Interaction and cross-talk between non-coding RNAs

Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors. SnoRNAs have also been reported to be precursors for PIWI-interacting RNAs (piRNAs) and thus may regulate the piRNAs as a precursor. These miRNAs and piRNAs target messenger RNAs (mRNAs) and regulate gene expression. In this review, we will present and discuss these interactions, cross-talk, and co-regulation of ncRNAs and gene regulation due to these interactions.     

Cytological evidence on the ability of the nucleolus organizing regions to assemble pre-existing nucleolar material

The treatment of Vicia faba root tips with 5-azacytidine caused unequal allotment of the chromosomes; after one cell cycle, a pair of daughter nuclei was produced, one of which carried the nucleolus organizing regions (NORs) and the other of which lacked them. The pre-existing nucleolar material brought into the NOR-carrying daughter nucleus by the chromosomes disappeared concurrently with the appearance of the new nucleoli, whereas in another daughter nucleus without the NOR a number of small nucleolus-like bodies became visible at random positions. These findings suggest that in addition to ribosomal RNA synthesis the NOR has another role in cells; to stimulate the pre-existing nucleolar material to assemble at the NOR itself.     

Cytological evidence on the ability of the nucleolus organizing regions to assemble pre-existing nucleolar material

Summary The treatment ofVicia faba root tips with 5-azacytidine caused unequal allotment of the chromosomes; after one cell cycle, a pair of daughter nuclei was produced, one of which carried the nucleolus organizing regions (NORs) and the other of which lacked them. The pre-existing nucleolar material brought into the NOR-carrying daughter nucleus by the chromosomes disappeared concurrently with the appearance of the new nucleoli, whereas in another daughter nucleus without the NOR a number of small nucleolus-like bodies became visible at random positions. These findings suggest that in addition to ribosomal RNA synthesis the NOR has another role in cells; to stimulate the pre-existing nucleolar material to assemble at the NOR itself.     

RNA processing and human disease

Gene expression involves multiple regulated steps leading from gene to active protein. Many of these steps involve some aspect of RNA processing. Diseases caused by mutations that directly affect RNA processing are relatively rare compared with mutations that disrupt protein function. The vast majority of diseases of RNA processing result from loss of function of a single gene due to mutations in cis-acting elements required for pre-messenger RNA (mRNA) splicing. However, a few diseases are caused by alterations in the trans-acting factors required for RNA processing and in the vast majority of cases it is the pre-mRNA splicing machinery that is affected. Clearly, alterations that disrupt splicing of pre-mRNAs from large numbers of genes would be lethal at the cellular level. A common theme among these diseases is that only subsets of genes are affected. This is consistent with an emerging view that different subsets of exons require different sets of cis-acting elements and trans-acting factors.     

Regulatory mechanisms of RNA function: emerging roles of DNA repair enzymes

The acquisition of an appropriate set of chemical modifications is required in order to establish correct structure of RNA molecules, and essential for their function. Modification of RNA bases affects RNA maturation, RNA processing, RNA quality control, and protein translation. Some RNA modifications are directly involved in the regulation of these processes. RNA epigenetics is emerging as a mechanism to achieve dynamic regulation of RNA function. Other modifications may prevent or be a signal for degradation. All types of RNA species are subject to processing or degradation, and numerous cellular mechanisms are involved. Unexpectedly, several studies during the last decade have established a connection between DNA and RNA surveillance mechanisms in eukaryotes. Several proteins that respond to DNA damage, either to process or to signal the presence of damaged DNA, have been shown to participate in RNA quality control, turnover or processing. Some enzymes that repair DNA damage may also process modified RNA substrates. In this review, we give an overview of the DNA repair proteins that function in RNA metabolism. We also discuss the roles of two base excision repair enzymes, SMUG1 and APE1, in RNA quality control.     

Ribosomal gene numbers in Microseridinae (Compositae: Cichorieae)

Summary 8 species of the subtribe Microseridinae contain between 1100 and 3400 genes for 25 and 18 S ribosomal RNA. The gene numbers seem to evolve by discrete steps. Their trend follows a general reduction in genome size during the evolution of the annual species ofMicroseris, but numbers remain high in one of them and inAgoseris grandiflora. 2 species ofPyrrhopappus differ by a duplication of the ribosomal gene numbers; 5 S ribosomal RNA genes in 4 species are repeated roughly 10,000 times.We thank Miss S. Werner, Miss A. Roth and Miss U. Krehan for help with some of the experiments. This paper is part of a project supported by grant Ba 536/1-5 from the Deutsche Forschungsgemeinschaft.     

Nucleotide sequence of the gene for the mitochondrial 15S ribosomal RNA of yeast

We have determined the nucleotide sequence of a DNA segment carrying the entire 15S ribosomal RNA gene of yeast mitochondrial genome. Many stretches of sequence are present which are homologous to the E. coli 16S ribosomal RNA gene. The gene sequence can be folded into a secondary structure according to the [1] model on bacterial ribosomal RNAs. The structure reveals a striking similarity between the two RNAs despite the large difference in their base compositions. In the middle of the gene, we found a guanine-cytosine rich sequence that is also present in several other regions of the mitochondrial genome.     

Diversity and roles of (t)RNA ligases

The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.     

Degradation of ribosomal RNA from Escherichia coli by ribonuclease U2 and in vitro transcription of "RNA-fragments" into complementary DNA]

Under well defined conditions ribosomal RNAs purified from Escherichia coli can be degraded by ribonuclease U2 giving rise to RNA fragments of 60--70 nucleotides. In vitro, these fragments are efficiently transcribed into a complementary DNA by DNA polymerase RNA dependent, partially purified from extracts of E. coli. In vivo, "RNA-fragments-U2" inhibit the development of plant tumors.     

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.     

Formaldehyde-Schiff's reagent as a nucleolar stain

Summary The use of formaldehyde-Schiff's reagent as a nucleolar stain has been described. Using different digestion procedures, it was confirmed that the stain is specific for RNA. It can be suitably used as a nucleolar stain, particularly in plant materials after a short TCA extraction, which probably extracts the nonbound RNA.     

Formaldehyde-Schiff's reagent as a nucleolar strain.

The use of formaldehyde-Schiff's reagent as a nucleolar stain has been described. Using different digestion procedures, it was confirmed that the stain is specific for RNA. It can be suitably used as a nucleolar stain, particularly in plant materials after a short TCA extraction, which probably extracts the nonbound RNA.     

Secondary and topographic structure of ribosomal RNA 16S of Escherichia coli

We present a model for the secondary structure of 16S ribosomal RNA from E. coli. This model has been deduced by restricting the total number of theoretical base pairings using the following criteria: (1) susceptibility of residues towards enzymatic probes that are specific for either paired or single stranded regions; (2) reactivity of certain residues to chemical modification; (3) evidence for medium and long range interactions; (4) comparative analysis of ribosomal RNA sequences from other organisms.     

Simultaneous syntheses of cytoplasmic and chloroplastic ribosomal RNA during the cell cycle ofDunaliella

Summary Chloroplastic and cytoplasmic ribosomal RNA syntheses were analyzed in synchromous culteres. All 4 rRNA species are simultaneously accumulated during the light period of the cell cycle. Cytoplasmic rRNA synthesis is repressed only during the later part of the S phase.