Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation

Abstract

RNAs are trafficked and localized with exquisite precision inside the cell. Studies of candidate messenger RNAs have shown the vital importance of RNA subcellular location in development and cellular function. New sequencing-and imaging-based methods are providing complementary insights into subcellular localization of RNAs transcriptome-wide. APEX-seq and ribosome profiling as well as proximity-labeling approaches have revealed thousands of transcript isoforms are localized to distinct cytotopic locations, including locations that defy biochemical fractionation and hence were missed by prior studies. Sequences in the 3′ and 5′ untranslated regions (UTRs) serve as "zip codes" to direct transcripts to particular locales, and it is clear that intronic and retrotransposable sequences within transcripts have been co-opted by cells to control localization. Molecular motors, nuclear-to-cytosol RNA export, liquid-liquid phase separation, RNA modifications, and RNA structure dynamically shape the subcellular transcriptome. Location-based RNA regulation continues to pose new mysteries for the field, yet promises to reveal insights into fundamental cell biology and disease mechanisms.

Subcellular Transcriptomics and Proteomics: A Comparative Methods Review

“…The biotinylated RNA could then be affinity purified with streptavidin beads and sequenced. The APEX-Seq approach was used to generate an atlas of human RNA localization covering nine different subcellular niches and to probe the spatial organization of transcripts associated with translation initiation complexes as well as repressive RNA granules ( 18 , 331 ). This study unveiled the dynamic, varied, and stress type–dependent nature of stress granules.…”

“…Spatial proteomics and transcriptomics have often been reviewed independently with technical details covered in previous articles ( 18 , 19 , 20 ). Here, we outline and directly compare methods (summarized in Table 1 ) that interrogate the spatial transcriptomic and proteomic within subcellular compartments of cells, rather than spatial information at the tissue level, and suggest gaps in technology in need of further advancement.…”

“…, APEX) that covalently labels molecules in immediate proximity of the bait with a small and exogenous substrate. The substrate can then be purified along with the labeled molecules BioID has revealed novel organellar components of the Trypanosoma brucei , flies, and worms ( 295 , 302 , 304 , 308 ) and identifying novel proteins involved in hyperpolarization that are linked to neurodegenerative diseases ( 314 , 315 ) APEX-Seq identified stress type–dependent RNA interactions with stress granules ( 18 , 331 ) Lysed, in vivo labeling Untargeted, label organelle(s) of interest The table includes a short description about the principle of each method, examples of their biological insights or applications, and basic comparisons of the characteristics of the methods. …”

How Do Bacteria Maximize Their Cellular Assets?

“…Both approaches utilizing fluorescent in situ hybridization with complex probe sets [38] and RNA localization by fractionation and sequencing [39] revealed that most mRNAs encoding membrane proteins were preferentially positioned at the membrane. Moreover, mRNAs encoding cytoplasmic and polar proteins were largely distributed throughout these respective cellular regions [40]. It is known that the cis-acting sequence in the transcript serves as a ZIP code [41] or signal recognition particle [38] that can determine protein targeting in a particular region through RNA localization.…”

Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu

“…Furthermore, centrifugation-based techniques such as Grad-seq (gradient sequencing), CeFraSeq (cell fractionation sequencing) and R-DeeP (RNA-dependent proteins) exist, charting the global RNA-protein co-sedimentation landscape, the shuttling of RNA to subcellular fractions and the RNA-dependence of protein complexes, respectively [ 16 , 20 , 21 , 22 , 23 ]. Such approaches were recently summarized elsewhere [ 24 , 25 ] and are not reiterated in detail in the present review. Also, common molecular principles guiding lncRNA interaction with individual molecules (proteins, mRNAs and microRNAs) in the cytoplasm and nucleus have recently been reviewed [ 2 , 11 , 12 ].…”