Spatial organization of RNA polymerase II transcription in the nucleus

In eukaryotic cells, mRNA synthesis is carried out by large, multifunctiona l complexes that are also involved in coordinating transcription with other nuclear processes. This survey focuses on the distribution and structural arrangement of these complexes within the nucleus, in relationship with the discrete positioning of particular chromosomal loci. To better understand the link between the spatial organization of the nucleus and the regulation of gene expression, it is necessary to combine information from biochemica l studies with results from microscopic observations of preserved nuclear s tructures. Recent experimental approaches have made this possible. The subn uclear locations of specific chromosome loci, RNA transcripts, RNA polymera ses, and transcription and pre-mRNA-processing factors can now be observed with computer-assisted microscopy and specific molecular probes. The result s indicate that RNA polymerase II (RNAPII) transcription takes place at dis crete sites scattered throughout the nucleoplasm, and that these sites are also the locations of pre-mRNA processing. Transcribing polymerases appear to be grouped into clusters at each transcription site, Cell cycle-dependen t zones of transcription and processing factors have been identified, and c ertain subnuclear domains appear specialized for expression or silencing of particular genes. The arrangement of transcription in the nucleus is dynam ic and depends on its transcriptional activity, with the RNAPII itself play ing a central role in marshalling the large complexes involved in gene expr ession.