Differently expressed genes potentially targeted by nutriregulated miRNA.

<p>In bold, miRNA or DEG whose expression are upregulated by the food deprivation. ABCC5: ATP-binding cassette, sub-family C (CFTR/MRP), member 5, ANKFY1: Ankyrin repeat and FYVE domain-containing protein 1, ARFIP1: Arfaptin-1, CD24: Signal transducer CD24 precursor, DCBLD1: Discoidin, CUB and LCCL domain-containing protein 1 precursor, DCUN1D3: DCN1, defective in cullin neddylation 1, domain containing 3, DPAGT1: UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase, EFHC1: EF-hand domain-containing protein 1, ESR1: Oestrogen receptor alpha, INSIG1: Insulin-induced gene 1 protein, IRF2BP2: Interferon regulatory factor 2 binding protein 2, KCNH8: Potassium voltage-gated channel subfamily H member 8, LEPREL2: Prolyl 3-hydroxylase 3 precursor, MYO1B: Myosin Ib, PHLDB1: Pleckstrin homology-like domain family B member 1, PLAGL2: Zinc finger protein PLAGL2, RAD9A: Cell cycle checkpoint control protein Rad9A, TMEM2: Transmembrane protein 2, TSPAN31: Tetraspanin-31, ZCCHC14: Zinc finger CCHC domain-containing protein 14.</p><p>Differently expressed genes potentially targeted by nutriregulated miRNA.</p

Nutriregulated miRNA which bovine equivalent is located in QTL associated with milk production and composition.

<p>Conservation between nutriregulated and bovine miRNA was checked and their localization in QTL (CattleQTLdb, <a href="http://www.animalgenome.org/cgi-bin/QTLdb/BT/" target="_blank">http://www.animalgenome.org/cgi-bin/QTLdb/BT/</a>) associated with milk was investigated.</p><p>Nutriregulated miRNA which bovine equivalent is located in QTL associated with milk production and composition.</p

Principal component analyses of miRNA in Control and FD goats.

<p>L0X: represent 1 library, FD: Food deprived. Analyses were performed on miRNA for libraries according to the diet received by the goats. The two different diets are labelled within their 95% inertia ellipse (Red: Control; Green: FD).</p

Amino acid transporters potentially targeted by nutriregulated miRNA.

<p>Putative targets were predicted from DIANA microT v5.0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140111#pone.0140111.ref036" target="_blank">36</a>] for known miRNA and Custom Target Scan v5.2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140111#pone.0140111.ref037" target="_blank">37</a>] for predicted miRNA.</p><p>Amino acid transporters potentially targeted by nutriregulated miRNA.</p

Summary of sequencing data.

<p>^ameans of data for the 4 Control goat libraries</p><p>^bmeans of data for the 6 FD goat libraries</p><p>^csequencing adapters removed</p><p>^d17-28 nt size filter, used by the miRDeep2 software</p><p>^ereads with at least one and at most five reported alignments, used by the miRDeep2 software.</p><p>Summary of sequencing data.</p

Potential involvement of nutriregulated miRNA in milk fat synthesis.

<p>In red, miRNA which expression was up-regulated in FD goat mammary glands compared with Controls, while those whose expression was down-regulated are in blue.</p

Nutriregulated miRNA binding sites on <i>ESR1</i> mRNA.

<p>Analyses were performed using DIANA microT v5.0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140111#pone.0140111.ref036" target="_blank">36</a>] for miR-125b-3p and miR-222-3p and Custom Target Scan v5.2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140111#pone.0140111.ref037" target="_blank">37</a>] for chr19_26739-5p. The interaction between 3’UTR of ESR1 and the seed region of miR-222-3p of one binding site is described in the box.</p

Potential contribution of nutriregulated miRNA to regulating PTEN and associated networks.

<p>GLUT1: GLUcose Transporter 1, mTOR: mechanistic Target Of Rapamycin, PTEN: Phosphatase and TENsin homolog, SREBF1: Sterol REsponsive Binding Factor 1.</p

Summary of sequencing data lactating mouse, bovine and AGO2 mammary gland miRNA libraries.

a<p>poly-A stretches removed.</p>b<p>17–28 nt size filtering,reads used by miRDeep2 quantification process.</p>c<p>reads with at least one and at most five reported alignments, used by the miRDeep2 prediction process.</p><p>* In AGO sample 2, many reads below 10 counts were present, subsequently discarded by miRDeep2 processes.</p

Characterisation of mouse AGO2-RISC loading.

<p>Proportion of miRNA expressed with an equivalent ( = ) or a different (> or <) abundance in AGO2-RISC and mammary gland miRNomes. A few representative examples are presented for each category and the complete data are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091938#pone.0091938.s008" target="_blank">Table S5</a>.</p