samples; ***, ** and * indicate respectively a p-value <0.001, <0.01 or <0.05.</p

The 3’-moR-128-2 is produced by the precursor sequence of miR-128-3p.

<p>A) The moRNA is derived from a region of the primary miRNA sequence exceeding the canonical hairpin precursor sequence, and it is not exaclty adjactent to the annotated miRNA. B) Minimum free energy (MFE) folding structure, predicted by RNAfold, for the canonical hairpin sequence and for the longer one, from which the moRNA is probably derived. C) Both the considered small RNAs are conserved in evolution through vertebrates.</p

Expression pattern of 18 mRNAs potentially targeted by miRNAs, according to qRT-PCR data.

<p>For each mRNA, miRNA and moRNA, we report if it is increased (I) or decreased (D) in the PMF VS CTR sample comparison; the mRNAs p-values associated to a significant difference are listed; the last column indicates if the expression of observed target mRNA variation is inversely related to the corresponding miRNA or moRNA.</p

Origin, sequence variability, and relations beween 3’-moR-128-2 and the adjacent miR-128-3p.

<p>A) 3’-moR-128-2 and miR-128-3p map to the same locus and both shows sequence variability (isomiRs and isomoRs). Both the major and the minor isomoRs are found in normal CD34+ cells and not in PMF samples. Red and blue colors indicate isomiR and isomoR groups that can be produced with an unique sequence cutting sites. The most expressed isomoR is not associated to the corresponding most expressed isomiR. Moreover, expression levels, in CTR and PMF samples, of isomiRs and isomoRs are poorly correlated intragroup. These observations, point against the moRNA being simply a by-product of the miRNA biogenesis. A similar indication is given by the fact that some abundant isomiRs are not associated to detected isomoR sequences. B) 3’-moR-128-2 and miR-128-3p have different, poorly overlapping, sets of predicted targets. C) 3’-moR-128-2 sequence can stably bind a target site in the 3’UTR of the RAN mRNA, causing post transcriptional silencing.</p

Summary of small RNAs expressed in CD34+ cells.

<p>Summary of small RNAs expressed in CD34+ cells.</p

Differential expression of small RNAs in PMF vs CTR CD34+.

<p>A) Log2 FC of 37 small RNA differentially expressed considering PMF vs CTR CD34+, according to RNA-seq data (FDR<0.05). When a small RNA was not expressed in one sample category, the ratio was infinite and we represent it as the arbitrary maximum value of 15. B) RT-PCR expression calculation of five selected miRNAs in granulocytes collected from an independent cohort of normal controls (n = 10) and of PMF (50) samples; ***, ** and * indicate respectively a p-value <0.001, <0.01 or <0.05.</p

Variability assessment of 14 SSR loci of <i>Chamelea gallina</i>.

<p>Variability, expressed in terms of number of different alleles, was assessed on 12 individuals collected in Chioggia in 2010 (off Venice lagoon, Italy). The table reports the name of each locus, taken from the contig number, the repeat content, the forward (F) and reverse (R) primer sequences, the fluorescent label, the annealing temperature (Ta) of PCR amplification, the size range of amplified fragments in bp, the allelic range in repeats, the number of alleles (Na) detected and the Hardy-Weinberg probability (pHWE). Significant p-values in bold (α = 0.05). Mean values for allele number, observed and expected heterozygosity are reported in the last row. Standard Deviation is reported in brackets (± SD).</p>*<p>Loci putatively affected by null alleles following MICRO-CHECKER 2.2.3. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044185#pone.0044185-vanOosterhout1" target="_blank">[51]</a>.</p>a<p>p-values were calculated based on a limited number of individuals (n = 12).</p