Dataset Information

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.

SUBMITTER: Fazal FM

PROVIDER: S-EPMC7426137 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation.

Fazal Furqan M FM Chang Howard Y HY

Cold Spring Harbor symposia on quantitative biology 20190101

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 cytotop ...[more]

PMID: 32482897

Similar Datasets

Project description:The surging demand for commodity crops has led to rapid and severe agricultural frontier expansion globally and has put producing regions increasingly under pressure. However, knowledge about spatial patterns of agricultural frontier dynamics, their leading spatial determinants, and socio-ecological trade-offs is often lacking, hindering contextualized decision making towards more sustainable food systems. Here, we used inventory data to map frontier dynamics of avocado production, a cash crop of increasing importance in global diets, for Michoacán, Mexico, before and after the implementation of the North American Free Trade Agreement (NAFTA). We compiled a set of environmental, accessibility and social variables and identified the leading determinants of avocado frontier expansion and their interactions using extreme gradient boosting. We predicted potential expansion patterns and assessed their impacts on areas important for biodiversity conservation. Avocado frontiers expanded more than tenfold from 12,909 ha (1974) to 152,493 ha (2011), particularly after NAFTA. Annual precipitation, distance to settlements, and land tenure were key factors explaining avocado expansion. Under favorable climatic and accessibility conditions, most avocado expansion occurred on private lands. Contrary, under suboptimal conditions, most avocado expansion occurred on communal lands. Large areas suitable for further avocado expansion overlapped with priority sites for restoration, highlighting an imminent conflict between conservation and economic revenues. This is the first analysis of avocado frontier dynamics and their spatial determinants across a major production region and our results provide entry points to implement government-based strategies to support small-scale farmers, mostly those on communal lands, while trying to minimize the socio-environmental impacts of avocado production.Supplementary informationThe online version contains supplementary material available at 10.1007/s10113-022-01883-6.

Dataset Information

Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation.

Publications

Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets