Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L.

Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play crucial roles in gene expression and regulation. However, the NATs in Cannabis Sativa L., a widely economic and medicinal plant rich in cannabinoids remain unknown. In this study, we comprehensively predicted C. sativa NATs genome-wide using strand-specific RNA sequencing (ssRNA-Seq) data, and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). Consequently, a total of 307 NATs were predicted in C. sativa, including 104 cis- and 203 trans- NATs. Functional enrichment analysis demonstrated the potential involvement of the C. sativa NATs in DNA polymerase activity, RNA-DNA hybrid ribonuclease activity, and nucleic acid binding. Finally, 18 cis- and 376 trans- NAT-ST pairs were predicted to produce 621 cis- and 5,679 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.

Critical evaluation of quantification methods for oligonucleotides formulated in lipid nanoparticles.

There is a very large variety in the types of nanoparticulate lipid formulations for oligonucleotides, and remarkably, also a very large heterogeneity in the methods that are used for analyzing oligonucleotide load, encapsulation efficiency and oligonucleotide release. Furthermore, a literature survey showed that the extent to which these procedures are reported in scientific literature varies greatly, with some of them not even reporting any quantification at all. This greatly hampers the reproducibility of nanoparticle preparation between different researchers and between different laboratories, which slows down the clinical translation of such nanomedicines. In this work, a standardized extraction method from liposomes is proposed, in which potential contaminants from the carrier are removed by a simple extraction of the oligonucleotides. These extracts were then analyzed with seven commonly used methods for oligonucleotide quantification, including several absorbance based methods and the most commonly applied dye binding assay. Strikingly, differences in absolute values up to fourfold were found when the same sample was analyzed using different methods which should be taken into consideration when reports using different methods are compared. Furthermore, these results indicate that the most commonly applied method, the dye binding assay, may -without adaptations- not be suitable for short oligonucleotides like siRNAs. The found differences in quantification methods as described here underscore the need for proper documentation of methods to correctly interpret published results, which -with regard to oligonucleotide analysis- is currently lacking in many reports.

Codelivery of DNA and siRNA via arginine-rich PEI-based polyplexes.

In this study, we formulated polyplexes with different compositions for codelivery of DNA and small-interfering RNA (siRNA). Since DNA and siRNA have distinctive and complementary morphological characteristics (DNA is long and winding and siRNA is short and rigid), we hypothesized that their codelivery using polyplex would enhance each other's transfection. To test this hypothesis, cationic polymer branched polyethylenimine (bPEI) as a standard transfecting agent and its derivative arginine-rich oligopeptide-grafted bPEI modified with polyethylene glycol (P(SiDAAr)5P3), synthesized in our laboratory, were used as carriers for transfection. Polyplexes at different nucleic acid to polymer weight ratios were characterized for transfection in breast cancer sensitive (MCF-7) and resistant (MCF-7/Adr) cell lines. Gene silencing effect of polyplexes was determined in MDA-MB-231-luc-D3H2LN cell line. The results demonstrated that the polyplexes formed with derivative P(SiDAAr)5P3 show significantly lower toxicity compared to polyplexes formed using bPEI. Further, codelivery resulted in 20-fold higher DNA transfection and 2-fold higher siRNA transfection as compared to the respective single nucleotide delivery. DNA transfection was ∼100-fold lower in resistant MCF-7/Adr cells than in sensitive MCF-7 cells. Confocal imaging and flow cytometry data demonstrated that enhanced transfection does not solely depend on DNA's cellular uptake, suggesting that other mechanisms contribute to increased transfection. DNA-co-siRNA delivery could be a promising therapeutic approach to achieve synergistic effects because it can simultaneously target and interfere with multiple regulatory levels in a cell to halt and reverse disease progression.

An interview with Hakim Djaballah, Ph.D. Interview by Vicki Glaser.

Dr. Hakim Djaballah is Director of the High-Throughput Screening (HTS) Core Facility at Memorial Sloan-Kettering Cancer Center (MSKCC), in New York City. He has several years of industrial experience in preclinical drug discovery, working in both pharmaceutical and biotechnology companies. He has been involved in developing and screening antibacterials, antivirals, and antifungals, as well as identifying targets in various therapeutic areas, including diabetes, central nervous system, cardiovascular system, oncology, and inflammation. He obtained his B.S. in biochemistry with biotechnology from the University of Birmingham and completed his Ph.D. in biochemistry at the University of Leicester, both in England. He was recruited to MSKCC in 2003 to set up and direct the HTS Core Facility, a drug discovery laboratory involved in both chemical and RNAi screening. Dr. Djaballah was the recipient of the 2007 Robots and Vision User Recognition Award. Sponsored by the Robotic Industries Association and the Automated Imaging Association, the award is presented every 2 years to individuals in institutions that have successfully implemented robots in their work.

Identification of small RNAs in late developmental stage of rice anthers.

Small RNAs including microRNA (miRNA) and small interfering RNA (siRNA) are known as repressors of gene expression. There are many plant proteins involved in small RNA-mediated gene silencing, such as Dicer ribonucleases and RNA-dependent RNA polymerases. However, most of these proteins have been reported to be absent in the late developmental stage of the plant male gamete, pollen. In order to clarify the existence of the small RNAs during maturation of pollen, we cloned and sequenced small RNAs from rice anthers including tricellular pollen. From fifty six candidates of small RNAs, we identified two known miRNAs (miR166 and miR167), eight potential miRNAs, and ten putative heterochromatic siRNAs (hc-siRNAs). RNA gel blot analyses clearly showed that miR166 and miR167 were accumulated in the uninuclear pollen stage of anther development and remained until the tricellular pollen stage. Our cloning and RNA gel blot analyses of small RNAs led us to propose a possible function of small RNA-mediated gene regulation for the development of male gametes in rice.