When LIN41 Comes to a Fork in the Road, It Takes BOTH Paths: Translational Repression OR mRNA Decay, Depending on the Target Site Position.

In this issue, Aeschimann et al. (2017) demonstrate that, depending on the target location site (5'UTR or 3'UTR), LIN41 triggers repression of translation or mRNA decay, suggesting that one factor may use two independent pathways of post-transcriptional gene regulation.

DNA methylation and miRNA-1296 act in concert to mediate spatiotemporal expression of KPNA7 during bovine oocyte and early embryonic development.

BACKGROUND: Epigenetic regulation of oocyte-specific maternal factors is essential for oocyte and early embryonic development. KPNA7 is an oocyte-specific maternal factor, which controls transportation of nuclear proteins important for early embryonic development. To elucidate the epigenetic mechanisms involved in the controlled expression of KPNA7, both DNA methylation associated transcriptional silencing and microRNA (miRNA)-mediated mRNA degradation of KPNA7 were examined. RESULTS: Comparison of DNA methylation profiles at the proximal promoter of KPNA7 gene between oocyte and 6 different somatic tissues identified 3 oocyte-specific differentially methylated CpG sites. Expression of KPNA7 mRNA was reintroduced in bovine kidney-derived CCL2 cells after treatment with the methylation inhibitor, 5-aza-2'-deoxycytidine (5-Aza-CdR). Analysis of the promoter region of KPNA7 gene in CCL2 cells treated with 5-Aza-CdR showed a lighter methylation rate in all the CpG sites. Bioinformatic analysis predicted 4 miRNA-1296 binding sites in the coding region of KPNA7 mRNA. Ectopic co-expression of miRNA-1296 and KPNA7 in HEK293 cells led to reduced expression of KPNA7 protein. Quantitative real time PCR (RT-qPCR) analysis revealed that miRNA-1296 is expressed in oocytes and early stage embryos, and the expression reaches a peak level in 8-cell stage embryos, coincident with the time of embryonic genome activation and the start of declining of KPNA7 expression. CONCLUSIONS: These results suggest that DNA methylation may account for oocyte-specific expression of KPNA7, and miRNA-1296 targeting the coding region of KPNA7 is a potential mechanism for KPNA7 transcript degradation during the maternal-to-zygotic transition.

Comparison of polyglactin-910 and polydioxanone for closure of the linea alba following caudal ventral midline laparotomy in sheep.

This study compared incisional complications after ventral midline laparotomy using 2 absorbable suture materials for apposition of the linea alba in sheep. The linea alba of 93 yearling sheep was sutured by 3 veterinarians in a simple continuous pattern using either polyglactin 910 (PG910; group PG) or polydioxanone (PDS; group PD). A blinded observer assessed surgical sites at the time of suture removal. Multivariate logistic regression was used to assess the association between incisional complications and variables (suture material used, veterinarian, skin suture removal time). The odds of incisional complications did not vary significantly with the type of suture material used (P = 0.11), veterinarian (P = 0.61) or skin suture removal time (P = 0.36). Most incisional complications were cutaneous suture sinus formation. Either PG910 or PDS may be used for linea alba closure in sheep.

Comparison de l'utilisation du polyglactin 910 et du polydioxanone pour suturer la ligne blanche lors de laparotomies ventrales médianes caudales chez la brebis. Cette étude compare les complications incisionnelles suite à une laparotomie ventrale médiane en utilisant 2 fils de sutures pour l'apposition de la ligne blanche chez la brebis. La ligne blanche de 93 brebis a été suturée par 3 vétérinaires en points simples continus avec du polyglactin 910 (PG910; groupe PG) ou du polydioxanone (PDS; groupe PD). Une observation à l'aveugle des sites chirurgicaux a été effectuée lors du retrait des points de suture. Une régression logistique multivariée a été utilisée pour déterminer l'association entre les complications incisionnelles et les variables (matériel de suture utilisé, vétérinaire et temps de retrait des sutures cutanées). Les chances de complications ne variaient pas selon le type de matériel de suture utilisé (P = 0,11), le vétérinaire (P = 0,61) ou la période de retrait des points cutanés (P = 0,36). La majorité des complications étaient des fistules associées aux sutures cutanées. Le PG910 ou le PDS peut être utilisé pour l'apposition de la ligne blanche chez la brebis.(Traduit par les auteurs).

Translation affects mRNA stability in a codon-dependent manner in human cells.

mRNA translation decodes nucleotide into amino acid sequences. However, translation has also been shown to affect mRNA stability depending on codon composition in model organisms, although universality of this mechanism remains unclear. Here, using three independent approaches to measure exogenous and endogenous mRNA decay, we define which codons are associated with stable or unstable mRNAs in human cells. We demonstrate that the regulatory information affecting mRNA stability is encoded in codons and not in nucleotides. Stabilizing codons tend to be associated with higher tRNA levels and higher charged/total tRNA ratios. While mRNAs enriched in destabilizing codons tend to possess shorter poly(A)-tails, the poly(A)-tail is not required for the codon-mediated mRNA stability. This mechanism depends on translation; however, the number of ribosome loads into a mRNA modulates the codon-mediated effects on gene expression. This work provides definitive evidence that translation strongly affects mRNA stability in a codon-dependent manner in human cells.

Discovery of a novel oocyte-specific Krüppel-associated box domain-containing zinc finger protein required for early embryogenesis in cattle.

Zinc finger (ZNF) transcription factors interact with DNA through zinc finger motifs and play important roles in a variety of cellular functions including cell growth, proliferation, development, apoptosis, and intracellular signal transduction. One-third of ZNF proteins in metazoans contain a highly conserved N-terminal motif known as the Krüppel-associated box (KRAB) domain, which acts as a potent, DNA-binding dependent transcriptional repression module. Analysis of RNA-Seq data generated from a bovine oocyte cDNA library identified a novel transcript, which encodes a KRAB-containing ZNF transcription factor (named ZNFO). Characterization of ZNFO mRNA expression revealed that it is exclusively expressed in bovine oocytes and early embryos. A GFP reporter assay demonstrated that ZNFO protein localizes specifically to the nucleus, supporting its role in transcriptional regulation. To test the role of ZNFO in early embryonic development, zygotes were generated by in vitro maturation and fertilization of oocytes, and injected with small interfering RNA (siRNA) designed to knockdown ZNFO. Cleavage rates were not affected by ZNFO siRNA injection. However, embryonic development to 8- to 16-cell stage and blastocyst stage was significantly reduced relative to the uninjected and negative control siRNA-injected embryos. Further, interaction of ZNFO with the highly conserved co-factor, KRAB-associated protein-1 (KAP1), was demonstrated, and evidence supporting transcriptional repression by ZNFO was demonstrated using a GAL4-luciferase reporter system. Results of described studies demonstrate that ZNFO is a maternally-derived oocyte-specific nuclear factor required for early embryonic development in cattle, presumably functioning by repressing transcription.

Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).

Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed from intergenic regions of genomes. To date, no lincRNAs in non-model teleost fish have been reported. In this report, we present the first reference catalog of 9674 rainbow trout lincRNAs based on analysis of RNA-Seq data from 15 tissues. Systematic analysis revealed that lincRNAs in rainbow trout share many characteristics with those in other mammalian species. They are shorter and lower in exon number and expression level compared with protein-coding genes. They show tissue-specific expression pattern and are typically co-expressed with their neighboring genes. Co-expression network analysis suggested that many lincRNAs are associated with immune response, muscle differentiation, and neural development. The study provides an opportunity for future experimental and computational studies to uncover the functions of lincRNAs in rainbow trout.