Detection of mRNA sequences in nuclear 30S ribonucleoprotein subcomplexes

RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities

RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.

Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics

Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe²⁺ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts

Heterogeneous nuclear ribonucleic acid (hnRNA) molecules in eucaryotic cell nuclei associate with a well-defined group of abundant, highly conserved proteins to form heterogeneous nuclear ribonucleoproteins (hnRNP). The exact manner in which these 30S complexes assemble on nuclear transcripts, however, has not been well documented. To determine whether any site selectivity in the formation of hnRNP can be detected (e.g., preferential recognition of intervening sequences or of premessage regions), we investigated the distribution of 30S hnRNP on a particular nuclear RNA, the polyoma virus late transcript. Hybridization studies showed not only that the majority of polyoma late nuclear RNA sequences can be isolated in the form of 30S complexes, but that the RNP were located equally on intervening sequences and premessage portions of the transcript. The latter conclusion was confirmed by ribonuclease T1 oligonucleotide fingerprint analysis of polyoma virus-specific RNA recovered from native 30S complexes. However, fingerprint analysis of the small segments of viral RNA in the 30S fraction that survived extensive ribonuclease treatment revealed that oligonucleotides corresponding to intervening sequences were preferentially lost. We discuss these findings in relation to the structure of 30S hnRNP and their function in RNA biogenesis.

Relatively stable population of c-myc RNA that lacks long poly(A)

We examined the turnover of c-myc RNA in the human promyelocytic cell line HL-60. In whole-cell RNA from rapidly growing cells we observed two major size classes of c-myc RNA, 2.4 and 2.2 kilobases (kb). When HL-60 cells were treated with actinomycin D for 30 min to inhibit transcription, the 2.4-kb c-myc RNA population was rapidly degraded, while the 2.2-kb c-myc RNA was degraded much more slowly. S1 nuclease transcript mapping and promoter-specific probes were utilized to show that both the stable 2.2-kb and the labile 2.4-kb c-myc RNA populations have 5' ends at the second promoter site (P2) and 3' ends at the second poly(A) addition site. To examine further possible structural differences between these two RNA populations, we fractionated RNA on an oligo(dT)-cellulose column to separate RNAs that contained long poly(A) tails from those which did not. We found that the labile 2.4-kb c-myc RNA population bound to oligo(dT)-cellulose, while the more stable 2.2-kb c-myc RNA population did not. Preliminary estimates of their half-lives (t1/2) showed that the poly(A)+ c-myc RNA had a t1/2 of 12 min, while the c-myc RNA that did not bind to oligo(dT)-cellulose had a t1/2 of greater than 1 h. Several other cell types contain both poly(A)+ and nonpoly(A)+ c-myc RNAs including HeLa cells, normal human bone marrow cells, and normal mouse fetal liver cells. In agreement with the results in HL-60 cell, HeLa cell poly(A)+ c-myc RNA was more labile than c-myc RNA that lacked poly(A). The stable, nonpoly(A)+ c-myc RNA population may be important in the posttranscriptional regulation of c-myc expression.

Relatively stable population of c-myc RNA that lacks long poly(A)

We examined the turnover of c-myc RNA in the human promyelocytic cell line HL-60. In whole-cell RNA from rapidly growing cells we observed two major size classes of c-myc RNA, 2.4 and 2.2 kilobases (kb). When HL-60 cells were treated with actinomycin D for 30 min to inhibit transcription, the 2.4-kb c-myc RNA population was rapidly degraded, while the 2.2-kb c-myc RNA was degraded much more slowly. S1 nuclease transcript mapping and promoter-specific probes were utilized to show that both the stable 2.2-kb and the labile 2.4-kb c-myc RNA populations have 5' ends at the second promoter site (P2) and 3' ends at the second poly(A) addition site. To examine further possible structural differences between these two RNA populations, we fractionated RNA on an oligo(dT)-cellulose column to separate RNAs that contained long poly(A) tails from those which did not. We found that the labile 2.4-kb c-myc RNA population bound to oligo(dT)-cellulose, while the more stable 2.2-kb c-myc RNA population did not. Preliminary estimates of their half-lives (t1/2) showed that the poly(A)+ c-myc RNA had a t1/2 of 12 min, while the c-myc RNA that did not bind to oligo(dT)-cellulose had a t1/2 of greater than 1 h. Several other cell types contain both poly(A)+ and nonpoly(A)+ c-myc RNAs including HeLa cells, normal human bone marrow cells, and normal mouse fetal liver cells. In agreement with the results in HL-60 cell, HeLa cell poly(A)+ c-myc RNA was more labile than c-myc RNA that lacked poly(A). The stable, nonpoly(A)+ c-myc RNA population may be important in the posttranscriptional regulation of c-myc expression.

In vitro assembly of a pre-messenger ribonucleoprotein

Transcription of the Bal I E restriction fragment of adenovirus DNA by RNA polymerase II in a HeLa cell extract produces a RNA transcript 1,712 nucleotides in length. This transcript contains the first two elements of the tripartite leader that, in vivo, is spliced onto the late mRNAs. We have found that this adenovirus 2 transcript forms a specific ribonucleoprotein complex (RNP) in this in vitro system. The RNP particle sediments in sucrose gradients as a monodisperse peak at 50 S and has a buoyant density of 1.34 g/cm3 in Cs2SO4, indicating the same 4:1 protein/RNA composition as native nuclear RNPs that contain pre-mRNA sequences (hnRNP). Moreover, the in vitro-assembled RNP is resistant to concentrations of NaCl that are known to dissociate nonspecific RNA-protein complexes. The adenovirus 2 transcript is precipitated by a monoclonal antibody for hnRNP core proteins. In addition, RNA-protein crosslinking of [alpha-32P]UTP-labeled transcript/RNP complexes reveals that the major proteins in contact with the RNA are the Mr 32,500-41,500 species known to be associated with hnRNA in vivo. These results demonstrate the in vitro assembly of a specific RNA polymerase II transcript into RNP. Moreover, because the 1,712-nucleotide adenovirus 2 transcript lacks poly(A) addition sites and because the leader sequences are not spliced appreciably in this in vitro system, it follows that RNP formation requires neither polyadenylylation nor splicing, nor is it sufficient to cause the latter.

An assessment of the evidence for the role of ribonucleoprotein particles in the maturation of eukaryote mRNA

This article has sought to draw together, on the one hand, what is known of mRNA processing and its control and, on the other hand, what is known of the structure and validity of hnRNP and snRNP particles. At the same time, it has attempted to synthesize these two themes into a critical assessment of the evidence which suggests that the particles are intimately involved in processing. It cannot be said that the case is proven. The evidence is compelling but circumstantial. The last few years have seen the development of the first in vitro splicing systems (Weingartner and Keller, 1981; Goldenberg and Raskus, 1981; Kole and Weissman, 1982), the isolation of monoclonal antibodies to defined snRNP (Lerner et al., 1981a; Billings et al., 1982) and hnRNP proteins (Hugle et al., 1982), and the ability to use artificial lipid vesicles to transfer antisera (Lenk et al., 1982) and radioactive snRNA (Gross and Cetron, 1982) into cells. It is to be hoped that further refinements of these and other techniques will allow us to solve this, one of the major outstanding problems of molecular biology.

Structure of nuclear ribonucleoprotein: identification of proteins in contact with poly(A)+ heterogeneous nuclear RNA in living HeLa cells

The processing of heterogeneous nuclear RNA into messenger RNA takes place in special nuclear ribonucleoprotein particles known as hnRNP. We report here the identification of proteins tightly complexed with poly(A)+ hnRNA in intact HeLa cells, as revealed by a novel in situ RNA-protein cross-linking technique. The set of cross-linked proteins includes the A, B, and C "core" hnRNP proteins, as well as the greater than 42,000 mol wt species previously identified in noncross-linked hnRNP. These proteins are shown to be cross-linked by virtue of remaining bound to the poly(A)+ hnRNA in the presence of 0.5% sodium dodecyl sulfate, 0.5 M NaCl, and 60% formamide, during subsequent oligo(dT)-cellulose chromatography, and in isopycnic banding in Cs2SO4 density gradients. These results establish that poly(A)+ hnRNA is in direct contact with a moderately complex set of nuclear proteins in vivo. This not only eliminates earlier models of hnRNP structure that were based upon the concept of a single protein component but also suggests that these proteins actively participate in modulating hnRNA structure and processing in the cell.

Turnover of the major polypeptides of 40-S monomer particles

The pulse-chase experiments with Friend erythroleukemia cells designed to reveal the metabolic properties of the protein complex of 40-S particles showed that the major polypeptides of this complex turn over with half-lives between 19 h and 206 h. the main conclusion from the experiments is that the complex does not degrade as a single unit. Since the individual polypeptides forming the complex live much longer than hnRNA, and in addition degrade at a different rate, we considered the following two modes of degradation as most likely. (1) The complex might not be subjected to a profound degradation at the end of the processing of associated pre-mRNA. In this case it should exist as a long-lived recyclable mosaic of metabolically differing polypeptides whose replacement takes place at a specific rate. (2) Alternatively, the protein complex might be completely degraded at the end of processing, but in a way that liberates free individual polypeptides available for recycling. The further experiments indicate that the 37 000-Mr, 34 000-Mr and 32 000-Mr core proteins in isolated 40-S particles and in particles associated with a nuclear fraction released from chromatin after micrococcal nuclease digestion degrade at different rates. These experiments suggest the existence of at least a metabolic heterogeneity among the population of nuclear particles carrying pre-mRNA.

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts

Heterogeneous nuclear ribonucleic acid (hnRNA) molecules in eucaryotic cell nuclei associate with a well-defined group of abundant, highly conserved proteins to form heterogeneous nuclear ribonucleoproteins (hnRNP). The exact manner in which these 30S complexes assemble on nuclear transcripts, however, has not been well documented. To determine whether any site selectivity in the formation of hnRNP can be detected (e.g., preferential recognition of intervening sequences or of premessage regions), we investigated the distribution of 30S hnRNP on a particular nuclear RNA, the polyoma virus late transcript. Hybridization studies showed not only that the majority of polyoma late nuclear RNA sequences can be isolated in the form of 30S complexes, but that the RNP were located equally on intervening sequences and premessage portions of the transcript. The latter conclusion was confirmed by ribonuclease T1 oligonucleotide fingerprint analysis of polyoma virus-specific RNA recovered from native 30S complexes. However, fingerprint analysis of the small segments of viral RNA in the 30S fraction that survived extensive ribonuclease treatment revealed that oligonucleotides corresponding to intervening sequences were preferentially lost. We discuss these findings in relation to the structure of 30S hnRNP and their function in RNA biogenesis.

Characterization of pre-messenger-RNA-containing nuclear ribonucleoprotein particles from avian erythroblasts

Ribonucleoprotein particles have been isolated from duck erythroblast nuclei using a procedure designed to produce maximal cytoplasmic dispersion with minimal release of endogenous hydrolytic enzymes. The RNA extracted from the purified nuclear ribonucleoprotein fraction is shown to contain globin messenger RNA sequences at a concentration comparable to that present in total nuclear RNA. The polypeptide composition of this fraction revealed by electrophoresis in two dimensions is complex, consisting of at least 65 acidic species and 21 basic species. Several lines of evidence suggest that these are authentic components of nuclear ribonucleoprotein. The so-called 'core' proteins of nuclear ribonucleoprotein which were previously shown to migrate as a single band on low-pH urea gels, and as six bands on sodium dodecyl sulphate gels are here shown to be considerably more complex being resolved by two-dimensional electrophoresis into a group of 15 basic and 6 more and less neutral polypeptides. Isoelectric focusing of nuclear ribonucleoprotein under non-denaturing conditions suggests that these latter species are not uniformly distributed along the pre-messenger RNA molecule.

Preformed Messenger RNAs and Early Wheat Embryo Germination

Wheat (Triticum aestivum L.) embryo homogenates have been fractionated into three cell fractions from which RNA was extracted and assayed for mRNA content by in vitro translation and by [(3)H]polyuridylic acid hybridization. In dry embryos the preformed mRNAs are distributed equally between a rapidly sedimenting "pellet" fraction and a cytoplasmic "ribosomal/subribosomal" fraction. During germination 25 to 40% of the total mRNA becomes polyribosomal. The remaining 60 to 75% is retained in the pellet and ribosomal/subribosomal fractions.To compare the nucleotide sequences of the different mRNA fractions, cDNAs were transcribed from polyribosomal (A+) RNA of 40-minute imbibed embryos and from total A(+) RNA of dry embryos, and the ability of these cDNAs to hybridize with the more prevalent classes of mRNA from the different cell fractions was analyzed. The results suggest that there is no significant difference between the preformed mRNAs that move into polyribosomes and those remaining in the nonpolyribosomal fractions. In addition there appears to be no difference between the mRNAs of polyribosomes from embryos germinated for 45 minutes and 5 hours. Between 5 hours and 2 days, however, there is a considerable change in the mRNA composition of the embryos. We conclude for the prevalent classes of message, that the preformed mRNAs of the wheat embryo are not involved in temporal regulation of early development but that they function primarily to allow a rapid resumption of growth upon exposure of the embryo to water.

Size distribution of rat liver nuclear RNA containing mRNA sequences

Total rat liver poly(A)-containing polysomal mRNA was size-fractionated on polyacrylamide gels in 98% formamide. Complementary DNA (cDNA) was prepared from the 8--14-S mRNA fraction and separated into sequences representing abundant and non-abundant mRNAs. The cDNA complementary to the abundant small mRNA of the rat liver cell (approximately 20 species) was hybridized to nuclear RNA of different lengths to determine the size distribution of nuclear RNA molecules which contain these messenger sequences. It was found that: 1. All abundant 8--14-S poly(A)-containing mRNAs have larger nuclear precursor molecules; 20% of the different messenger sequences are found in nuclear RNA of several times their cytoplasmic length. 2. 70% of the mass of the examined nuclear messenger sequences is in RNA molecules of a size similar to their polysomal mRNA; 30% are in larger than 18-S RNA and 2% are between 37 S and 44 S. 3. The majority of small messenger-containing RNA molecules in the RNA prepared from isolated nuclei are of true nuclear origin, since their frequency distribution differs significantly from that of the polysomal 8--14-S mRNA.

A comparative study on the two classes of heterogeneous nuclear ribonucleoprotein particles separated in metrizamide density gradient, by electrophoresis of proteins and chase experiments. Evidence for two distinct subfractions of HnRNP in mammalian nuclei

Heterogeneous nuclear ribonucleoprotein particles (HnRNP) were separated in metrizamide density gradients, into two fractions migrating to 1.31 g ml-1 and 1.18 g ml-1, respectively. Proteins associated with each of these fractions were analysed by SDS-acrylamide gel electrophoresis. It is shown that the whole proteins extracted from these two metrizamide fractions exhibit clearly different electrophoretic patterns: 1.31 HnRNP particles contain as major polypeptide chains molecules with molecular weights ranging from 40,000 to 65,000, while major polypeptides of 1.18 HnRNP are banding in the 30,000-40,000 molecular weight region of the gels. Both fractions contain numerous other associated polypeptide chains whose molecular weights are above 65,000. A possible kinetic relationship between these two HnRNP classes was investigated in vivo by performing chase experiments. No clear evidence for a precursor-product relationship was found. Implications arising from these structural and kinetic observations, and problems relating to nuclear maturation of pre-messenger RNA, are discussed.