In a paper published online in advance in Genome Biology this week, Harvard Medical School's Kate Broadbent and her colleagues report their use of "high-resolution DNA tiling microarrays to survey transcriptional activity across 22.6 [percent] of the P. [Plasmodium] falciparum strain 3D7 genome." Among other things, the team identified and characterized a family of 22 telomere-associated long, non-coding RNAs. Broadbent et al. say that this family of lncRNA telomere-associated repetitive element transcripts, or lncRNA-TAREs, along with "other promising lncRNA candidates may provide mechanistic insight into P. falciparum transcriptional regulation."
In another Genome Biology advance online publication, the University of Pennsylvania's Daniel Simola and Junhyong Kim present Sniper, a "novel multi-locus Bayesian probabilistic model and a computationally efficient algorithm that explicitly incorporates sequence reads that map to multiple genomic loci" for the purpose of next-generation sequencing-based SNP discovery. Simola and Kim say that Sniper "fully accounts for sequencing error, template bias, and multi-locus SNP combinations, maintaining high sensitivity and specificity under a broad range of conditions."
The University of California, Los Angeles' Steven Jacobsen and his colleagues this week show that 5-hydroxymethylcytosine, or 5hmC, "may be targeted to certain genomic regions based both on gene expression and sequence composition." In generating a genome-wide map of 5hmC in human embryonic stem cells using hmeDIP-seq, the team "found that 5hmC is enriched in enhancers as well as in gene bodies," and that it "was also enriched in … protein-DNA interaction sites."
Researchers at the Chinese Academy of Sciences report in a Genome Biology paper published online on the "differences in composition and expression profile of miRNAs between developing pollen and sporophytes," to which "novel and non-conserved known miRNAs [are] the main contributors." The team pyrosequenced small RNA populations from Oryza sativa "uninucleate microspores to tricellular pollen and control sporophytic tissues at the genome-wide level" and found 202 miRNAs expressed in developing pollen, 103 of which were enriched. Of the novel miRNAs it identified, the team says that more than half "displayed pollen- or stage-specific expression."