On pre-messenger RNA and transcriptions. A review

Proteomics and Bioinformatics Analysis of Cartilage in Post-Traumatic Osteoarthritis in a Mini-Pig Model of Anterior Cruciate Ligament Repair

Background

Although osteoarthritis (OA) is a degenerative disease that is increasingly common with age, the pathogenesis of post-traumatic OA (PTOA) is poorly understood. This study aimed to undertake proteomics and bioinformatics analysis of cartilage in PTOA in a mini-pig model of anterior cruciate ligament repair (ACLR).

Material/Methods

The mini-pig model of PTOA involved autologous orthotopic ACLR. Screening and identification of differentially expressed proteins in the knee joint cartilage in the OA cartilage group were compared with the control group using tandem mass tag (TMT)-labeling liquid chromatography with tandem mass spectrometry (LC-MS-MS). A protein expression level >1.2 fold-change represented protein upregulation and <0.83 fold-change represented protein down-regulation Bioinformatics analysis included Gene Ontology (GO) functional annotation and the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis to determine the biological functions and pathways of proteins showing altered expression profiles associated with OA.

Results

There were 2,950 proteins screened from the knee cartilage tissues of the OA model group using quantitative TMT-labeling LC-MS-MS. There were 491 proteins identified with altered expression profiles, 198 proteins were upregulated and 293 proteins were down-regulated in the OA cartilage group. GO function and KEGG pathway enrichment analysis of the 491 proteins identified their functions in cellular processes, metabolic processes, and biological regulation.

Conclusions

Proteomics and bioinformatics analysis of cartilage in PTOA in a mini-pig model of ACLR identified OA-related proteins.

Conditional control of alternative splicing through light-triggered splice-switching oligonucleotides

The spliceosome machinery is composed of several proteins and multiple small RNA molecules that are involved in gene regulation through the removal of introns from pre-mRNAs in order to assemble exon-based mRNA containing protein-coding sequences. Splice-switching oligonucleotides (SSOs) are genetic control elements that can be used to specifically control the expression of genes through correction of aberrant splicing pathways. A current limitation with SSO methodologies is the inability to achieve conditional control of their function paired with high spatial and temporal resolution. We addressed this limitation through site-specific installation of light-removable nucleobase-caging groups as well as photocleavable backbone linkers into synthetic SSOs. This enables optochemical OFF → ON and ON → OFF switching of their activity and thus precise control of alternative splicing. The use of light as a regulatory element allows for tight spatial and temporal control of splice switching in mammalian cells and animals.

Expression studies of the core+1 protein of the hepatitis C virus 1a in mammalian cells. The influence of the core protein and proteasomes on the intracellular levels of core+1

Recent studies have suggested the existence of a novel protein of hepatitis C virus (HCV) encoded by an ORF overlapping the core gene in the +1 frame (core+1 ORF). Two alternative translation mechanisms have been proposed for expression of the core+1 ORF of HCV-1a in cultured cells; a frameshift mechanism within codons 8-11, yielding a protein known as core+1/F, and/or translation initiation from internal codons in the core+1 ORF, yielding a shorter protein known as core+1/S. To date, the main evidence for the expression of this protein in vivo has been the specific humoral and cellular immune responses against the protein in HCV-infected patients, inasmuch as its detection in biopsies or the HCV infectious system remains elusive. In this study, we characterized the expression properties of the HCV-1a core+1 protein in mammalian cells in order to identify conditions that facilitate its detection. We showed that core+1/S is a very unstable protein, and that expression of the core protein in addition to proteosome activity can downregulate its intracellular levels. Also, we showed that in the Huh-7/T7 cytoplasmic expression system the core+1 ORF from the HCV-1 isolate supports the synthesis of both the core+1/S and core+1/F proteins. Finally, immunofluorescence and subcellular fractionation analyses indicated that core+1/S and core+1/F are cytoplasmic proteins with partial endoplasmic reticulum distribution in interphase cells, whereas in dividing cells they also localize to the microtubules of the mitotic spindle.

The mammalian transcriptome and the function of non-coding DNA sequences

Many non-coding sequences transcribed from the mammalian genome are proving to have important regulatory roles, but the functions of the majority remain mysterious.

For decades, researchers have focused most of their attention on protein-coding genes and proteins. With the completion of the human and mouse genomes and the accumulation of data on the mammalian transcriptome, the focus now shifts to non-coding DNA sequences, RNA-coding genes and their transcripts. Many non-coding transcribed sequences are proving to have important regulatory roles, but the functions of the majority remain mysterious.

Historical review: the discovery of 'giant' RNA and RNA processing: 40 years of enigma

RNA processing is a primordial paradigm of gene expression. Iconoclastic when discovered, after 40 years there is still no general rationale for this apparent 'wasting' of up to 90% of RNA transcripts. This article tells the story of the discovery of RNA in the laboratory of J.E. Darnell. The discovery of 'giant' RNA and its conversion into rRNA revealed the phenomenon of RNA processing and pre-rRNA. Genuine mRNA was also identified, but the majority of DNA-like nuclear RNA was also found to be giant and unstable. In spite of early evidence, pre-mRNA processing was only accepted in 1977 when the discovery of gene fragmentation in DNA made it obvious.

In chicken leukemia cells globin genes are fully transcribed but their rnas are retained in the perinucleolar area

Using hybridization in situ with a ribo-probe recognizing transcripts of the chicken alpha A globin gene, we show here that in proliferating AEV-transformed erythroblasts this gene is strongly transcribed, but the corresponding transcripts are retained in the nuclei. Most surprisingly, this globin RNA accumulates in the perinucleolar areas in a pattern never observed before. Upon induction of cells to differentiate, leading to productive expression of the hemoglobins, the transcripts of the alpha A globin gene were found for the most part in the cytoplasm. In the nuclei of differentiated cells, the globin RNA is concentrated in one or two specific spots, which are likely to represent the "processing centers" (PCs) of the globin RNA. The results presented indicate that posttranscriptional steps of regulation involving in particular the perinuclear areas are of major importance for erythroid differentiation.

Transcription of the alpha globin gene domain in normal and AEV-transformed chicken erythroblasts: mapping of giant globin-specific RNA including embryonic and adult genes

The genomic domain of about 20 kbp of the chicken alpha-type globin genes, framed by AT-rich linkers (ATRLs; Moreau et al. 1982) and repetitive sequences (Broders et al. 1986), was cut into 13 fragments and subcloned. The in vitro labelled individual restriction fragments were used to test the extent of the transcribed domain by blot-hybridization of nuclear RNA in large excess from normal adult chicken and Avian Erythroblastosis Virus (AEV)-transformed erythroblasts. In both these types of cells, the AT-rich segments situated 6 kbp upstream of the first gene as well as all the domain including the embryonic pi and the adult alpha D and alpha A genes down to the AT-rich segment placed 3 kbp downstream were found to be transcribed. Electrophoresis of nuclear RNA, Northern blotting and hybridization with most of the nick-translated DNA probes revealed in all cases the presence of heterogeneous globin RNA molecules in the 3-12 kb range, as well as some distinct RNA bands. Single-stranded RNA probes of some genomic segments indicated asymmetrical transcription of the minus strand. A 12 kb globin-specific RNA including the pi and alpha A genes but not the intervening alpha D gene was observed in AEV-transformed cells: it includes sequences located far upstream and downstream from the alpha globin genes and might represent a processing product of a full length transcript spanning the whole domain. Reverse transcription by extension of primers placed in the first exon of each of the three globin genes confirmed the presence of continuous transcripts of the domain including the two adult and the embryonic globin genes.

Correlations of repetitive and AT-rich DNA segments within the chicken globin gene domains

The repetitive DNA segments were mapped within a 30 Kbp genomic domain including (in 5' to 3' order) the chicken embryonic pi and adult alpha D (minor) and alpha A (major) globin genes. Two repeats map 5 and 8 Kbp upstream from the embryonic pi gene and another 3 Kbp downstream of the adult alpha A gene. These repetitive DNA sequences are placed within, or immediately adjacent to the AT-rich DNA segments framing this domain. Similar correlations exist also within the chicken beta globin gene domain. The positions of these AT-rich and repetitive DNA segments framing the alpha globin gene domain also correlate with other already explored features of long range DNA organisation, as clusters of sites of DNAse I hypersensitivity and differential methylation, sites of Matrix-DNA attachment, and with the beginning and end of the transcribed domain.

Nature and origin of the RNA associated with simian virus 40 large tumor antigen

Simian virus 40 (SV40) large tumor (T) antigen isolated from mammalian cells undergoing lytic or transforming infection is associated with small RNA fragments ("T-antigen RNA") that are protected from nuclease digestion. The rather high complexity of the ribonuclease T1 fingerprints of T-antigen RNA suggested that it is mainly derived from cellular heterogeneous nuclear RNAs. In the present study, 5'-32P-labeled T-antigen RNA was hybridized to monkey, mouse, and human Alu and SV40 DNA, and the nucleotide sequence of 37 T1 oligonucleotides was determined. The results suggest that the bulk of T-antigen RNA is derived from noncoding, double-stranded, ordered regions of cellular heterogeneous nuclear RNAs that exhibit sequence homologies with interspersed repetitive elements of the cellular genome. The possible biological implications of these results are discussed.

Sequential stimulation of cellular RNA synthesis in polyoma-infected mouse kidney cell cultures

Lytic infection with polyoma virus leads in Go-arrested primary mouse kidney cell cultures to a mitotic host response. In the present work we focused our attention on cellular RNA synthesis shortly after onset of polyoma T-antigen synthesis. Onset of polyoma-induced stimulation of 45S pre-rRNA synthesis was determined by hybridization of total cellular RNA with a plasmid (pMrSalB) containing the 5'-end of the mouse ribosomal gene and of the other cellular RNA species by standard biochemical analysis of cellular fractions. The results showed that polyoma-induced stimulation of cellular hnRNA (hnRNP) synthesis, the earliest presently known host cell reaction, preceded onset of stimulated 45S pre-rRNA synthesis and that the latter was paralleled by polyoma-induced stimulation of 5S RNA, tRNA and overall protein synthesis. The polyoma-induced mitotic response is similar to that triggered by simian virus 40 and by certain nonviral mitogens.

Determination of the primary sequence of the duck alpha D globin mRNA and comparison of all adult duck and chick globin mRNA sequences

The nucleotide sequence of the duck alpha D globin mRNA was determined. Its main feature is an exceptionally short 3' non-coding segment of only 46 nucleotides, placed after the coding sequence of 141 codons. The last of the 6 adult globin mRNA of duck and chicken being thus sequenced, a comparison of all their features has become possible. Comparing the duck alpha D mRNA to the related sequence in the chicken, we found greater homology than comparing it to the linked alpha A globin sequence in the same species. Extensive homology can be found for a same globin chain alpha A, alpha D or beta in between different avian species including also the goose and the ostrich; the avian alpha globin chains show a lower degree of sequence conservation in between species than the beta chains. In contrast, within one species the three globin sequences have further diverged. The divergence between the alpha A and alpha D globin within a same species point to individual functional specificity and hence independent evolution and suggest that a mechanism of 'gene conversion' did not operate in between the avian alpha globin genes. Two segments of the amino acid sequence which we named 'A alpha' and 'B alpha' remain homologous in all avian alpha globins; two other regions 'A beta' and 'B beta' are identical in between the beta globins. Segment A is placed at the 5' end of exon II, and segment B at the 3' end of the same exon; some amino acids in those segments are involved in the Heme binding site. Being almost identical in all know mammalian and avian globins of the alpha respectively the beta type, regions A and B seem to represent the best conserved sequences in adult globin mRNA maintained during the divergence of species.

Serum-induced stimulation of nucleoplasmic and nucleolar transcription in mouse 3T3 fibroblasts revisited

Transition of 3T3 mouse fibroblasts from a quiescent to a growing state was induced by the addition of 10% fresh bovine serum to the culture medium. The number of DNA-synthesizing cells began to increase 10-11 h after the addition of serum and reached a maximum of 70-80% around 24 h. In quiescent cells, maintained in 0.5% serum, residual RNA synthesis represented mainly nucleoplasmic transcription (hnRNA, 5-S RNA and tRNA). Synthesis of tRNA was 2-3-fold increased by 1-2 h after addition of serum; however, a significant stimulation of hnRNA, 5-S RNA and 45-S pre-rRNA synthesis could only be observed around 4h. The experimental data also revealed a close temporal relationship between the onset of serum-stimulated hnRNA and overall protein synthesis. Determined colorimetrically, the cellular RNA and protein content began to increase by 4-5 h and had doubled by 24 h. Virtually the same results on RNA and protein synthesis were obtained when the experiments were performed in the presence of cytosine arabinoside, an inhibitor of DNA synthesis. From our results we concluded that serum-stimulated overall RNA and protein synthesis preceded by several hours serum-induced S phase and was independent of DNA replication.

Polyoma-induced stimulation of nucleoplasmic transcription is paralleled by development of resistance against actinomycin D

Polyoma virus induced in quiescent, Go-arrested mouse kidney cells a lytic infection. Synthesis of the polyoma T-antigens began 7-8 h after infection and was followed by a mitotic reaction of the host cell comprising stimulated synthesis and accumulation of cellular (mainly ribosomal) RNA and protein and duplication of the host cell chromatin (S-phase). In the present work we focused attention on nucleoplasmic transcription, i.e. synthesis of hnRNA, 5S RNA and tRNA. To inhibit selectively nucleolar transcription we used low concentrations of actinomycin D (act. D). Synthesis of 45S precursor- ribosomal RNA in mock- and polyoma-infected mouse kidney cells was completely blocked by 0.05 micrograms/ml act.D within 2 h. In mock-infected cells also nucleoplasmic transcription was rather sensitive against 0.05 micrograms/ml act.D. Polyoma- induced stimulation of nucleoplasmic transcription began around 12 h and was paralleled by the development of resistance against act.D. Resistance of nucleoplasmic transcription in virus-infected cells was thus similar to that observed by others in uninfected, proliferating mammalian cells. The possible biological implications of these results are discussed.

The effect of inhibition of RNA synthesis by actinomycin D on the population of basic polypeptides of the 30S unclear ribonucleoprotein particles

In rats injected intraperitoneally with actinomycin D (2 mg/kg body weight) 12 h earlier, the yield of the 30S ribonucleoprotein particles isolated from liver nuclei by extraction with 0.1 M NaCl at pH 8.0 decreased by 60 per cent. The protein-to-RNA ratio of these particles increased to 32:1 from the ratio 4.4:1 found in the same particles isolated from the nuclei of liver of control rats. The particles isolated from the liver nuclei of rats injected with actinomycin D were depleted of all charge isomers of the two most prominent polypeptides (33,000 and 39,000 daltons) present in the particles of liver of control animals. The most abundant protein in these particles was a 43,000 dalton polypeptide. This polypeptide is the least prominent of the 3 major polypeptides present in the control particles. The same charge isomers of the 43,000 dalton polypeptide were present in the nuclear ribonucleoprotein particles isolated from the liver of control animals and from the liver of animals treated with actinomycin D 12 h earlier. In control animals the nuclear ribonucleoprotein monoparticles isolated from kidney contained 3 major polypeptides of the same molecular weight with the same distribution of their charge isomers as were present in the particles isolated from liver nuclei. The injection of actinomycin D 12 h earlier was without any effect on the protein composition of the 30S nuclear ribonucleoprotein particles of rat kidney.

Nucleotide sequence analysis of a cloned duck beta-globin cDNA

The primary structure of the duck beta-globin mRNA was obtained from sequence analysis of the double-stranded in vitro-transcribed DNA cloned in plasma pBR322. The 646-bp long globin DNA insert comprises a coding sequence of 438 bp corresponding to 146 amino acids, a 5'-noncoding region 63 bp long, and a 3'-noncoding region of 113 bp prior to a stretch of adenosine residues. The salient features of each of these regions are discussed and compared with beta-globin mRNAs of other vertebrates.

Isolation of globin pre-messenger RNA on thiol-agarose by terminally mercurated complementary DNA

A mercurated DNA complementary to globin mRNA was prepared by the addition of mercurated poly(dC) tails to the 3'-end of the molecule using the enzyme terminal deoxynucleotidyl transferase. The mercurated complementary DNA was retained efficiently on thiol-agarose from which it was eluted by 2-mercaptoethanol. Hybridization of the mercurated probe to globin mRNA led to a specific selection of the latter from a mixed population of RNA through hybrid retention on thiol-agarose. In some pilot experiments this technique was applied for the isolation of globin gene-specific pre-mRNA. Pulse-labeled RNA up to 3 X 10(6) MW was thus isolated with prominent peaks of 1.5 kb ('15 S'), 4.0 kb ('28 S') and up to about 10 kb. Electron microscopical analysis revealed pre-mRNA molecules of up to 1.2 mu (about 4.5 kb) in length isolated by hybridization to (Hg)cDNA; in control experiments, hybridization of this high MW RNA was competed out by highly purified globin mRNA. These data provide another indication for the existence of globin gene transcripts in the 10 kb range, i.e. transcripts larger than the about 1 500 nucleotides long '15 S' pre-mRNA, the substrate to final splicing. Such 'giant' transcripts can be interpreted as either the obligatory primary pre-mRNA or only facultative transcripts of the globin genes.

Systematic punctuation of eukaryotic DNA by A+T-rich sequences

Isodenaturation of avian and mammalian DNA of Mr greater than 2.5 X 10(8) in 85% (vol/vol) formamide led to the observation by electron microscopy of A+T-rich zones ("AT-rich linkers") of 300-3000 base pairs which are distributed over the entire genome in a characteristic pattern. Linkers of mean length 800 base pairs are found either isolated or in clusters of about four to six linkers of more heterogeneous size separated on average by 2500 base pairs (in duck DNA). In between clusters, single linkers segment the DNA at distances of 10 to more than 100 kilobase pairs, with a majority in the range of 10-30 kilobase pairs. An analogous organization of linkers is found in rat and mouse DNA. The internal organization of the clusters varies, however, in a fashion that might be related to the large amount of light satellite DNA in the mouse and its apparent absence in rat and avian DNA. It is possible to fragment the DNA under appropriate conditions by the single-strand-specific nuclease S1 at the site of these A+T-rich zones and to obtain, on alkaline sucrose gradients, a bimodal pattern of DNA fragments of the size corresponding to the pattern observed by electron microscopy. The implications of this observation for DNA organization, chromatin structure, units of transcription and replication, and possible targets of A+T-specific drugs are discussed.

Restriction mapping of cDNA recombinants including the adult chicken and duck globin messenger sequences: a comparative study

A comparison of the organization of six avian adult globin messenger sequences is based on previously reported recombinant duck adult globin cDNA plasmids (Therwath et al., 1980) and the actual construction and characterization of pBR322 recombinant plasmids including the beta and the normal alpha A and alpha D chicken adult globin mRNA sequences. Identification of the cloned DNA was performed using hybridization-selection under conditions permitting complete purification in one step of the three globin mRNAs, and translation of the corresponding mRNA. Orientation of the globin insert in the vector was determined, taking into account the computer prediction of the restriction sites based on the known amino acid sequences of the three globin chains (Roizès and Pelaquier, 1980) and those actually observed, and by identification of restriction fragments using 3'-specific probes. Identification, orientation and restriction mapping of these cloned DNAs reveals extensive homologies in organisation of beta sequences between duck and chicken, as well as among the alpha sequences in every two possible combinations.