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RNA localization in prokaryotes: Where, when, how, and why.
Wiley Interdiscip Rev RNA
March 2021
Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
Only recently has it been recognized that the transcriptome of bacteria and archaea can be spatiotemporally regulated. All types of prokaryotic transcripts-rRNAs, tRNAs, mRNAs, and regulatory RNAs-may acquire specific localization and these patterns can be temporally regulated. In some cases bacterial RNAs reside in the vicinity of the transcription site, but in many others, transcripts show distinct localizations to the cytoplasm, the inner membrane, or the pole of rod-shaped species.
View Article and Find Full Text PDFZipSeq: barcoding for real-time mapping of single cell transcriptomes.
Nat Methods
August 2020
Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns.
View Article and Find Full Text PDFMechanisms and consequences of subcellular RNA localization across diverse cell types.
Traffic
June 2020
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
Essentially all cells contain a variety of spatially restricted regions that are important for carrying out specialized functions. Often, these regions contain specialized transcriptomes that facilitate these functions by providing transcripts for localized translation. These transcripts play a functional role in maintaining cell physiology by enabling a quick response to changes in the cellular environment.
View Article and Find Full Text PDFPum2 Shapes the Transcriptome in Developing Axons through Retention of Target mRNAs in the Cell Body.
Neuron
December 2019
The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA. Electronic address:
Localized protein synthesis is fundamental for neuronal development, maintenance, and function. Transcriptomes in axons and soma are distinct, but the mechanisms governing the composition of axonal transcriptomes and their developmental regulation are only partially understood. We found that the binding motif for the RNA-binding proteins Pumilio 1 and 2 (Pum1 and Pum2) is underrepresented in transcriptomes of developing axons.
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