Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

TL;DR: This article outlines several promising directions in neuroscience that could be integrated with single-cell RNA sequencing, including neurodevelopment, the identification of novel brain microstructures, cognition and behavior, neuronal cell positioning, molecules and cells related to advanced brain functions, sleep-wake cycles/circadian rhythms, and computational modeling of brain function.

TL;DR: Researchers developed a fluorescence imaging method to visualize nascent RNA in cells using 4-thiouridine as a metabolic tag and DNA-templated oxidative amination, enabling selective labeling of target mRNAs in HeLa cells.

TL;DR: The fluorescent labeling strategy of chromatin in live cells will be summarized, followed by a systematic comparison of live cell imaging instrumentation and practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation purposes are given.

TL;DR: Proximity RNA-seq is introduced, which identifies colocalization preferences for pairs or groups of nascent and fully transcribed RNAs in the nucleus, based on massive-throughput RNA barcoding of subnuclear particles in water-in-oil emulsion droplets, followed by cDNA sequencing.

TL;DR: In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.

TL;DR: Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together.

TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.

TL;DR: It is shown that RNA velocity—the time derivative of the gene expression state—can be directly estimated by distinguishing between unspliced and spliced mRNAs in common single-cell RNA sequencing protocols, and expected to greatly aid the analysis of developmental lineages and cellular dynamics, particularly in humans.