Massively parallel sequencing of millions of <30-nt class="search-term-highlight">RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (βTC-3) reveals that ∼50% of the mature miRNAs representing mostly the mmu-let-7 family display internal insertion/deletions and substitutions when compared to precursor miRNA and the mouse genome reference sequences.

Approximately, 12%–20% of species associated with mmu-let-7 populations exhibit sequence discrepancies that are dramatically reduced in nucleotides 3–7 (5′-seed) and 10–15 (cleavage and anchor sites). This observation is inconsistent with sequencing error and leads us to propose that the changes arise predominantly from post-transcriptional RNA-editing activity operating on miRNA:target mRNA complexes.

Internal nucleotide modifications are most enriched at the ninth nucleotide position. A common ninth base edit of U-to-G results in a significant increase in stability of down-regulated let-7a targets in inhibin-deficient mice (Inha^−/−). An excess of U-insertions (14.8%) over U-deletions (1.5%) and the presence of cleaved intermediates suggest that a mammalian TUTase (terminal uridylyl transferase) mediated dUTP-dependent U-insertion/U-deletion cycle may be a possible mechanism.

We speculate that mRNA target site-directed editing of mmu-let-7a duplex-bulges stabilizes “loose” miRNA:mRNA target associations and functions to expand the target repertoire and/or enhance mRNA decay over translational repression. Our results also demonstrate that the systematic study of sequence variation within specific RNA classes in a given cell type from millions of sequences generated by next-generation sequencing (NGS) technologies (“intranomics”) can be used broadly to infer functional constraints on specific parts of completely uncharacterized RNAs.

Source - http://genome.cshlp.org/content/18/10/1571.abstract?sid=40206306-7c2e-4b18-96b3-8319fa594a4b

We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp.

genome sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including four members of a ncRNA family in the asexual blood stage. These transcripts represent novel structured ncRNAs in P. falciparumand are not represented in any RNA databases.

We provide supporting evidence for purifying selection acting on the experimentally verified ncRNAs by comparing the nucleotide substitutions in the predicted ncRNA candidate structures in P. falciparum with the closely related chimp malaria parasite P. reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism’s life cycle.

Source - http://genome.cshlp.org/content/18/2/281.abstract?sid=40206306-7c2e-4b18-96b3-8319fa594a4b

We have conducted a survey of RNA editing in human brain by comparing sequences of clones from a human brain cDNA library to the reference human genome sequence and to genomic DNA from the same individual. In the RNA sample from which the library was constructed, 01:2000 nucleotides were edited out of >3 Mb surveyed. All edits were adenosine to inosine (A→I) and were predominantly in intronic and in intergenic RNAs.

No edits were found in translated exons and few in untranslated exons. Most edits were in high-copy-number repeats, usually Alus. Analysis of the genome in the vicinity of edited sequences strongly supports the idea that formation of intramolecular double-stranded RNAwith an inverted copy underlies most A→I editing.

The likelihood of editing is increased by the presence of two inverted copies of a sequence within the same intron, proximity of the two sequences to each other (preferably within 2 kb), and by a high density of inverted copies in the vicinity. Editing exhibits sequence preferences and is less likely at an adenosine 3′ to a guanosine and more likely at an adenosine 5′ to a guanosine. Simulation by BLAST alignment of the double-stranded RNA molecules that underlie known edits indicates that there is a greater likelihood of A→I editing at A:C mismatches than editing at other mismatches or at A:U matches. However, because A:U matches in double-stranded RNA are more common than all mismatches, overall the likely effect of editing is to increase the number of mismatches in double-stranded RNA.

Source - http://genome.cshlp.org/content/14/12/2379.abstract?sid=4be18750-d5af-4896-b05e-eeb49c944425

One dose of vaccine may be effective to protect infants and children and reduce transmission of the H1N1 virus, according to a study in JAMA, just published online because of its public health implications. The study will appear in the January 6 print edition of the journal.

Initial reports of 2009 influenza A(H1N1) infection in many countries have largely involved children, especially those attending school. Reports have also indicated high hospitalization rates of children younger than 5 years of age in the current pandemic, according to background information provided by the authors. "The Advisory Committee on Immunization Practices also currently recommends that infants and children aged 9 years or younger receive two doses of H1N1 influenza vaccine at least 21 days apart, based on existing experience with seasonal trivalent influenza vaccines in this age group."

Terry Nolan, M.B.B.S., Ph.D., from the University of Melbourne, Australia and colleagues assessed the effectiveness and safety of two doses of a 2009 influenza A(H1N1) vaccine in 370 healthy infants and children ages six-months to less than 9 years living in Australia. The children were randomized into groups that received a two-injection regimen 21 days apart in doses of either 15-micrograms or 30-micrograms of the vaccine.

"Following the first dose of vaccine, antibody titers of 1:40 or greater were observed in 161 of 174 infants and children in the 15-microgram group (92.5 percent) and in 168 of 172 infants and children in the 30 microgram group (97.7 percent)," the authors report. "All participants demonstrated antibody titers of 1:40 or greater after the second vaccine dose," [which means that every child achieved an antibody level considered high enough to protect against the H1N1 virus]. The researchers note that the majority of adverse reactions to the vaccine were mild to moderate in severity. The immune responses to the vaccine were strong regardless of age, baseline antibody status, or whether the child had received a seasonal influenza vaccination prior to this study.

"Our findings suggest that a single dose 15-microgram dose vaccine regimen may be effective and well tolerated in children, and may have positive implications for disease protection and reduced transmission of pandemic H1N1 in the wider population," the authors conclude.

Editor's Note: This study was sponsored by CSL Limited with funding from the Australian government's Department of Health and Ageing.

Editorial: 2009 Influenza A(H1N1) Vaccines for Children

"Even though influenza activity has decreased in recent weeks in some states, there remains the possibility of continued activity through the traditional winter influenza season and the prospect of normal winter circulation of seasonal influenza viruses," and the authors of the editorial note that this pandemic has highlighted the fact the children have no measurable immunity against the H1N1 virus.

Anthony E. Fiore, M.D., M.P.H., from the National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, and Kathleen M. Neuzil, M.D., M.P.H., of PATH, Seattle, write that children have been a primary source of illness in community outbreaks of pandemic influenza with more severe complications, hospitalizations and deaths from this virus than what is usually seen for seasonal influenza.

The editorial authors urge caution at interpretation of the results of the study. "The hemagglutinin antigen content administered to six-month-old infants and children younger than 3 years in this study was 15-micrograms, the equivalent of two doses of the 7.5-microgram vaccine currently licensed in the United States for this age group."

"The immunogenicity data presented by Nolan et al suggest that at least some children will be protected after a single 15-microgram dose of the H1N1 vaccine used in this study, but the findings cannot be generalized with confidence to all children, epidemiological circumstances in every country, or different vaccine formulations."

In conclusion, the authors write: "… it remains prudent to continue to follow current recommendations for administering two doses to infants and young children while awaiting definitive vaccine effectiveness data."