Data Ghanipoor-Samami and Javadmanesh et al. for PLoS ONE 2018.xlsx

Real time qPCR data<br><br><br

Tissue-specific expression profiles of IGF system binding proteins in bovine pre- and postnatal developmental stages.

<p>Abundances of transcripts for <i>IGFBP1</i>, <i>IGFBP2</i>, <i>IGFBP3</i>, <i>IGFBP4</i>, <i>IGFBP5</i>, <i>IGFBP6</i>, <i>IGFBP7</i> and <i>IGFBP8</i> were measured in tissues of Day 48 embryos, Day 153 fetuses and 12–14 month-old juveniles. Placental samples were obtained from Day 48 embryos, Day 153 fetuses and term calves born by Caesarean section (C-section) at Day 277/278 of gestation. Means and standard deviations of means for each transcript and tissue were calculated based on triplicate measures of pooled cDNA comprising up to 60 embryonic cDNA samples, 73 fetal cDNA samples, 5 placental cDNA samples of C-section calves and 17 juvenile cDNA samples. Transcript abundances were calculated by the standard curve method and expressed in relative units, and are presented in logarithmic scale. ‘m’ denotes missing tissue such as kidney that is not yet present in embryos, where transcript abundances could not be determined.</p

Tissue-specific expression profiles of IGF system ligands in bovine pre- and postnatal developmental stages.

<p>Abundances of global <i>IGF1</i> transcript and splice variants <i>IGF1</i> class 1 and 2, global <i>IGF2</i> transcript and promoter and splice variant-specific <i>IGF2</i>-P0, <i>IGF2</i>-P1e2, <i>IGF2</i>-P1e3, <i>IGF2</i>-P2e4, <i>IGF2</i>-P2e5, <i>IGF2</i>-P3 and <i>IGF2</i>-P4 transcript were measured in tissues of Day 48 embryos, Day 153 fetuses and 12–14 month-old juveniles. Placental samples were obtained from Day 48 embryos, Day 153 fetuses and term calves born by Caesarean section (C-section) at Day 277/278 of gestation. Means and standard deviations of means for each transcript and tissue were calculated based on triplicate measures of pooled cDNA comprising up to 60 embryonic cDNA samples, 73 fetal cDNA samples, 5 placental cDNA samples of C-section calves and 17 juvenile cDNA samples. Transcript abundances were calculated by the standard curve method and expressed in relative units, and are presented in logarithmic scale. ‘m’ denotes missing tissue such as kidney that is not yet present in embryos, where transcript abundances could not be determined.</p

Bovine IGF2 gene and transcript structure with primer locations for amplification of promoter specific transcripts and splice variants.

<p>The exon-intron structure of bovine insulin/insulin-like growth factor 2 (<i>INS/IGF2</i>, GenBank accession no. EU518675.1) with locations of five promoters (P0, P1, P2, P3 and P4) is shown at the top with promoters (<i>IGF2</i>-P0 –P4) and splice variant specific transcripts indicated below. Red and green boxes depict untranslated and protein coding exons, respectively. Forward (F) and reverse (R) primers are indicated with region spanned, including intron where applicable, symbolized by a black bar between primers above the transcript. According to the transcription initiation site of human <i>IGF2</i>-P0 transcript, the putative orthologous bovine transcript is predicted to originate from a highly conserved region located upstream of the splice donor site of transcript P1 exon 2. We could specifically amplify bovine <i>IGF2</i>-P0 using a strategically designed forward primer within this unique 5’-UTR sequence and the reverse primer located within exon 2. The two splice variants of P1 promoter transcripts include leading exon 1 which is alternatively spliced onto exons 2 and 3 (<i>IGF2</i>-P1e2) and exon 3 (<i>IGF2</i>-P1e3) plus the coding exons. In order to amplify the P1 promoter transcripts, two pairs of primers located within exon 2 (for <i>IGF2</i>-P1e2) and exons 3 and 8 (for <i>IGF2</i>-P1e3) were used. This approach was necessary because specific amplification of transcripts derived from P1 promoter failed due to lack of suitable PCR primer sequence in exon 1. Since <i>IGF2</i>-transcript P1 exon 2 is part of the first exonic region of transcript <i>IGF2</i>-P0, and exon 3 is present in both <i>IGF2-</i>P0 and <i>IGF2-</i>P1 transcripts, the <i>IGF2</i>-P1e2 and -P1e3 amplicons could potentially derive from P0 and/or P1 promoters, depending on tissue and developmental stage. We quantified transcript abundances for two splice variants derived from <i>IGF2-</i>P2 promoter which comprise leading exon 4 (<i>IGF2</i>-P2e4) or leading exons 4 and 5 (<i>IGF2</i>-P2e5) as well as the protein coding exons. The forward primer for <i>IGF2</i>-P2e4 was designed to span the junction of exons 4 and 8, and for <i>IGF2</i>-P2e5 was in exon 5 with the reverse primer for both splice variants in exon 8. To amplify <i>IGF2</i>-P3 and <i>IGF2</i>-P4 transcripts, forward primers were designed within exons 6 and 7 with the reverse primer located within exon 8. All primers are detailed in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200466#pone.0200466.s003" target="_blank">S3 Table</a></b>.</p

Tissue-specific expression profiles of IGF system receptors in bovine pre- and postnatal developmental stages.

<p>Abundances of global <i>IR</i> transcript and splice variants <i>IR</i>-A and <i>IR</i>-B, <i>IGF1R</i> and <i>IGF2R</i> were measured in tissues of Day 48 embryos, Day 153 fetuses and 12–14 month-old juveniles. Placental samples were obtained from Day 48 embryos, Day 153 fetuses and term calves born by Caesarean section (C-section) at Day 277/278 of gestation. Means and standard deviations of means for each transcript and tissue were calculated based on triplicate measures of pooled cDNA comprising up to 60 embryonic cDNA samples, 73 fetal cDNA samples, 5 placental cDNA samples of C-section calves and 17 juvenile cDNA samples. Transcript abundances were calculated by the standard curve method and expressed in relative units, and are presented in logarithmic scale. ‘m’ denotes missing tissue such as kidney that is not yet present in embryos, where transcript abundances could not be determined.</p

Tissue-specific expression profiles of long non-coding RNAs associated with the IGF system in bovine pre- and postnatal developmental stages.

<p>Abundances of <i>H19</i> and <i>AIRN</i> transcript were measured in tissues of Day 48 embryos, Day 153 fetuses and 12–14 month-old juveniles. Placental samples were obtained from Day 48 embryos, Day 153 fetuses and term calves born by Caesarean section (C-section) at Day 277/278 of gestation. Means and standard deviations of means for each transcript and tissue were calculated based on triplicate measures of pooled cDNA comprising up to 60 embryonic cDNA samples, 73 fetal cDNA samples, 5 placental cDNA samples of C-section calves and 17 juvenile cDNA samples. Transcript abundances were calculated by the standard curve method and expressed in relative units, and are presented in logarithmic scale. ‘m’ denotes missing tissue such as kidney that is not yet present in embryos, where transcript abundances could not be determined.</p

Relative contribution of promoter and splice variant-specific <i>IGF2</i> transcripts to global <i>IGF2</i> transcript abundance in fetal tissues and placenta.

<p><i>IGF2</i>-P0, <i>IGF2</i>-P3 and <i>IGF2</i>-P4 are percent transcript abundance derived from P0, P3 and P4 promoters, respectively. Splice variants of promoter P2 transcript are <i>IGF2</i>-P2e4 with untranslated leader exon 4 and <i>IGF2</i>-P2e5 with untranslated leader exons 4 and 5. Estimated means are from 73 fetal cDNA samples per tissue and 95% confidence intervals are detailed in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0200466#pone.0200466.s009" target="_blank">S9 Table</a></b>. Transcript abundances were calculated by the standard curve method, normalized with reference genes and expressed in relative units. The relative contribution of each promoter-specific transcript to global <i>IGF2</i> transcript abundance was calculated by Johnson’s Relative Weight procedure.</p

Effects of interaction of maternal and paternal genomes, fetal sex and final maternal weight nested within maternal genetics on <i>H19</i> transcript abundance in fetal <i>M. semitendinosus</i> at midgestation.

<p>Least square means with standard error of means and <i>P</i>-values for significant differences (<i>t</i>-test) between means (<b>A</b>) and significant regressions of final maternal weight nested within Bt and Bi maternal genomes (<b>B</b>) are shown. Bt: <i>Bos taurus taurus</i>, Angus. Bi: <i>Bos taurus indicus</i>, Brahman.</p

Specific effects of maternal genomes, paternal genomes and fetal sex on fetal absolute muscle weights at midgestation.

<p>Least square means with standard errors of means are shown and <i>P</i>-values for significant differences (<i>t</i>-test) between means for <i>M. supraspinatus</i> (<b>A</b>), <i>M. longissimus dorsi</i> (<b>B</b>), <i>M. quadriceps femoris</i> (<b>C</b>), <i>M. semimembranosus</i> (<b>D</b>) and combined muscle weight (sum of weights of dissected muscles) (<b>E</b>) are indicated. ND: Not determined because of significant nested effect of final maternal weight (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053402#pone-0053402-g005" target="_blank"><b>Figure 5</b></a>). Bt: <i>Bos taurus taurus</i>, Angus. Bi: <i>Bos taurus indicus</i>, Brahman.</p

Relative contributions of maternal and paternal genome to genetic variation in fetal myofibre characteristics, absolute and relative muscle weights, and <i>H19</i> transcript abundance.

<p>Myofibre characteristics were determined in <i>M. semitendinosus.</i> CSA: Cross-sectional area. Total cell: All myofibres measured regardless of cell type. Combined muscle weights: Sum of <i>M. supraspinatus, M. longissimus dorsi</i>, <i>M. semimembranosus</i> and <i>M. quadriceps femoris</i> weight. Relative muscle weight: Absolute muscle weight divided by decapitated and eviscerated fetal carcass weight.</p