Sequencing-guided design of genetically encoded small RNAs targeting CAG repeats for selective inhibition of mutant huntingtin.

Huntington's disease (HD) is an incurable neurodegenerative disorder caused by genetic expansion of a CAG repeat sequence in one allele of the huntingtin (HTT) gene. Reducing expression of the mutant HTT (mutHTT) protein has remained a clear therapeutic goal, but reduction of wild-type HTT (wtHTT) is undesirable, as it compromises gene function and potential therapeutic efficacy. One promising allele-selective approach involves targeting the CAG repeat expansion with steric binding small RNAs bearing central mismatches. However, successful genetic encoding requires consistent placement of mismatches to the target within the small RNA guide sequence, which involves 5' processing precision by cellular enzymes. Here, we used small RNA sequencing (RNA-seq) to monitor the processing precision of a limited set of CAG repeat-targeted small RNAs expressed from multiple scaffold contexts. Small RNA-seq identified expression constructs with high-guide strand 5' processing precision and promising allele-selective inhibition of mutHTT. Transcriptome-wide mRNA-seq also identified an allele-selective small RNA with a favorable off-target profile. These results support continued investigation and optimization of genetically encoded repeat-targeted small RNAs for allele-selective HD gene therapy and underscore the value of sequencing methods to balance specificity with allele selectivity during the design and selection process.

Substrate promiscuity of Dicer toward precursors of the let-7 family and their 3'-end modifications.

The human let-7 miRNA family consists of thirteen members that play critical roles in many biological processes, including development timing and tumor suppression, and their levels are disrupted in several diseases. Dicer is the endoribonuclease responsible for processing the precursor miRNA (pre-miRNA) to yield the mature miRNA, and thereby plays a crucial role in controlling the cellular levels of let-7 miRNAs. It is well established that the sequence and structural features of pre-miRNA hairpins such as the 5'-phosphate, the apical loop, and the 2-nt 3'-overhang are important for the processing activity of Dicer. Exceptionally, nine precursors of the let-7 family (pre-let-7) contain a 1-nt 3'-overhang and get mono-uridylated in vivo, presumably to allow efficient processing by Dicer. Pre-let-7 are also oligo-uridylated in vivo to promote their degradation and likely prevent their efficient processing by Dicer. In this study, we systematically investigated the impact of sequence and structural features of all human let-7 pre-miRNAs, including their 3'-end modifications, on Dicer binding and processing. Through the combination of SHAPE structural probing, in vitro binding and kinetic studies using purified human Dicer, we show that despite structural discrepancies among pre-let-7 RNAs, Dicer exhibits remarkable promiscuity in binding and cleaving these substrates. Moreover, the 1- or 2-nt 3'-overhang, 3'-mono-uridylation, and 3'-oligo-uridylation of pre-let-7 substrates appear to have little effect on Dicer binding and cleavage rates. Thus, this study extends current knowledge regarding the broad substrate specificity of Dicer and provides novel insight regarding the effect of 3'-modifications on binding and cleavage by Dicer.

Linking the Electrical Conductivity and Non-Stoichiometry of Thin Film Ce1-xZrxO2-δ by a Resonant Nanobalance Approach.

Bulk ceria-zirconia solid solutions (Ce1-xZrxO2-δ, CZO) are highly suited for application as oxygen storage materials in automotive three-way catalytic converters (TWC) due to the high levels of achievable oxygen non-stoichiometry δ. In thin film CZO, the oxygen storage properties are expected to be further enhanced. The present study addresses this aspect. CZO thin films with 0 ≤ x ≤ 1 were investigated. A unique nano-thermogravimetric method for thin films that is based on the resonant nanobalance approach for high-temperature characterization of oxygen non-stoichiometry in CZO was implemented. The high-temperature electrical conductivity and the non-stoichiometry δ of CZO were measured under oxygen partial pressures pO2 in the range of 10-24-0.2 bar. Markedly enhanced reducibility and electronic conductivity of CeO2-ZrO2 as compared to CeO2-δ and ZrO2 were observed. A comparison of temperature- and pO2-dependences of the non-stoichiometry of thin films with literature data for bulk Ce1-xZrxO2-δ shows enhanced reducibility in the former. The maximum conductivity was found for Ce0.8Zr0.2O2-δ, whereas Ce0.5Zr0.5O2-δ showed the highest non-stoichiometry, yielding δ = 0.16 at 900 °C and pO2 of 10-14 bar. The defect interactions in Ce1-xZrxO2-δ are analyzed in the framework of defect models for ceria and zirconia.