Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

TL;DR: The results indicate that C-FISH potentially enables tens of thousands of different transcripts or genomic loci to be precisely profiled in individual cells in situ.

TL;DR: The results indicate that the variability in viral gene expression and replication are not due to defective genomes but due to host cell heterogeneity, and demonstrate the importance of cell-to-cell variability measurements for understanding transcription and replication in viral infections.

TL;DR: Hi-M was used to study chromosome organization during the awakening of the zygotic genome in intact Drosophila embryos and was able to unveil the changes in 3D chromatin organization occurring upon transcriptional activation and homologous chromosome un-pairing.

TL;DR: TriBE (targets of RNA binding proteins identified by editing), RNA tagging, and STAMP (surveying targets by APOBEC-mediated profiling) are new genetic tools useful for the study of post-transcriptional regulation and RBP identification as discussed by the authors .

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.