PubMed · 14970453
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Richard A Shimkets. 2004. Technical considerations in quantitating gene expression.. https://doi.org/10.1385/1-59259-751-3%3A1
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STALARD (selective target amplification for low-abundance RNA detection) enables isoform-level quantification of low-abundance RNAs using conventional laboratory equipment. Here, we describe steps for RNA isolation, primer design, reverse transcription, selective target amplification, and downstream analysis. The protocol couples selective pre-amplification with a quantitative reverse-transcription PCR (RT-qPCR) readout and optional nanopore sequencing. Using 1 μg input RNA and 12 pre-amplification cycles, STALARD reduces Cq values by approximately 10-12 cycles, bringing the target into a reliably quantifiable range. For complete details on the use and execution of this protocol, please refer to Jeong et al.1.
Mutations in BRCA1 predominantly lead to elevated risks of breast and ovarian cancers. In contrast to the tissue-specific nature of BRCA1tumors, the normal BRCA1 gene product functions in diverse nuclear events including transcription, DNA repair, and DNA damage checkpoint. Recent findings of physical and functional associations between BRCA1 and the RNA polymerase II (RNAPII)-dependent transcription machinery may shed some light on this longstanding paradox of BRCA1 biology. Eukaryotic gene expression is now known to be a continuous process, whereby each step is physically and functionally connected to the next. In particular, RNAPII plays a pivotal role in coordinating transcription with various pre-mRNA processing events and stress response. Interestingly, BRCA1 preferentially interacts with the processive form of RNAPII and proteins that regulate RNAPII activity and movement during transcription elongation. In response to DNA damage, BRCA1 dissociates from RNAPII and localizes to DNA damage sites. We propose that BRCA1 may coordinate multiple steps in gene expression, including transcription initiation, elongation, and pre-mRNA processing via its interactions with the transcription machinery at selected gene loci. The same BRCA1-associated transcription apparatus may serve as a sensor for stress signals and facilitate the transition from a transcription state to checkpoint/DNA repair state. Such a coordinating role of BRCA1 in gene expression may ensure the appropriate quantity and quality of the mature transcripts for certain breast and ovarian cancer-related genes, as well as the genetic integrity of the breast and ovary tissues.
Today, plant biotechnology relies on two processes for delivery and expression of heterologous genes in plants: stable genetic transformation and transient infection with viral vectors. Although much faster, the transient route until recently was limited because of virus' low infectivity and its inability to carry average-size or larger transgenes. A recently developed new generation transfection technology overcomes these limitations by relying on Agrobacterium as an infective systemic agent that delivers viral replicons. This improved process is being used to simultaneously start transient gene amplification and high-level expression in all mature leaves of a plant, and such a transfection can be done on an industrial scale. This eclectic technology, called 'magnifection', combines advantages of three biological systems: vector efficiency and efficient systemic DNA delivery of Agrobacterium, speed and expression level/yield of a plant RNA virus, as well as posttranslational capabilities and low production costs of a plant. The proposed process allows for industrial production that does not require genetic modification of plants, that is much faster than previous methods, and that is biologically safe. Numerous applications in the area of vaccine manufacturing are being discussed.