Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.

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A census of human RNA-binding proteins.

Linear arrays of spherical chromatin particles (nu bodies) about 70 angstroms in diameter have been observed in preparations of isolated eukaryotic nuclei swollen in water, centrifuged onto carbon films, and positively or negatively stained. These bodies have been found in isolated rat thymus, rat liver, and chicken erythrocyte nuclei. Favorable views also reveal connecting strands about 15 angstroms wide between adjacent particles.

https://science.sciencemag.org/content/sci/183/4122/330.full.pdf

Spheroid Chromatin Units (ν Bodies)

Electron microscopic and biochemical evidence that chromatin structure is a repeating unit

Models for replication and transcription often display polymerases that track like locomotives along their DNA templates However, recent evidence supports an alternative model in which DNA and RNA polymerases are immobilized by attachment to larger structures, where they reel in their templates and extrude newly made nucleic acids These polymerases do not act independently; they are concentrated in discrete “factories,” where they work together on many different templates Evidence for models involving tracking and immobile polymerases is reviewed

https://science.sciencemag.org/content/sci/284/5421/1790.full.pdf

The Organization of Replication and Transcription

Although the U3 small nucleolar RNA (snoRNA), a member of the box C/D class of snoRNAs, was identified with the spliceosomal small nuclear RNAs (snRNAs) over 30 years ago, its function and its associated protein components have remained more elusive. The U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA in all organisms where it has been tested. Biochemical and genetic analyses suggest that U3 pre-rRNA base-pairing interactions mediate endonucleolytic pre-rRNA cleavages. Here we have purified a large ribonucleoprotein (RNP) complex from Saccharomyces cerevisiae that contains the U3 snoRNA and 28 proteins. Seventeen new proteins (Utp1 17) and Rrp5 were present, as were ten known components. The Utp proteins are nucleolar and specifically associated with the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. On the basis of its large size (80S; calculated relative molecular mass of at least 2,200,000) and function, this complex may correspond to the terminal knobs present at the 5' ends of nascent pre-rRNAs. We have termed this large RNP the small subunit (SSU) processome.

A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis

The presence of extrachromosomal nucleoli in amphibian oocytes has permitted isolation and electron microscopic observation of the genes coding for ribosomal RNA precursor molecules. Visualization of these genes is possible because many precursor molecules are simultaneously synthesized on each gene. Individual genes are separated by stretches of DNA that apparently are not transcribed at the time of synthesis of precursor rRNA in the extrachromosomal nucleoli.

https://science.sciencemag.org/content/sci/164/3882/955.full.pdf

Visualization of Nucleolar Genes

The morphology of active structural and putative ribosomal RNA genes was observed by electron microscopy after lysis of fragile Escherichia coli cells. Conclusions drawn are: most of the chromosome is not genetically active at any one instant; translation is completely coupled with transcription; the 16S and 23S ribosomal RNA cistrons occur in tandem, in regions which are widely spaced on the chromosome.

https://science.sciencemag.org/content/sci/169/3943/392.full.pdf

Visualization of Bacterial Genes in Action

Morphological studies of transcription

Publisher Summary The numerous electron microscope autoradiographic studies of eukaryotic cells show that RNA synthesis is localized in dispersed chromatin in both nucleolar and non-nucleolar compartments of the nucleus. Alternatively, autoradiography of thin sections of pulse-labeled bacteria shows the localization of RNA synthesis near the interface of the ribosome-containing areas of the cell and the nucleoid regions that contain most of the bacterial DNA. An example of the structural resolution of genetic activity obtainable by thin-sectioning methods is presented in this chapter. In none of the thin-section studies with either eukaryotic or prokaryotic cells, however, could a distinct genetic unit be resolved within the regions active in RNA synthesis. More recently, direct visualization of the fine structure of individual, active genes in both cell types has been accomplished through novel isolation techniques. This chapter discusses the current status of these studies. Structural aspects of the activity of specific genes are demonstrated here using representatives of both eukaryotic and prokaryotic cell types. In both cases, inherent characteristics of the cells permitted the use of relatively simple techniques for isolating portions of active genomes.

O. L. Miller

Papers

Visualization of Nucleolar Genes

Visualization of Bacterial Genes in Action

Morphological studies of transcription

Visualization of RNA synthesis on chromosomes.

Electron Microscopic Visualization of Transcription