Genomic analysis of RNA localization

Abstract

The localization of mRNAs to specific subcellular sites is widespread, allowing cells to spatially restrict and regulate protein production, and playing important roles in development and cellular physiology. This process has been studied in mechanistic detail for several RNAs. However, the generality or specificity of RNA localization systems and mechanisms that impact the many thousands of localized mRNAs has been difficult to assess. In this review, we discuss the current state of the field in determining which RNAs localize, which RNA sequences mediate localization, the protein factors involved, and the biological implications of localization. For each question, we examine prominent systems and techniques that are used to study individual messages, highlight recent genome-wide studies of RNA localization, and discuss the potential for adapting other high-throughput approaches to the study of localization.

Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs

“…Other recent studies are also beginning to imply similar levels of localization in other organisms (Taliaferro et al 2014;Weil 2014;Jambor et al 2015;Liao et al 2015). However, functional studies that validate the relative importance and underlying mechanisms behind the majority of these localization events are lagging behind.…”

Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application

“…These types of methods can be based on protein immunoprecipitation, intact organelle purification, or partitioning through sucrose gradients [173]. Then, RNA-seq (biochemical cell fractionation combined with RNA-seq, CeFra-seq) was performed to detect specific RNAs at the transcriptome scale [83]. Fractionation-based methods have high sensitivity for low-abundance transcripts due to aggregation across many cells; however, they are restricted by isolation protocols and the purity of resulting isolates, which possibly induce technical noise by contamination across fractions [24,174,175].…”

Neuronal messenger ribonucleoprotein transport follows an aging Lévy walk

“…The mRNP particles are exported from the nucleus to the cytoplasm to be translated into proteins. However, certain mRNA molecules are not immediately translated into proteins but are rather stored in a translationally repressed state and transported to specific regions inside a cell 1 , 2 . In neurons, about one-third of mRNA species are transported from the cell body to the dendrites and axons 3 and locally translated into proteins upon signal transduction 4 – 6 .…”