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Morphology of nuclear transcription - PubMed

Review

Morphology of nuclear transcription

Klara Weipoltshammer et al. Histochem Cell Biol. 2016 Apr.

Abstract

Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.

Keywords: Chromatin; Epigenetic gene regulation; Loop formation; Nuclear architecture; Nucleoli; Transcription factory.

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Figures

Fig. 1
Fig. 1

a BrU incorporation to visualize nascent transcripts, HeLa cell, confocal image (projection) Bar 5 µm b Nucleolus of HeLa cell, sketch of Christmas tree in relation to the fibrillar complex where transcription takes place (inset), TEM Bar 1 µm c In situ hybridization to detect rRNA which is present in df and gc, HeLa cell, TEM, Bar 1 µm, fc fibrillar center, df dense fibrillar component, gc granular component

Fig. 2
Fig. 2

a Detection of a fragment of the transcription unit (red) and of the intergenic spacer (green) of rDNA, FISH on stretched DNA fibers, nuclear halo preparation, Bar 5 µm, b HeLa cell expressing histones H2B (green) and histone H3 variant H3.3 (red) which has been associated with transcriptional activity (Ahmad and Henikoff 2002), note that nucleoli are largely devoid of signal, structured illumination imaging, Bar 5 µm, c FISH with a probe covering the entire rDNA repeat showing an extracted rDNA loop, nuclear halo preparation

Fig. 3
Fig. 3

Sketch to compare morphology of transcription a in nucleoli and b in transcription factories. The transcription factory core (tf) is functionally related to the fibrillar center (fc), and transcription takes place at the surface of both entities. Active genes come into contact with the polymerases by chromatin loop formation out of silenced chromatin (gray dots). In nucleoli, nascent transcripts (brown) are predominately found in the dense fibrillar component (df) where RNA processing commences. A similar zone can be postulated for the transcription factory, Pol I…green dots, Pol II pink dots, gc granular component

Fig. 4
Fig. 4

Human peripheral lymphocytes a unstimulated and b after 72-h stimulation, FISH to detect part of the TU of rDNA showing significant alterations of rDNA arrangement in the course of differentiation, nuclear outline indicated (yellow)

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