LINC24065 is a monoallelically expressed long intergenic noncoding RNA located in the cattle DLK1–DIO3 cluster

Long noncoding RNAs (lncRNAs) are important regulators of biological processes, and regulate genomic imprinting in cis and/or trans to induce monoallelic expression with parent-origin-specific pattern. DLK1–DIO3 domain is one of the largest imprinted clusters in mammals, and maternally expressed noncoding RNAs of this region is related to the pluripotency of the embryonic stem cells. Previously, we sequenced the cDNA of two maternally expressed noncoding RNAs, MEG8 and MEG9, and mapped a lncRNA (LINC24061) between the two genes in the cattle DLK1–DIO3 domain on chromosome 21. In this study, we identified LINC24065, a novel long intergenic noncoding RNA (lincRNA), which was also located between MEG8 and MEG9. We identified four variants of LINC24065 (LINC24065-v1, LINC24065-v2, LINC24065-v3 and LINC24065-v4) that were a result of alternative splicing from 18 exons. LINC24065-v1 and LINC24065-v2 showed tissue-specific expression patterns in adultbovine tissues, and LINC24065-v3 and LINC24065-v4 were detected in all eight analysed tissues (heart, liver, spleen, lung, kidney, skeletal muscle, adipose and brain). Using single-nucleotide polymorphism (SNP)-based method, LINC24065 was identified to have monoallelic expression in adult tissues, suggesting that it is imprinted in cows. These results provide a foundation for further investigation about whether LINC24065 plays a role in regulating imprinting of the DLK1–DIO3 domain.

Genome-wide gene expression patterns in dikaryon of the basidiomycete fungus Pleurotus ostreatus

Abstract Dikarya is a subkingdom of fungi that includes Ascomycota and Basidiomycota. The gene expression patterns of dikaryon are poorly understood. In this study, we bred a dikaryon DK13 × 3 by mating monokaryons MK13 and MK3, which were from the basidiospores of Pleurotus ostreatus TD300. Using RNA-Seq, we obtained the transcriptomes of the three strains. We found that the total transcript numbers in the transcriptomes of the three strains were all more than ten thousand, and the expression profile in DK13 × 3 was more similar to MK13 than MK3. However, the genes involved in macromolecule utilization, cellular material synthesis, stress-resistance and signal transduction were much more up-regulated in the dikaryon than its constituent monokaryons. All possible modes of differential gene expression, when compared to constituent monokaryons, including the presence/absence variation, and additivity/nonadditivity gene expression in the dikaryon may contribute to heterosis. By sequencing the urease gene poure sequences and mRNA sequences, we identified the monoallelic expression of the poure gene in the dikaryon, and its transcript was from the parental monokaryon MK13. Furthermore, we discovered RNA editing in the poure gene mRNA of the three strains. These results suggest that the gene expression patterns in dikaryons should be similar to that of diploids during vegetative growth.