Effectiveness of Three Doses of mRNA COVID-19 Vaccines in the Hemodialysis Population during the Omicron Period

BACKGROUND

Coronavirus disease 2019 (COVID-19) vaccine effectiveness studies in the hemodialysis population have demonstrated that two doses of mRNA COVID-19 vaccines are effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severe complications when Alpha and Delta were predominant variants of concern. Vaccine effectiveness after a third dose versus two doses for preventing SARS-CoV-2 infection and severe COVID-19 in the hemodialysis population against Omicron is not known.

METHODS

We conducted a retrospective cohort study in Ontario, Canada, between December 1, 2021, and February 28, 2022, in the maintenance hemodialysis population who had received two versus three doses of mRNA COVID-19 vaccines. COVID-19 vaccination, SARS-CoV-2 infection, and related hospitalization and death were determined from provincial databases. The primary outcome was the first RT-PCR confirmed SARS-CoV-2 infection, and the secondary outcome was a SARS-CoV-2-related severe outcome, defined as either hospitalization or death.

RESULTS

A total of 8457 individuals receiving in-center hemodialysis were included. At study initiation, 2334 (28%) individuals received three doses, which increased to 7468 (88%) individuals by the end of the study period. The adjusted hazard ratios (aHR) for SARS-CoV-2 infection (aHR, 0.58; 95% confidence interval [CI], 0.50 to 0.67) and severe outcomes (hospitalization or death) (aHR, 0.40; 95% CI, 0.28 to 0.56) were lower after three versus two doses of mRNA vaccine. Prior infection, independent of vaccine status, was associated with a lower risk of reinfection, with an aHR of 0.44 (95% CI, 0.27 to 0.73).

CONCLUSIONS

Three-dose mRNA COVID-19 vaccination was associated with lower incidence of SARS-CoV-2 infection and severe SARS-CoV-2-related outcomes during the Omicron period compared with two doses.

Disease-associated human genetic variation through the lens of precursor and mature RNA structure

Disease-associated variants (DAVs) are commonly considered either through a genomic lens that describes variant function at the DNA level, or at the protein function level if the variant is translated. Although the genomic and proteomic effects of variation are well-characterized, genetic variants disrupting post-transcriptional regulation is another mechanism of disease that remains understudied. Specific RNA sequence motifs mediate post-transcriptional regulation both in the nucleus and cytoplasm of eukaryotic cells, often by binding to RNA-binding proteins or other RNAs. However, many DAVs map far from these motifs, which suggests deeper layers of post-transcriptional mechanistic control. Here, we consider a transcriptomic framework to outline the importance of post-transcriptional regulation as a mechanism of disease-causing single-nucleotide variation in the human genome. We first describe the composition of the human transcriptome and the importance of abundant yet overlooked components such as introns and untranslated regions (UTRs) of messenger RNAs (mRNAs). We present an analysis of Human Gene Mutation Database variants mapping to mRNAs and examine the distribution of causative disease-associated variation across the transcriptome. Although our analysis confirms the importance of post-transcriptional regulatory motifs, a majority of DAVs do not directly map to known regulatory motifs. Therefore, we review evidence that regions outside these well-characterized motifs can regulate function by RNA structure-mediated mechanisms in all four elements of an mRNA: exons, introns, 5' and 3' UTRs. To this end, we review published examples of riboSNitches, which are single-nucleotide variants that result in a change in RNA structure that is causative of the disease phenotype. In this review, we present the current state of knowledge of how DAVs act at the transcriptome level, both through altering post-transcriptional regulatory motifs and by the effects of RNA structure.

Research advance in lipid nanoparticle-mRNA delivery system and its application in CAR-T cell therapy

Chimeric antigen receptor (CAR) T cell therapy has shown significant efficacy for hematological malignancies, however, it needs to be further optimized. Recently, the lipid nanoparticle (LNP)-mRNA delivery system as a nonviral gene transfer vector has gained rapid progress in CAR-T cell therapy. The claudin-6 (CLDN6) mRNA is delivered to antigen presenting cells (APCs) through LNP system, thereby enhancing the function of CLDN6 CAR-T cells for the clearance of solid tumor cells. For treatment of acute cardiac injury, the fibroblast activation protein (FAP) CAR mRNA can be delivered to T cells through LNP system for the in vivo production of FAP CAR-T cells, thereby blocking the process of myocardial fibrosis. The LNP-mRNA delivery system has advantages including having no integration in host genome, inexpensiveness, low toxicity and modifiability; on the other hand, it has certain disadvantages such as limited cell persistence caused by transient protein expression and limitations in preparation techniques. This article reviews the research advance in LNP-mRNA in vivo delivery system and its application in CAR-T cell therapy.

Longitudinal Analyses of Blood Transcriptome During Conversion to Psychosis

The biological processes associated with the onset of schizophrenia remain largely unknown. Current hypotheses favor gene × environment interactions as supported by our recent report about DNA methylation changes during the onset of psychosis. Here, we conducted the first longitudinal transcriptomic analysis of blood samples from 31 at-risk individuals who later converted to psychosis and 63 at-risk individuals who did not. Individuals were followed for a maximum of 1 year. Blood samples were collected at baseline and at the end of follow-up and individuals served as their own controls. Differentially expressed genes between the 2 groups were identified using the RNA sequencing of an initial discovery subgroup (n = 15 individuals). The most promising results were replicated using high-throughput real-time qPCR in the whole cohort (n = 94 individuals). We identified longitudinal changes in 4 brain-expressed genes based on RNAseq analysis. One of these genes (CPT1A) was replicated in the whole cohort. The previously observed hypermethylation in NRP1 and GSTM5 during the onset of psychosis correlated with a decrease in corresponding gene expression. RNA sequencing also identified 2 co-expression networks that were impaired after conversion compared with baseline-the Wnt pathway including AKT1, CPT1A and semaphorins, and the Toll-like receptor pathway, related to innate immunity. This longitudinal study of transcriptomic changes in individuals with at-risk mental state revealed alterations during conversion to psychosis in pathways and genes relevant to schizophrenia. These results may be a first step toward better understanding psychosis onset. They may also help to identify new biomarkers and targets for disease-modifying therapeutic strategies.

mRNA expression of CDH3, IGF2BP3, and BIRC5 in biliary brush cytology specimens is a useful adjunctive tool of cytology for the diagnosis of malignant biliary stricture

Although advances have been made in diagnostic tools, the distinction between malignant and benign biliary strictures still remains challenging. Intraductal brush cytology is a convenient and safe method that is used for the diagnosis of biliary stricture, but, low sensitivity limits its usefulness. This study aimed to demonstrate the usefulness of mRNA expression levels of target genes in brush cytology specimens combined with cytology for the diagnosis of malignant biliary stricture. Immunohistochemistry for cadherin 3 (CDH3), p53, insulin-like growth factor II mRNA-binding protein 3 (IGF2BP3), homeobox B7 (HOXB7), and baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5) was performed in 4 benign and 4 malignant bile duct tissues. Through endoscopic or interventional radiologic procedures, brush cytology specimens were prospectively obtained in 21 and 35 paitents with biliary strictures. In the brush cytology specimens, the mRNA expressions levels of 5 genes were determined by real-time polymerase chain reaction. Immunohistochemistry for CDH3, p53, IGF2BP3, HOXB7, and BIRC5 all showed positive staining in malignant tissues in contrast to benign tissues, which were negative. In the brush cytology specimens, the mRNA expression levels of CDH3, IGF2BP3, HOXB7, and BIRC5 were significantly higher in cases of malignant biliary stricture compared with cases of benign stricture (P = 0.006, P < 0.001, P < 0.001, and P = 0.001). The receiver-operating characteristic curves of these 4 mRNAs demonstrated that mRNA expression levels are useful for the prediction of malignant biliary stricture (P = 0.006, P < 0.001, P < 0.001, and P = 0.002). The sensitivity and specificity, respectively, for malignant biliary stricture were 57.1% and 100% for cytology, 57.1% and 64.3% for CDH3, 76.2% and 100% for IGF2BP3, 71.4% and 57.1% for HOXB7, and 76.2% and 64.3% for BIRC5. When cytology was combined with the mRNA levels of CDH3, IGF2BP3, or BIRC5, the sensitivity for malignant biliary stricture improved to 90.5%. The measurement of the mRNA expression levels of CDH3, IGF2BP3, and BIRC5 by real-time polymerase chain reaction combined with cytology was useful for the differentiation of malignant and benign biliary strictures in brush cytology specimens.

Messenger RNA expression patterns of p75 neurotrophin receptor and tropomyosin-receptor-kinase A following spinal cord injury

BACKGROUND

Induction of p75 neurotrophin receptor (p75NTR) could be one of the first steps that initiate apoptotic cascade after injury, or it may indicate regeneration responses undertaken by the injured system, possibly in collaboration with resident tropomyosin-receptor-kinase (Trk).

OBJECTIVE

To measure quantitative changes in messenger RNA (mRNA) expression levels of p75NTR, Trk A, and caspase-9 in rat's injured spinal cord (SCI). The reciprocal interaction between Trk and p75NTR signaling pathways can dictate cellular responses to neurotrophins. p75NTR can regulate Trk-dependent responses, but the role of Trk in regulating p75NTR-dependent signaling is not well documented.

DESIGN

Using real-time polymerase chain reaction, this study analyzed changes in the mRNA abundance of the mentioned genes at 6, 24, and 72 hours and 7 and 10 days after SCI in adult male rats. SCI was induced at T9 level by transsection.

RESULTS

Results show a complicated temporal and spatial pattern of alteration with different degrees and direction (up- or down-regulation) in p75NTR, Trk A, and caspase-9 mRNA expression levels after SCI. The greatest variation was seen in center regions following SCI. This study shows that alteration in p75NTR, Trk A, and caspase-9 expression starts as early as 6 hours after SCI. Alterations in p75NTR, Trk A, and caspase-9 expression within the spinal cord may play a key role in the apoptotic cell death.

CONCLUSION

Results suggest that the role of p75NTR is to eliminate damaged cells by activating the apoptotic machinery, especially at the center of damage and during first week after injury.

Quantitation and localization of inflammatory cytokines interleukin-6 and interleukin-8 in the lower uterine segment during cervical dilatation

PURPOSE

Cervical dilatation during parturition is associated with a significant increase of interleukin (IL)-6 and IL-8. The purpose of this study was to localize the respective messenger RNA and to quantitate their protein levels during various stages of dilatation.

METHODS

Protein extracts from 34 biopsy specimens of the lower uterine segment at various stages of cervical dilatation (<2, 2 to <4, 4-6, and >6 cm) were subjected to enzyme linked immunosorbent assay for IL-6 and IL-8 to document their concentration. The respective mRNA expression was studied using reverse transcriptase PCR using IL-6 and IL-8 specific primers. Localization of IL-6 and IL-8 was done by in situ hybridization using biotinylated probes.

RESULTS

The IL-6 and IL-8 concentrations increased significantly in the lower uterine segment tissues at 4-6 cm of dilatation. Expression of IL-8 was seen in all the tissues at or more than 4 cm dilatation, whereas IL-6 expression was inconsistent. In situ hybridization localized IL-6 and IL-8 mRNA to the glandular epithelium.

CONCLUSIONS

The increase in the inflammatory cytokines (IL-6 and IL-8) during parturition is associated with cervical effacement.

Demystified.... Transcription

The transcription of genes could be defined as the intricate molecular manoeuvres occurring in the nuclei of cells, which allow the translation of genetic information held in the DNA into the proteins required for life. Gene transcription is the dominant control point in the production of any protein, and is initiated and regulated through the combined activities of a highly specialised set of nuclear proteins. This review examines the role of these protein "transcription factors" in the production of messenger RNA, the information intermediary produced in the nucleus, and transferred to the cytoplasm to serve as a template for protein synthesis. In combination with RNA polymerase, an extraordinary and complex enzyme required to synthesise new RNA molecules, a multitude of transcription factors combine their activities to orchestrate and control this elegant process.

Differential regulation of corticotropin-releasing hormone and vasopressin gene transcription in the hypothalamus by norepinephrine

All stress-related inputs are conveyed to the hypothalamus via several brain areas and integrated in the parvocellular division of the paraventricular nucleus (PVN) where corticotropin-releasing hormone (CRH) is synthesized. Arginine vasopressin (AVP) is present in both magnocellular and parvocellular divisions of the PVN, and the latter population of AVP is colocalized with CRH. CRH and AVP are co-secreted in the face of certain stressful stimuli, and synthesis of both peptides is suppressed by glucocorticoid. CRH and AVP stimulate corticotropin (ACTH) secretion synergistically, but the physiological relevance of the dual corticotroph regulation is not understood. Norepinephrine (NE) is a well known neurotransmitter that regulates CRH neurons in the PVN. We explored the mode of action of NE on CRH and AVP gene transcription in the PVN to examine the effect of the neurotransmitter on multiple genes that are responsible for a common physiological function. After NE injection into the PVN of conscious rats, CRH heteronuclear (hn) RNA increased rapidly and markedly in the parvocellular division of the PVN. AVP hnRNA did not change significantly in either the parvocellular or magnocellular division of the PVN after NE injection. The present results show that the transcription of CRH and AVP genes is differentially regulated by NE, indicating the complexity of neurotransmitter regulation of multiple releasing hormone genes in a discrete hypothalamic neuronal population.

Characterization of beta-adrenoceptor mediated smooth muscle relaxation and the detection of mRNA for beta1-, beta2- and beta3-adrenoceptors in rat ileum

1. Functional and molecular approaches were used to characterize the beta-AR subtypes mediating relaxation of rat ileal smooth muscle. 2. In functional studies, (-)-isoprenaline relaxation was unchanged by CGP20712A (beta1-AR antagonist) or ICI118551 (beta2-AR antagonist) but shifted by propranolol (pKB=6.69). (+/-)-Cyanopindolol, CGP12177 and ICID7114 did not cause relaxation but antagonized (-)-isoprenaline relaxation. 3. BRL37344 (beta3-AR agonist) caused biphasic relaxation. The high affinity component was shifted with low affinity by propranolol, (+/-)-cyanopindolol, tertatolol and alprenolol. CL316243 (beta3-AR agonist) relaxation was unaffected by CGP20712A or ICI118551 but blocked by SR58894A (beta3-AR antagonist; pA2 = 7.80). Enhanced relaxation after exposure to forskolin and pertussis toxin showed that beta3-AR relaxation can be altered by manipulation of components of the adenylate cyclase signalling pathway. 4. The beta-AR agonist RO363 relaxed the ileum (pEC50=6.18) and was blocked by CGP20712A. Relaxation by the beta2-AR agonist zinterol (pEC50=5.71) was blocked by SR58894A but not by ICI118551. 5. In rat ileum, beta1-, beta2- and beta3-AR mRNA was detected. Comparison of tissues showed that beta3-AR mRNA expression was greatest in WAT>colon=ileum >cerebral cortex>soleus; beta1-AR mRNA was most abundant in cerebral cortex > WAT > ileum = colon > soleus; beta2-AR mRNA was expressed in soleus > WAT > ileum = colon > cerebral cortex. 6. These results show that beta3-ARs are the predominant beta-AR subtype mediating rat ileal relaxation while beta1-ARs may produce a small relaxation. The beta2-AR agonist zinterol produces relaxation through beta3-ARs and there was no evidence for the involvement of beta2-ARs in relaxation despite the detection of beta2-AR mRNA.

Functional and molecular evidence for beta 1-, beta 2- and beta 3- adrenoceptors in human colon

1. Relaxation of carbachol pre-contracted human colonic muscle to (-)-isoprenaline was examined in circular, longitudinal and taenia coli preparations to determine the beta-adrenoceptor subtypes involved. beta 1-, beta 2- and beta 3-Adrenoceptor mRNAs were also measured in colonic muscle and mucosa. 2. (-)-isoprenaline caused relaxation of longitudinal smooth muscle preparations with pEC50-7.39 +/- 0.12, and this response was inhibited by both propranolol (0.1 microM, pKB 8.55 +/- 0.12) and the selective beta 1-antagonist, CGP 20712A (0.1 microM, pKB 8.80 +/- 0.20), while the selective beta 2-antagonist, ICI 118551 (0.1 microM) failed to inhibit isoprenaline relaxation consistently. 3. (-)-Isoprenaline caused relaxation of taenia coli with a pEC50 of 6.70 +/- 0.17. Propranolol (0.1 microM). CGP 20712A (0.1 microM) and ICI 118551 (0.1 microM) inhibited the isoprenaline response with similar low affinities (pKB values 7.93, 7.71 and 7.54, respectively). Carbachol pre-contracted circular smooth muscle preparations failed to relax consistently to isoprenaline and these responses were not characterized. 4. beta 1- and beta 2-Adrenoceptor mRNAs were present in circular longitudinal muscle samples and taenia coli samples, and lower levels were detected in mucosa. beta 3-mRNA was also present in both muscle preparations but was not detected in human colonic mucosa. 5. In summary, beta 1-adrenoceptors are the predominant subtype mediating isoprenaline-induced relaxation of the thin longitudinal smooth muscle of human colon, while beta 1-receptors do not appear to be involved in these responses. However, beta 3-adrenoceptors may play a role in relaxation of the taenia coli as conventional antagonist affinities are low. beta 3-Adrenoceptor mRNA was present in taenia coli and circular/longitudinal smooth muscle but absent from human colonic mucosa.

Molecular indices of neuronal and glial plasticity in the hippocampal formation in a rodent model of age-induced spatial learning impairment

Spatial learning ability was quantitated in young and aged Long-Evans rats, and molecular markers were assessed in the striatum and hippocampal formation using immunocytochemical, immunoblotting, and in situ hybridization histochemical procedures. The mRNA for beta-amyloid precursor protein (beta APP), most likely the transcript encoding the 695-amino acid form of this protein, was elevated in pyramidal and granule cells in the hippocampus of aged rats exhibiting poorer spatial learning. In immunoblots of hippocampal protein extracts, however, the level of beta APP-like immunoreactivity was depressed in the more impaired subjects. Similarly, the level in hippocampus of the mRNA for manganese-dependent superoxide dismutase (Mn-SOD), a marker of oxidative stress, was positively correlated with the degree of behavioral impairment, but immunoblotting revealed that Mn-SOD protein was depressed in the aged hippocampus compared with young. The mRNAs for the neuronal form of nitric oxide synthase and for the astrocyte marker glial fibrillary acidic protein (GFAP) were elevated in the hippocampus in correlation with the extent of learning impairment. In the striatum, the levels of mRNA and protein for several candidate genes, including GFAP, were elevated in parallel with the learning index, but these were age effects. Several hippocampal proteins were unchanged (GFAP) or depressed (beta APP and Mn-SOD) in level, despite elevations in corresponding mRNAs. In the aged cohort, hippocampal GFAP mRNA, Mn-SOD mRNA, and beta APP emerged as predictors of behavioral impairment, suggesting the involvement of these hippocampal systems in age-related cognitive impairment.

Developmental profile of messenger RNA for the corticotropin-releasing hormone receptor in the rat limbic system

The ontogeny of corticotropin-releasing hormone (CRH) receptor messenger ribonucleic acid (mRNA) in rat brain, using in situ hybridization, is the focus of this study. The developmental profile of CRH receptor using binding assays and receptor autoradiography has been reported, but may be confounded by the presence of a binding protein. The recent cloning of the rat CRH receptor gene has permitted the use of in situ hybridization histochemistry to map the distribution of cells expressing CRH receptor mRNA in the developing brain. We used antisense 35S-labeled oligodeoxynucleotide probes for the two reported splice-variants of the CRH receptor mRNA, which yielded essentially identical localization patterns. CRH receptor mRNA was clearly detectable in infant brain starting on the second postnatal day. Signal in hippocampal CA1, CA2 and CA3a increased to 300-600% of adult levels by postnatal day 6 with a subsequent gradual decline. In the amygdala, in contrast, CRH receptor mRNA abundance increased steadily between the second and the ninth postnatal days, to levels twice higher than those in the adult. In the cortex, CRH receptor mRNA levels were high on postnatal day 2 and decreased to adult levels by day 12. Transient signal over the hypothalamic paraventricular nucleus, observed on the second postnatal day, was not evident at older ages. These results demonstrate robust synthesis of CRH receptor as early as on the second postnatal day and unique region-specific developmental profiles for CRH receptor gene expression.

Developmental profile of corticotropin releasing hormone messenger RNA in the rat inferior olive

Corticotropin releasing hormone is a neurotransmitter in the inferior olive complex of marsupials and mammals. The ontogeny of corticotropin releasing hormone gene expression in the rat inferior olive has not been described. Using in-situ hybridization histochemistry in 25 animals, we established the developmental profile of the peptide's messenger ribonucleic acid in the postnatal rat. CRH-messenger RNA was first detectable in two of four animals on the fifth postnatal day. Subsequently, gene expression increased linearly with age: by day 14, CRH was expressed in all olivary complex nuclei, and the distribution and relative abundance on day 18 were comparable to those in the adult. The developmental profile of CRH-mRNA in the rat inferior olive differs from those in the mouse and opossum, and from the pattern in the rat hypothalamus, suggesting species- and site-specificity of the peptide's function.

Effects of maternal and sibling deprivation on basal and stress induced hypothalamic-pituitary-adrenal components in the infant rat

Prolonged maternal deprivation during early infancy increases basal- and stress-induced corticosterone (CORT) levels, but the underlying mechanism is not clear. In general, stressors activate the hypothalamic-pituitary-adrenal (HPA) axis, with secretion and compensatory synthesis of hypothalamic cortcotropin-releasing hormone (CRH). In the infant rat, we have demonstrated that maximally tolerated acute cold stress induced a robust elevation of plasma CORT throughout the first 2 postnatal weeks. However CRH messenger RNA (CRH-mRNA) abundance 4 h subsequent to cold stress was enhanced only in rats aged 9 days or older. This suggests a developmental regulation of the CRH component of the HPA-response to this stressor. The present study examined whether increased basal and cold stress-induced CORT levels after 24 h of maternal deprivation were due to enhanced CRH-mRNA abundance in the hypothalamic paraventricular nucleus (PVN). CRH-mRNA abundance, and basal- and cold-induced plasma CORT levels were measured in maternally deprived 6 and 9-day-old pups compared to non-deprived controls. Maternal deprivation increased basal and cold-induced CORT levels on both 6 and 9-day-old rats. CRH-mRNA abundance in the PVN of deprived rats did not differ from that in non-deprived rats. Our results indicate that the enhanced basal and stress-induced plasma CORT observed after 24 h maternal deprivation is not due to increased CRH-mRNA abundance in the PVN.

Hemoglobin switching in sheep: only the gamma gene is in the active conformation in fetal liver but all the beta and gamma genes are in the active conformation in bone marrow

Differential expression of the closely linked gamma, beta(A) (or beta(B)), and beta(C) globin genes in sheep results in the production of fetal hemoglobin (Hb F, alpha(2)gamma(2)) during gestation and the adult hemoglobins (Hb A, alpha(2)beta(2) (A), and Hb B, alpha(2)beta(2) (B)) after birth. Erythropoietic stress in certain animals leads to production of Hb C (alpha(2)beta(2) (C)). The molecular mechanism of differential expression of these genes in nuclei of fetal and adult erythroid cells has been investigated by analysis of their susceptibility to digestion by DNase I (genes that are in the conformation associated with active transcription are sensitive to this nuclease). The concentration of globin gene sequences in DNA from control and DNase I-digested nuclei was determined by annealing to synthetic DNAs and analogous cDNA probes derived from recombinant plasmids containing one of the sheep globin genes. In nuclei from sheep fetal liver erythroid cells, the gamma genes but not the beta genes were digested by DNase I; the gamma locus was open but the beta(A) or beta(C) loci was closed, consistent with synthesis of only Hb F by these cells. DNase I digestion of nuclei from bone marrow of anemic sheep making only Hb C or Hb B resulted in equivalent digestion of the beta and gamma gene sequences, although gamma mRNA was not detected in these cells. Digestion by DNase I did not decrease the globin gene sequence concentration in residual DNA of spleen nuclei. As a further control, DNA from digested bone marrow and spleen nuclei were shown to anneal equally well to a cDNA prepared from liver polysomal mRNA. Differential expression of the gamma and beta globin genes in sheep fetal erythroid cell appears to be based on differences in chromatin structure. The gamma globin gene remains in the active conformation in adult erythroid cells; failure of gamma mRNA to accumulate in these cells probably reflects transcriptional or post-transcriptional regulation.

Replacement of ribosomal protein S1 by interference factor ialpha in ribosomal binding of phage Ms2 RNA

The MS2 RNA binding capacity of 30S ribosomal subunits, which is lost when protein S1 is removed, can be restored following incubation with interference factor ialpha and repelleting. Polyacrylamide-agarose gel electrophoresis shows that, under these conditions, a faster moving, non-RNA binding 30S species, which contains no S1, is converted to a slower moving RNA-binding one, having the same mobility as the 30S species that contains protein S1. Factor ialpha binds to single-stranded RNAs in a pattern that closely resembles the RNA binding pattern of initiation factor IF-3.

Transcription of polydeoxythymidylate sequences in the genome of the cellular slime mold, Dictyostelium discoideum

Messenger RNA of the cellular slime mold, Dictyostelium discoideum, contains about equimolar amounts of two classes of poly(adenylic acid) [poly(A)]; one is about 25 nucleotides long and the second about 100 nucleotides long. At least half of the messenger RNA molecules contain one sequence each of poly(A)(25) and poly(A)(100); both poly(A) sequences are located near the 3' end of messenger RNA, and the kinetics of their appearance on messenger RNA precursor indicates that poly(A)(25) is added before poly(A)(100). Dictyostelium nuclear DNA contains 14,000-15,000 sequences of poly(dT)(25) which could code for the smaller poly(A) residues. The poly(A)(100) must be added post-transcriptionally. The poly(dT)(25) sequences are interspersed throughout the genome and may well represent transcription termination regions.

Differential metabolism of large and small poly(A) sequences in the heterogeneous nuclear RNA of HeLa cells

The heterogeneous RNA of the HeLa cell nucleus contains short internal poly(A) sequences which, in contrast to the longer poly(A) sequences at the 3' ends, are not found in messenger RNA of the cytoplasm. A distinct origin for each of these homologous sequences is evident when the effects of actinomycin D and 3'-deoxyadenosine on their biosynthesis are compared. The shorter poly(A) appears to be transcribed, while the longer one does not. A kinetic analysis of the metabolism of each type of poly(A) sequence within different size classes of HnRNA after treatment of the cells with 3'-deoxyadenosine reveals distinctive distribution and metabolism of these sequences and also provides insight into mechanisms proposed for the generation of messenger RNA from these large RNA molecules in the nucleus.

Tissue-specific transcription of the globin gene in isolated chromatin

RNA was transcribed from chrmation from mouse fetal liver or brain, by use of DNA-dependent RNA polymerase of Escherichia coli. Globin messenger RNA sequences in the transcript were measured with complementary DNA copied from globin messenger RNA with RNA-dependent DNA polymerase. Globin messenger RNA sequences were found in RNA newly transcribed from chromatin from erythropoietic tissue but not in that transcribed from brain chromatin.

Application of fingerprinting techniques to iodinated nucleic acids

Several techniques of RNA and DNA finger-printing and determination of sequence have been applied to nucleic acids labeled with (125)I. Fingerprints of human 5S RNA and bacteriophage f2 RNA resemble those of their noniodinated counterparts both in complexity and in specific pattern. Iodination as used here is thus a general labeling procedure, and appears principally to label cytidine residues. This iodination method shows little sensitivity to potential structure in single-stranded RNA molecules, yields stable oligonucleotide products in a reproducible manner, and does not change the specificity of several ribonucleases and deoxyribonucleases.

Discriminatory ribosome rebinding of isolated regions of protein synthesis initiation from the ribonucleic acid of bacteriophage R17

To determine whether bacterial ribosomes recognize a distinguishing feature in the immediate vicinity of actual initiator codons or are directed to these sites through involvement of other portion(s) of the mRNA molecule, the interaction between ribosomes and defined (32)P-labeled initiator fragments from R17 RNA was studied. When incubated with mixtures of the three sites, ribosomes from Bacillus stearothermophilus (which initiate only the A protein on intact phage RNA) are able to select out the A fragment and discriminate against the coat and replicase initiator regions. By contrast, Escherichia coli ribosomes do not rebind that coat-protein region of R17 most efficiently, as they in the native RNA, but likewise prefer the A-protein initiator fragment. In both cases, ribosome binding of the isolated A site is comparable by several criteria to normal polypeptide-chain initiation on an intact R17 messenger RNA in vitro. E. coli ribosomal preference for the A site is confirmed in experiments with randomly fragmented R17 RNA, by both the initiation dipeptide and ribosome protection assay. Thus the A-protein ribosome-binding site of R17 RNA appears intrinsically to be a good initiator, while efficient recognition of the coat and replicase regions requires the participation of some portion of the remainder of the phage RNA molecule.

Glutamine synthetase induction in embryonic neural retina: immunochemical identification of polysomes involved in enzyme synthesis

Glutamine synthetase (EC 6.3.1.2) in embryonic neural retina in culture is rapidly induced by hydrocortisone. Retina polysomes involved in translation of this enzyme were precipitated with a high degree of specificity by the gammaglobulin isolated from antiserum against the enzyme (anti-enzyme gammaglobulin). Using immunoprecipitation procedures, we determined that the amount of polysome-bound nascent enzyme was maximal in polysomes comprising 9-14 ribosomes and was about 3-fold higher in the induced than in the noninduced retina. Within this size group of polysomes, those comprising 11-13 ribosomes showed consistently greater binding of anti-enzyme [(125)I]gammaglobulin than of normal [(125)I]-gammaglobulin. This size of polysomes corresponds to that calculated for a monocistronic messenger RNA for the subunit of this enzyme, which has a molecular weight of 42,000. The application of immunochemical techniques to identification of templates for synthesis of an enzyme in embryonic cells that constitutes less than 1% of the total cellular proteins indicates the usefulness of this method for detailed studies on regulation of other quantitatively minor products significant in cell differentiation.

Double-stranded RNA as an inhibitor of protein synthesis and as a substrate for a nuclease in extracts of Krebs II ascites cells

Concentrations of double-stranded RNA above about 0.1 mug/ml inhibit translation of encephalo-myocarditis viral RNA and mouse globin messenger RNA in extracts of Krebs II ascites cells. Protein synthesis initially proceeds at the control rate, then abruptly shuts off in a manner similar to that observed in reticulocyte lysates [Hunt, T. & Ehrenfeld, E. (1971) Nature New Biol. 230, 91-94]. Substantially higher concentrations of double-stranded RNA are required to give this effect in ascites extracts. Subcellular fractions of Krebs II ascites cells contain a nucleolytic activity capable of digesting several natural and synthetic double-stranded RNAs. This nuclease is most active under conditions of protein synthesis, and part of the activity remains associated with ribosomes upon sedimentation. It is probably because of digestion of double-stranded RNA by this nuclease that higher concentrations of double-stranded RNA are required for inhibition of protein synthesis in Krebs cell extracts than in reticulocyte lysates.

Occurrence of uridylate-rich oligonucleotide regions in heterogeneous nuclear RNA of HeLa cells

Heterogeneous nuclear RNA molecules from HeLa cells contain a specific segment of about 30 nucleotides length that is largely (about 80%) uridylic acid. This oligo(U) segment is located predominantly in the larger (70S-90S) heterogeneous nuclear RNA molecules, and is essentially absent in messenger RNA and 45S ribosomal precursor RNA molecules. The oligo(U) hybridizes rapidly to cellular DNA, suggesting that it is transcribed from the repeated regions of the DNA.

Induction of avidin synthesis by RNA obtained from chick oviduct

RNA was extracted from oviduct, shell gland, and liver of chicks treated with diethylstilbestrol and a combination of diethylstilbestrol and progesterone. Preparations containing 500 or 2500 mug of RNA were put in the oviductal lumen of diethylstilbestrol-treated chicks for 24 hr, and the avidin content of the oviduct was determined by measurement of [(14)C]biotin binding. The results of the present study demonstrate that oviduct RNA from chicks treated with progesterone induces synthesis of avidin in chick oviduct. In contrast, liver or shell gland RNA from chicks treated with progesterone, and liver or oviduct RNA from chicks treated with diethylstilbestrol are incapable of inducing avidin synthesis. The inducing capacity of oviduct RNA is destroyed when it is treated with ribonuclease. It is hypothesized that progesterone induces the synthesis of new species of oviduct RNA, which serve as messenger(s) for avidin synthesis. This hypothesis is offered in consideration of the findings: (i) that the residual amount of progesterone present as a contaminant in oviduct RNA from chicks treated with progesterone is far too low to account for the induced avidin synthesis; (ii) that such oviduct RNA from chicks treated with progesterone induces a slight synthesis of avidin in chick shell gland, which ordinarily does not produce avidin in response to progesterone administration and; (iii) that such RNA added in vitro to minces of oviductal tissues incubated in biotin-free medium for 24 hr induces synthesis of avidin.

Double-stranded regions in heterogeneous nuclear RNA from Hela cells

Heterogeneous nuclear RNA from HeLa cells contains double-stranded regions that arise by base pairing of complementary sequences that exist as parts of the same molecule (intramolecular base pairing). When denatured, the RNA sequences that form the double-stranded regions hybridize rapidly to HeLa cell DNA, suggesting that they are transcribed from reiterated sites in the genome. The messenger RNA does not contain the same class or amount of double-stranded RNA regions found in heterogeneous nuclear RNA.

Calf crystallin synthesis in frog cells: the translation of lens-cell 14S RNA in oocytes

14S RNA isolated from calf-lens polyribosomes was injected into oocytes of the frog Xenopus laevis. Oocytes injected with 14S RNA and buffer contained a protein resembling the A2 chain of calf alpha-crystallin; oocytes injected with buffer alone contained no crystallin-like material. alphaA2 crystallin polypeptides were identified by various criteria: urea-gel electrophoresis under acidic and basic conditions, gel electrophoresis in sodium dodecyl sulfate, N-terminal analysis, and paper chromatography of methionine-containing tryptic peptides. It is concluded that when it is injected into a living frog oocyte, the 14S RNA from lens tissue is reasonably stable and has the properties of an alphaA2 crystallin messenger. The messenger requires no lens cell-specific components for translation within the oocyte, and the translational machinery of the frog cell will accept messenger RNA from a totally different cell type from another species. The A2 chains of alpha-crystallin extracted from lens tissue possess an acetylated N-terminal methionine residue; the N-terminal methionine of alphaA2 chains derived from frog oocytes injected with 14S RNA was also acetylated.

Evidence for induction by cortisol in vitro of a protein inhibitor of transport and phosphorylation processes in rat thymocytes

Studies of intact rat thymocytes incubated in vitro with cortisol, actinomycin D, puromycin, and cycloheximide indicate that distinct inhibitory effects of cortisol on transport and phosphorylation are due to an action on mRNA synthesis with consequent induction of synthesis of protein(s) with inhibitory influence. Incubation of thymocytes with cortisol results in inhibition of the rate of labeled orthophosphate incorporation into ATP and the entry of rubidium ion and hexoses into the cells. Continuing protein synthesis is required for the progressive and persistent manifestation of the inhibitory effects of the steroid. RNA synthesis is also required during the initial phase of incubation of cells with cortisol, but significant inhibitory effects of cortisol, once initiated, are evident for at least 60-120 min after addition of actinomycin D. In contrast, addition of cycloheximide some time after cortisol results in prevention or reversal of the effects of the steroid. In the absence of cortisol, the antibiotics exert relatively little effect on orthophosphate incorporation and on the transport processes studied. It is suggested that the sequence of events leading to dissolution of thymocytes exposed to cortisol is initiated by the synthesis of mRNA coding for inhibitory protein(s) with more rapid turnover rates than that of the mRNA, and that these events are modulated by the relative sensitivity of different cellular processes to the protein inhibitor(s).

Polyadenylic acid sequences in the heterogeneous nuclear RNA and rapidly-labeled polyribosomal RNA of HeLa cells: possible evidence for a precursor relationship

Polyadenylate sequences have been found covalently linked in heterogeneous DNA-like nuclear RNA of HeLa cells. This poly(A) material seems homogeneous in size and accounts for about 0.5% of such RNA. Similar poly(A) sequences were found in rapidly-labeled polyribosomal RNA, thought to be messenger RNA. A possible model for mRNA synthesis from large heterogeneous nuclear RNA precursor molecules is discussed.