In the PNAS Early Edition this week, a trio of researchers at the University of Texas, Austin, reports their investigation of double-strand break repairs in the chloroplast genome of Arabidopsis. They've developed an inducible system in the plant that "employs a psbA intron endonuclease from Chlamydomonas, I-CreII, that is targeted to the chloroplast using the rbcS1 transit peptide." Using this, the team found an "alternative DSB repair pathways in the Arabidopsis chloroplast that resemble the nuclear, microhomology-mediated and nonhomologous end joining pathways, in terms of the homology requirement." The authors suggest that their work suggests that "an evolutionary relationship may exist between the repeat structure of the genome and the organelle's ability to repair broken chromosomes."
An international research team shows that "22-nucleotide RNAs trigger secondary siRNA biogenesis in plants." Using a bioinformatics-based approach, the investigators found that "secondary siRNA triggers are miRNAs and transacting siRNAs of 22 nt, rather than the more typical 21-nt length." In addition, they show that miR173 and miR828 "are effective as triggers only if expressed in a 22-nt form," while "increasing the length of miR319 from 21 to 22 nt converts it to an siRNA trigger."
Luís Amaral and colleagues at Northwestern University discuss a "physically grounded approach for estimating gene expression from microarray data" in PNAS this week. Their method, the team writes, "separately model[s] the noises specific to sample amplification, hybridization, and fluorescence detection, combining these into a parsimonious description of the variability sources in a microarray experiment." Amaral et al. suggest that their approach is " broadly applicable to other molecular biology technologies," beyond gene-expression microarray analysis.
Also in PNAS this week, investigators at the University of Hawaii and their colleagues describe their RNAi screen for telomerase reverse transcriptase transcriptional regulators and report their discovery that "HIF1α as critical for telomerase function in murine embryonic stem cells." HIF1α — or hypoxia inducible factor 1 alpha — "may have a physiologically relevant role in maintenance of functional levels of telomerase in stem cells," the authors suggest.