Project description:MiRNA expression profiling on 14.5 day old testis from sterile (PWD x B6)F1, (PWK x B6)F1 and fertile (B6 x PWD)F1 inter-subspecific hybrids were performed to study the genome wide variation in miRNA expression between different inter-subspecific hybrids during meiosis.
Project description:At critically short telomeres TERRA RNA-DNA hybrids become stabilized and drive homology-directed repair (HDR) to delay replicative senescence. However, even at long- and intermediate-length telomeres, not subject to HDR, transient TERRA RNA-DNA hybrids form, suggestive of additional roles. Here, we report that hybrids at telomeres prevent resection by the Exo1 nuclease when telomeres become non-functional. We employed the well-characterized cdc13-1 allele, where telomere resection can be induced in a temperature dependent manner, to demonstrate that ssDNA generation at telomeres is either prevented or augmented when RNA-DNA hybrids are stabilized or destabilized, respectively. The viability of cdc13-1 cells is affected by the presence or absence of hybrids accordingly. These results give insights into an additional role of TERRA at dysfunctional telomeres suggesting that it not only affects replicative senescence rates through HDR activation at critically short telomeres, but may also affect resection rates at intermediate length telomeres in pre-senescent cells.
Project description:MiRNA expression profiling on 14.5 day old testis from sterile (PWD x B6)F1, (PWK x B6)F1 and fertile (B6 x PWD)F1 inter-subspecific hybrids were performed to study the genome wide variation in miRNA expression between different inter-subspecific hybrids during meiosis. The total RNA (120 ng) samples were extracted from 14.5 days juvenile testes (pool of 4 samples), converted to cDNA using the Affymetrix 3 IVT Express Kit and hybridized to Affymetrix Mouse miRNA Gene 1.0ST GeneChips (core facility of the Institute of Molecular Genetics AS CR, Prague, Czech Rep.)
Project description:The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents and more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community.