Time, dose and ataxia telangiectasia mutated (ATM) status dependency of coding and noncoding RNA expression after ionizing radiation exposure.

Studies of gene expression have proved important in defining the molecular mechanisms of radiation action and identifying biomarkers of ionizing radiation exposure and susceptibility. The full transcriptional response to radiation is very complex since it also involves epigenetic mechanisms triggered by radiation exposure such as modifications of expression of noncoding RNA such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) that have not been fully characterized. To improve our understanding of the transcriptional response to radiation, we simultaneously monitored the expression of ten protein-coding genes, as well as 19 miRNAs and 3 lncRNAs in a time- and dose-dependent manner in stimulated human T lymphocytes obtained from two healthy donors (C1 and C2) and one patient with ataxia telangiectasia (AT), which is a well characterized radiosensitivity disorder. After 2 Gy X irradiation, expression levels were monitored at time points ranging from 15 min up to 24 h postirradiation. The majority of genes investigated responded rapidly to radiation exposure, with the peak up-regulation (CDKN1A, SESN1, ATF3, MDM2, PUMA and GADD45A) or down-regulation (CCNB1) occurring 2-3 h postirradiation, while DDB2, FDXR and CCNG1 responded with slower kinetics reaching a peak of expression between 5 and 24 h. A significant modification of expression after radiation exposure was observed for miR-34a-5p and miR-182-5p, with an up-regulation occurring at late time points reaching two to threefold at 24 h. Differences between two donors in miR-182-5p response to radiation were detected: for C2, up-regulation reached a plateau-phase around 5 Gy, while for C1, up-regulation was at its maximum around 3 Gy and then decreased at higher doses. Among the three lncRNAs studied, TP53TG1 demonstrated a weak up-regulation, reaching a maximum of 1.5-fold at 24 h after radiation exposure. Conversely, FAS-AS1 was up-regulated up to fivefold by 5 Gy irradiation. Our results indicate that expression of the majority of protein-coding genes allows discrimination of the AT from healthy donors when analyzed at 2 h. However, differences in expression between AT and healthy donors are no longer detectable 24 h postirradiation although, interestingly, linear dose responses for some of the genes studied are obtained at this time point. Furthermore, our study shows that miRNAs miR-34a-5p and miR-182-5p are responsive to radiation exposure in a dose- and time-dependent manner. Additionally, to the best of our knowledge, this is the first study to report that FAS-AS1 lncRNA is up-regulated by radiation exposure in an ATM-dependent fashion in human T lymphocytes.

Complete genome sequence and analyses of the subgenomic RNAs of sweet potato chlorotic stunt virus reveal several new features for the genus Crinivirus.

The complete nucleotide sequences of genomic RNA1 (9,407 nucleotides [nt]) and RNA2 (8,223 nt) of Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae) were determined, revealing that SPCSV possesses the second largest identified positive-strand single-stranded RNA genome among plant viruses after Citrus tristeza virus. RNA1 contains two overlapping open reading frames (ORFs) that encode the replication module, consisting of the putative papain-like cysteine proteinase, methyltransferase, helicase, and polymerase domains. RNA2 contains the Closteroviridae hallmark gene array represented by a heat shock protein homologue (Hsp70h), a protein of 50 to 60 kDa depending on the virus, the major coat protein, and a divergent copy of the coat protein. This grouping resembles the genome organization of Lettuce infectious yellows virus (LIYV), the only other crinivirus for which the whole genomic sequence is available. However, in striking contrast to LIYV, the two genomic RNAs of SPCSV contained nearly identical 208-nt-long 3' terminal sequences, and the ORF for a putative small hydrophobic protein present in LIYV RNA2 was found at a novel position in SPCSV RNA1. Furthermore, unlike any other plant or animal virus, SPCSV carried an ORF for a putative RNase III-like protein (ORF2 on RNA1). Several subgenomic RNAs (sgRNAs) were detected in SPCSV-infected plants, indicating that the sgRNAs formed from RNA1 accumulated earlier in infection than those of RNA2. The 5' ends of seven sgRNAs were cloned and sequenced by an approach that provided compelling evidence that the sgRNAs are capped in infected plants, a novel finding for members of the Closteroviridae.

Functional analysis of the Saccharomyces cerevisiae YFR021w/YGR223c/YPL100w ORF family suggests relations to mitochondrial/peroxisomal functions and amino acid signalling pathways.

Saccharomyces cerevisiae YFR021w, YGR223c and YPL100w are paralogous ORFs of unknown function. Phenotypic analysis of overexpression, single-, double- and triple-ORF deletion strains under various growth conditions indicated mitochondria-related functions for all three ORFs. Two-hybrid screens of a yeast genomic library identified potentially interacting proteins for the three ORFs. Among these, the transcriptional activator Rtg3p interacted with both Yfr021wp and Ypl100wp and both ORF single deletions reduced the constitutive expression of the RTG-regulated CIT2 and DLD3 genes and caused typical retrograde response of CIT2 and DLD3 under growth conditions requiring functional mitochondria, indicating that YFR021w and YPL100w are also involved in unidentified mitochondrial functions. Ptr3p, a component of the amino acid sensor Ssy1p/Ptr3p, was also found as a two-hybrid interactant of Yfr021wp. Of the three single-ORF deletions, ypl100w Delta exhibited ptr3 Delta-similar phenotypes. These findings, combined with the fact that RTG-dependent expression is modulated by specific amino acids, suggested possible relations of Yfr021wp and Ypl100wp to amino acid signalling pathways. Under most conditions examined, the effects of the single- and double-ORF deletions indicated that YFR021w, YPL100w and YGR223c are not parts of the same pathway. We found no unique phenotype attributed to the deletion of YGR223c. However, its function interferes with the function of the other two ORFs, as revealed by the effects of double- and triple-ORF deletions.