On May 4, 2022, Dr. Rasim Barutcu from the university of Toronto presented how he, co-first author Mingkun Wu and their colleagues applied APEX labeling to survey the distribution of RNA transcripts in the cell nucleus. The work led in Dr. Benjamin Blencowe’s lab at the University of Toronto was recently reported in a Molecular Cell article: https://doi.org/10.1016/j.molcel.2021.12.010
Rasim explained how they used markers for several membrane-less organelles to label transcripts located in specific locations in the nucleus, including nuclear speckles, cajal bodies, PML bodies, the nucleolus, Sam68 bodies, histone locus bodies and the lamina. Labeled transcripts were then identified using RNA-Seq and select candidates were cross-validated using orthologous methods such as FISH. This method allowed them to find hundreds of protein-coding and lncRNA transcripts that are enriched in nuclear speckles and the nuclear lamina.
Interestingly, while both speckle- and lamina-associated transcripts displayed clear evidence of intron retention, retained introns associated with the speckles are GC-rich, short, are often found in genes that code for proteins involved in RNA processing and cell cycle regulation, and many are “detained introns”, a class of introns that can be spliced out and exported out of the nucleus upon specific signaling. Sets of retained introns in the speckles also show clear periodicities that are in phase with the cell cycle.
The work brings some very interesting insight on the identity and the characteristics of transcripts that are regionally regulated in the nucleus. It also raises a number of questions that will require further investigation. For example, how is the regulation of these regionally enriched transcripts important for the cell, in particular for the cell cycle?
A recording of Rasim’s presentation is available for all to enjoy from the ISCBacademy channel: https://youtu.be/lrXiGJN74h4