Amplification of 5′ end cDNA with 'new RACE'

LncRNA CHKB-DT Downregulation Enhances Dilated Cardiomyopathy Through ALDH2

BACKGROUND

Human cardiac long noncoding RNA (lncRNA) profiles in patients with dilated cardiomyopathy (DCM) were previously analyzed, and the long noncoding RNA CHKB (choline kinase beta) divergent transcript (CHKB-DT) levels were found to be mostly downregulated in the heart. In this study, the function of CHKB-DT in DCM was determined.

METHODS

Long noncoding RNA expression levels in the human heart tissues were measured via quantitative reverse transcription-polymerase chain reaction and in situ hybridization assays. A CHKB-DT heterozygous or homozygous knockout mouse model was generated using the clustered regularly interspaced palindromic repeat (CRISPR)/CRISPR-associated protein 9 system, and the adeno-associated virus with a cardiac-specific promoter was used to deliver the RNA in vivo. Sarcomere shortening was performed to assess the primary cardiomyocyte contractility. The Seahorse XF cell mitochondrial stress test was performed to determine the energy metabolism and ATP production. Furthermore, the underlying mechanisms were explored using quantitative proteomics, ribosome profiling, RNA antisense purification assays, mass spectrometry, RNA pull-down, luciferase assay, RNA-fluorescence in situ hybridization, and Western blotting.

RESULTS

CHKB-DT levels were remarkably decreased in patients with DCM and mice with transverse aortic constriction-induced heart failure. Heterozygous knockout of CHKB-DT in cardiomyocytes caused cardiac dilation and dysfunction and reduced the contractility of primary cardiomyocytes. Moreover, CHKB-DT heterozygous knockout impaired mitochondrial function and decreased ATP production as well as cardiac energy metabolism. Mechanistically, ALDH2 (aldehyde dehydrogenase 2) was a direct target of CHKB-DT. CHKB-DT physically interacted with the mRNA of ALDH2 and fused in sarcoma (FUS) through the GGUG motif. CHKB-DT knockdown aggravated ALDH2 mRNA degradation and 4-HNE (4-hydroxy-2-nonenal) production, whereas overexpression of CHKB-DT reversed these molecular changes. Furthermore, restoring ALDH2 expression in CHKB-DT+/- mice alleviated cardiac dilation and dysfunction.

CONCLUSIONS

CHKB-DT is significantly downregulated in DCM. CHKB-DT acts as an energy metabolism-associated long noncoding RNA and represents a promising therapeutic target against DCM.

A standard workflow for community-driven manual curation of Strongyloides genome annotations

Advances in the functional genomics and bioinformatics toolkits for Strongyloides species have positioned these species as genetically tractable model systems for gastrointestinal parasitic nematodes. As community interest in mechanistic studies of Strongyloides species continues to grow, publicly accessible reference genomes and associated genome annotations are critical resources for researchers. Genome annotations for multiple Strongyloides species are broadly available via the WormBase and WormBase ParaSite online repositories. However, a recent phylogenetic analysis of the receptor-type guanylate cyclase (rGC) gene family in two Strongyloides species highlights the potential for errors in a large percentage of current Strongyloides gene models. Here, we present three examples of gene annotation updates within the Strongyloides rGC gene family; each example illustrates a type of error that may occur frequently within the annotation data for Strongyloides genomes. We also extend our analysis to 405 previously curated Strongyloides genes to confirm that gene model errors are found at high rates across gene families. Finally, we introduce a standard manual curation workflow for assessing gene annotation quality and generating corrections, and we discuss how it may be used to facilitate community-driven curation of parasitic nematode biodata. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Genome-Wide Mapping of 5' Isoforms with 5'-Seq

The transcriptome is far more complex than previously assumed. Transcripts from the same gene can differ in terms of transcription start site, transcription end site, or pattern of splicing, and growing evidence supports the functional importance of these distinct transcript isoforms. Easily identifying these isoforms experimentally via library construction and high-throughput sequencing is crucial. Current library construction methods for identifying transcription start sites (5' transcript isoforms) involve large number of steps and (expensive) reagents, utilization of cDNA intermediates for adapter ligation, and are less suitable for studying low-abundance isoforms. Here, I describe a quick protocol for the generation of sequencing libraries to define capped 5' isoforms (5'-Seq) of various abundances in yeast and suggest a 5' isoform data analysis pipeline. The protocol relies on the utilization of a dephosphorylation-decapping method (oligo-capping) to generate a sequencing library from mRNA fragments and is a simplification of previously published 5' isoform protocols in terms of the handling steps, time, and cost. This method is exemplified using Saccharomyces cerevisiae mRNA, but it can be applied to various cellular conditions to study the effects of 5' transcript isoforms on transcriptional and/or translational regulation. © 2023 Wiley Periodicals LLC. Basic Protocol: Construction of a DNA sequencing library from capped 5' isoforms Support Protocol: Sequencing data analysis.

A versatile 5′ RACE-Seq methodology for the accurate identification of the 5′ termini of mRNAs

Background

Technological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5′ ends of mRNAs are significantly underrepresented in these datasets, hindering the efficient analysis of the complex human transcriptome. The implementation of the template-switching mechanism at the reverse transcription stage along with 5′ rapid amplification of cDNA ends (RACE) constitutes the most prominent and efficient strategy to specify the actual 5′ ends of cDNAs. In the current study, we developed a 5′ RACE-seq method by coupling a custom template-switching and 5′ RACE assay with targeted nanopore sequencing, to accurately unveil 5′ termini of mRNA targets.

Results

The optimization of the described 5′ RACE-seq method was accomplished using the human BCL2L12 as control gene. We unveiled that the selection of hybrid DNA/RNA template-switching oligonucleotides as well as the complete separation of the cDNA extension incubation from the template-switching process, significantly increase the overall efficiency of the downstream 5′ RACE. Collectively, our results support the existence of two distinct 5′ termini for BCL2L12, being in complete accordance with the results derived from both direct RNA and PCR-cDNA sequencing approaches from Oxford Nanopore Technologies. As proof of concept, we implemented the described 5′ RACE-seq methodology to investigate the 5′ UTRs of several kallikrein-related peptidases (KLKs) gene family members. Our results confirmed the existence of multiple annotated 5′ UTRs of the human KLK gene family members, but also identified novel, previously uncharacterized ones.

Conclusions

In this work we present an in-house developed 5′ RACE-seq method, based on the template-switching mechanism and targeted nanopore sequencing. This approach enables the broad and in-depth study of 5′ UTRs of any mRNA of interest, by offering a tremendous sequencing depth, while significantly reducing the cost-per reaction compared to commercially available kits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08386-y.

A gene regulatory network for antenna size control in carbon dioxide-deprived Chlamydomonas reinhardtii cells

In green microalgae, prolonged exposure to inorganic carbon depletion requires long-term acclimation responses, involving modulated gene expression and the adjustment of photosynthetic activity to the prevailing supply of carbon dioxide. Here, we describe a microalgal regulatory cycle that adjusts the light-harvesting capacity at photosystem II (PSII) to the prevailing supply of carbon dioxide in Chlamydomonas (Chlamydomonas reinhardtii). It engages low carbon dioxide response factor (LCRF), a member of the squamosa promoter-binding protein (SBP) family of transcription factors, and the previously characterized cytosolic translation repressor nucleic acid-binding protein 1 (NAB1). LCRF combines a DNA-binding SBP domain with a conserved domain for protein-protein interaction. LCRF transcription is rapidly induced by carbon dioxide depletion. LCRF activates NAB1 transcription by specifically binding to tetranucleotide motifs present in its promoter. Accumulation of the NAB1 protein enhances translational repression of its prime target mRNA, encoding the PSII-associated major light-harvesting protein LHCBM6. The resulting truncation of the PSII antenna size helps maintaining a low excitation during carbon dioxide limitation. Analyses of low carbon dioxide acclimation in nuclear insertion mutants devoid of a functional LCRF gene confirm the essentiality of this novel transcription factor for the regulatory circuit.

Genomic Sequencing and Comparison of Sacbrood Viruses from Apis cerana and Apis mellifera in Taiwan

Sacbrood virus (SBV) was the first identified bee virus and shown to cause serious epizootic infections in the population of Apis cerana in Taiwan in 2015. Herein, the whole genome sequences of SBVs in A. cerana and A. mellifera were decoded and designated AcSBV-TW and AmSBV-TW, respectively. The whole genomes of AcSBV-TW and AmSBV-TW were 8776 and 8885 bp, respectively, and shared 90% identity. Each viral genome encoded a polyprotein, which consisted of 2841 aa in AcSBV-TW and 2859 aa in AmSBV-TW, and these sequences shared 95% identity. Compared to 54 other SBVs, the structural protein and protease regions showed high variation, while the helicase was the most highly conserved region among SBVs. Moreover, a 17-amino-acid deletion was found in viral protein 1 (VP1) region of AcSBV-TW compared to AmSBV-TW. The phylogenetic analysis based on the polyprotein sequences and partial VP1 region indicated that AcSBV-TW was grouped into the SBV clade with the AC-genotype (17-aa deletion) and was closely related to AmSBV-SDLY and CSBV-FZ, while AmSBV-TW was grouped into the AM-genotype clade but branched independently from other AmSBVs, indicating that the divergent genomic characteristics of AmSBV-TW might be a consequence of geographic distance driving evolution, and AcSBV-TW was closely related to CSBV-FZ, which originated from China. This 17-amino-acid deletion could be found in either AcSBV or AmSBV in Taiwan, indicating cross-infection between the two viruses. Our data revealed geographic and host specificities between SBVs. The amino acid difference in the VP1 region might serve as a molecular marker for describing SBV cross-infection.

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.

Evolving methods for rational de novo design of functional RNA molecules

Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to experimental screening and selection pipelines. In this review, we describe methods common to many such computational approaches, thoroughly dissect these methods and highlight open questions for the individual steps. Initially, it is essential to investigate the biological target system, the regulatory mechanism that will be exploited, as well as the desired components in order to define design objectives. Subsequent computational design is needed to combine the selected components and to obtain novel functionality. This process can usually be split into constrained sequence sampling, the formulation of an optimization problem and an in silico analysis to narrow down the number of candidates with respect to secondary goals. Finally, experimental analysis is important to check whether the defined design objectives are indeed met in the target environment and detailed characterization experiments should be performed to improve the mechanistic models and detect missing design requirements.

ESR2 Is Essential for Gonadotropin-Induced Kiss1 Expression in Granulosa Cells

Hypothalamic expression of Kiss1 plays an essential role in the onset of puberty, gonadal development, and ovulation. Estrogens regulate the expression of Kiss1 in the hypothalamus through estrogen receptor-α. Kiss1 is also expressed in the ovary, where its expression correlates with the onset of puberty and progression of the estrous cycle. To date, estrogen regulation of Kiss1 expression in the ovary has not been investigated. We recently observed that gonadotropin-induced Kiss1 expression was absent in Esr2-null rat ovaries even though Esr1 was present. Wild-type granulosa cells abundantly expressed Kiss1 and oocytes expressed the Kiss1 receptor. We characterized estrogen receptor-β (ESR2) regulation of Kiss1 expression in granulosa cells by identifying granulosa cell-specific transcript variants and potential regulatory regions. The Kiss1 promoter, an upstream enhancer, and a downstream enhancer all possessed conserved estrogen response elements (EREs) and showed active histone marks in gonadotropin-stimulated granulosa cells. The transcriptionally active Kiss1 promoter, as well as the enhancers, also revealed enrichment for ESR2 binding. Furthermore, activity of a Kiss1 promoter construct was induced after overexpression of ESR2 and was blocked upon mutation of an ERE within the promoter. Finally, pregnant mare serum gonadotropin and human chorionic gonadotropin administration induced phosphorylation of ESR2 and upregulated the AP-1 proteins FOSL2 and JUNB in granulosa cells. Activated MAPK ERK2 was associated with the ESR2 phosphorylation in granulosa cells, and AP-1 factors could synergistically activate the Kiss1 promoter activity. These gonadotropin-induced changes paralleled Kiss1 expression in granulosa cells. We conclude that gonadotropin-stimulated Kiss1 expression in granulosa cells is dependent on both the activation of ESR2 and the upregulation of AP-1.

Microprocessor Recruitment to Elongating RNA Polymerase II Is Required for Differential Expression of MicroRNAs

The cellular abundance of mature microRNAs (miRNAs) is dictated by the efficiency of nuclear processing of primary miRNA transcripts (pri-miRNAs) into pre-miRNA intermediates. The Microprocessor complex of Drosha and DGCR8 carries this out, but it has been unclear what controls Microprocessor's differential processing of various pri-miRNAs. Here, we show that Drosophila DGCR8 (Pasha) directly associates with the C-terminal domain of the RNA polymerase II elongation complex when it is phosphorylated by the Cdk9 kinase (pTEFb). When association is blocked by loss of Cdk9 activity, a global change in pri-miRNA processing is detected. Processing of pri-miRNAs with a UGU sequence motif in their apical junction domain increases, while processing of pri-miRNAs lacking this motif decreases. Therefore, phosphorylation of RNA polymerase II recruits Microprocessor for co-transcriptional processing of non-UGU pri-miRNAs that would otherwise be poorly processed. In contrast, UGU-positive pri-miRNAs are robustly processed by Microprocessor independent of RNA polymerase association.

Rapid Amplification of cDNA Ends for RNA Transcript Sequencing in Staphylococcus

Rapid amplification of cDNA ends (RACE) is a technique that was developed to swiftly and efficiently amplify full-length RNA molecules in which the terminal ends have not been characterized. Current usage of this procedure has been more focused on sequencing and characterizing RNA 5' and 3' untranslated regions. Herein is described an adapted RACE protocol to amplify bacterial RNA transcripts.

Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi

Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3' poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNA (Met)-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5' end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.

Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics

Co-translational mRNA degradation is a widespread process in which 5'-3' exonucleolytic degradation follows the last translating ribosome, thus producing an in vivo ribosomal footprint that delimits the 5' position of the mRNA molecule within the ribosome. To study this degradation process and ribosome dynamics, we developed 5PSeq, which is a method that profiles the genome-wide abundance of mRNA degradation intermediates by virtue of their 5'-phosphorylated (5'P) ends. The approach involves targeted ligation of an oligonucleotide to the 5'P end of mRNA degradation intermediates, followed by depletion of rRNA molecules, reverse transcription of 5'P mRNAs and Illumina high-throughput sequencing. 5PSeq can identify translational pauses at rare codons that are often masked when using alternative methods. This approach can be applied to previously extracted RNA samples, and it is straightforward and does not require polyribosome purification or in vitro RNA footprinting. The protocol we describe here can be applied to Saccharomyces cerevisiae and potentially to other eukaryotic organisms. Three days are required to generate 5PSeq libraries.

An efficient full-length cDNA amplification strategy based on bioinformatics technology and multiplexed PCR methods

A novel strategy for amplification full-length cDNA and promoter sequences has been developed using bioinformatics technology and multiplexed PCR methods in this study. The amplification of 3′ ends of cDNA is performed according to the modified classic 3′ RACE techniques, therein the more efficient and effective oligo(dT)-anchor primer with hairpin structure is specially designed. For the amplification of 5′ ends of cDNA, two or three-round TAIL-PCR or touch-down PCR using arbitrary degenerate (AD) and sequence-specific reverse (SPR) primers is performed until the 5′ sequence of multi-assembled fragment reaches the exon1 region identified by aligning this fragment to reference genome database. Then another TAIL-PCR or touch-down PCR using genomic DNA as template is conducted to obtain the remaining 5′ and promoter sequences. The 5′ end sites of cDNA are predicted by aligning finally assembled fragment to homologous reference genes of other species, and screening the relative locations of common characteristic cis-elements in silico on promoter. The putative 5′ ends are further validated by primers corresponding to these predicted sites in cDNAs. This method is suitable for researchers to isolate limited full-length cDNA sequences due to its operability, inexpensiveness, efficiency and speediness.

Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells

Complement receptor 2 (CR2/CD21) is predominantly expressed on the surface of mature B cells where it forms part of a coreceptor complex that functions, in part, to modulate B-cell receptor signal strength. CR2/CD21 expression is tightly regulated throughout B-cell development such that CR2/CD21 cannot be detected on pre-B or terminally differentiated plasma cells. CR2/CD21 expression is upregulated at B-cell maturation and can be induced by IL-4 and CD40 signaling pathways. We have previously characterized elements in the proximal promoter and first intron of CR2/CD21 that are involved in regulating basal and tissue-specific expression. We now extend these analyses to the CR2/CD21 core promoter. We show that in mature B cells, CR2/CD21 transcription proceeds from a focused TSS regulated by a non-consensus TATA box, an initiator element and a downstream promoter element. Furthermore, occupancy of the general transcriptional machinery in pre-B versus mature B-cell lines correlate with CR2/CD21 expression level and indicate that promoter accessibility must switch from inactive to active during the transitional B-cell window.

SpBADH of the halophyte Sesuvium portulacastrum strongly confers drought tolerance through ROS scavenging in transgenic Arabidopsis

Glycine betaine (GB) accumulation is involved in abiotic stress. However, it is not known whether BADH, the key enzyme of GB synthesis, utilizes the antioxidant system to confer drought stress tolerance. In this study, a novel member of the ALDH10 gene family, SpBADH, was isolated from Sesuvium portulacastrum. The expression of this gene was up-regulated by NaCl, PEG6000, H2O2, ABA and high temperature in S. portulacastrum. SpBADH overexpression in Arabidopsis resulted in higher BADH activity and GB content and might increase tolerance to drought/osmotic stresses, specifically strong tolerance to drought stress. Transgenic lines exhibited lower MDA and H2O2 contents but higher proline, POD, SOD and CAT contents than the wild type under drought and osmotic stresses. SpBADH overexpression in Arabidopsis also enhanced the expression of ROS-related genes including AtSOD, AtPOD, AtCAT, AtAPX and Atpsb under drought and osmotic stresses. Thus, SpBADH increases plant tolerance to drought or osmotic stresses by reducing H2O2, increasing proline, and activating antioxidative enzymes to improve ROS scavenging.

Identification and complete genome analysis of kobuvirus in faecal samples of European roller (Coracias garrulus): for the first time in a bird

The genus Kobuvirus (Picornaviridae) consists of three species, Aichivirus A (e.g., Aichi virus, which infects humans), Aichivirus B and Aichivirus C. Kobuvirus have not been detected in non-mammal species including birds. In this study, a novel kobuvirus was identified in 3 (17 %) out of 18 faecal samples collected from European rollers (Coracias garrulus) in Hungary. The complete genome sequence of strain SZAL6-KoV/2011/HUN (KJ934637), which was determined using a novel 5'/3' RACE method (dsRNA-RACE) involving a double-stranded (ds)RNA intermediate, has a type-V IRES at the 5' end and a cis-acting element (CRE) in the 3C gene and encodes L and 2A(H-box/NC) proteins, but it does not contain the sequence forming a "barbell-like" secondary RNA structure in the 3'UTR. SZAL6-KoV/2011/HUN has 72 %, 73 %, and 81 % amino acid sequence identity to the P1, P2, and P3 protein, respectively, of Aichi virus. Evolutionary analysis showed that SZAL6-KoV/2011/HUN shares a common ancestor with other kobuviruses but belongs to a more ancient lineage in the species Aichivirus A. Investigation of the known kobuviruses in different animals and discovery of novel kobuviruses in potential host species helps to clarify the evolutionary connection and zoonotic potential of kobuviruses.

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

Hundreds of transcript isoforms with varying boundaries and alternative regulatory signals are transcribed from the genome, even in a genetically homogeneous population of cells. To study this transcriptional heterogeneity, we developed transcript isoform sequencing (TIF-seq), a method that allows the genome-wide profiling of full-length transcript isoforms defined by their exact 5' and 3' boundaries. TIF-seq entails the generation of full-length cDNA libraries, followed by their circularization and the sequencing of the junction fragments spanning the 5' and 3' transcript ends. By determining the respective co-occurrence of start and end sites of individual transcript molecules, TIF-seq can distinguish variations that conventional approaches for mapping single ends cannot, such as short abortive transcripts, bicistronic messages and overlapping transcripts that differ in lengths. The TIF-seq protocol we describe here can be applied to any eukaryotic organism (e.g., yeast, human), and it requires 6-10 d for generating TIF-seq libraries, 10 d for sequencing and 2-3 d for analysis.

Localization and divergent profiles of estrogen receptors and aromatase in the vocal and auditory networks of a fish with alternative mating tactics

Estrogens play a salient role in the development and maintenance of both male and female nervous systems and behaviors. The plainfin midshipman (Porichthys notatus), a teleost fish, has two male reproductive morphs that follow alternative mating tactics and diverge in multiple somatic, hormonal, and neural traits, including the central control of morph-specific vocal behaviors. After we identified duplicate estrogen receptors (ERβ1 and ERβ2) in midshipman, we developed antibodies to localize protein expression in the central vocal-acoustic networks and saccule, the auditory division of the inner ear. As in other teleost species, ERβ1 and ERβ2 were robustly expressed in the telencephalon and hypothalamus in vocal-acoustic and other brain regions shown previously to exhibit strong expression of ERα and aromatase (estrogen synthetase, CYP19) in midshipman. Like aromatase, ERβ1 label colocalized with glial fibrillary acidic protein (GFAP) in telencephalic radial glial cells. Quantitative polymerase chain reaction revealed similar patterns of transcript abundance across reproductive morphs for ERβ1, ERβ2, ERα, and aromatase in the forebrain and saccule. In contrast, transcript abundance for ERs and aromatase varied significantly between morphs in and around the sexually polymorphic vocal motor nucleus (VMN). Together, the results suggest that VMN is the major estrogen target within the estrogen-sensitive hindbrain vocal network that directly determines the duration, frequency, and amplitude of morph-specific vocalizations. Comparable regional differences in steroid receptor abundances likely regulate morph-specific behaviors in males and females of other species exhibiting alternative reproductive tactics.

Temporal classification and mapping of non-polyadenylated transcripts of an invertebrate iridovirus

The temporal expression of the 54 Chilo iridescent virus (CIV) virion protein genes was investigated by combining drug treatments that inhibit protein or DNA synthesis and an RT-PCR strategy particularly suitable for non-polyadenylated mRNAs. This method generates a uniform 3′ terminus by ligation of a 5′-phosphorylated oligonucleotide to the 3′ end of the transcript that is recognized by a complementary primer during RT-PCR. This analysis showed that CIV virion proteins are encoded by genes in all three predetermined temporal classes: 23 immediate-early, 11 delayed-early and seven late virion gene transcripts were identified and assigned to ORFs. Early transcription of many virion protein genes supports the notion that virion proteins may also play essential roles in the initial stages of infection. In addition, some of the early gene products present in the virion may reflect the intracellular path that the virus follows during infection.

Glucocorticoid and androgen signaling pathways diverge between advertisement calling and non-calling fish

Behavioral and neuroendocrine mechanisms of social vocalization in teleost fish are influenced by the glucocorticoid cortisol and the androgen 11-ketotestosterone (11kT). The relative abundance of both 11kT, which binds to androgen receptors (ARα, ARβ), and cortisol, which binds to glucocorticoid receptors (GR-1, GR-2), is regulated by 11β-hydroxylase (11βH) that converts 11-deoxycortisol to cortisol and testosterone to 11β-OH-testosterone, and 11β-hydroxysteroid dehydrogenase (11βHSD) that converts cortisol to the inactive metabolite cortisone and 11β-OH-testosterone to 11kT. In midshipman fish, we tested the hypothesis that plasma steroid levels, mRNA abundance for 11βH and 11βHSD in the vocal muscle and testis (known site of 11kT synthesis), and mRNA abundances for ARs and GRs in vocal muscle, would differ between males that did or did not recently produce 'hum' advertisement calls. Quantitative real-time PCR demonstrated that non-calling male vocal muscle had significantly higher mRNA levels for all receptors except ARα, and a strong trend for higher 11βHSD; 11βH was similar to that in calling males. Calling males had higher plasma and testis 11kT, but lower plasma cortisol, levels. Testis enzyme levels did not differ between male groups, although calling males showed a positive linear correlation between plasma 11kT and testis 11βHSD mRNA levels, consistent with testis being the main source of plasma 11kT. We propose that higher vocal muscle 11βHSD levels in non-calling males reflect increased local conversion of elevated cortisol to cortisone, providing protection from cortisol-related toxicity, while increased receptor expression in non-calling males functions as a preparatory mechanism for meeting the physiological demands of future vocalization.

The genetic basis of pollinator adaptation in a sexually deceptive orchid

In plants, pollinator adaptation is considered to be a major driving force for floral diversification and speciation. However, the genetic basis of pollinator adaptation is poorly understood. The orchid genus Ophrys mimics its pollinators' mating signals and is pollinated by male insects during mating attempts. In many species of this genus, chemical mimicry of the pollinators' pheromones, especially of alkenes with different double-bond positions, plays a key role for specific pollinator attraction. Thus, different alkenes produced in different species are probably a consequence of pollinator adaptation. In this study, we identify genes that are likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturases (SAD), in three closely related Ophrys species, O. garganica, O. sphegodes, and O. exaltata. Combining floral odor and gene expression analyses, two SAD homologs (SAD1/2) showed significant association with the production of (Z)-9- and (Z)-12-alkenes that were abundant in O. garganica and O. sphegodes, supporting previous biochemical data. In contrast, two other newly identified homologs (SAD5/6) were significantly associated with (Z)-7-alkenes that were highly abundant only in O. exaltata. Both molecular evolutionary analyses and pollinator preference tests suggest that the alkenes associated with SAD1/2 and SAD5/6 are under pollinator-mediated divergent selection among species. The expression patterns of these genes in F₁ hybrids indicate that species-specific expression differences in SAD1/2 are likely due to cis-regulation, while changes in SAD5/6 are likely due to trans-regulation. Taken together, we report a genetic mechanism for pollinator-mediated divergent selection that drives adaptive changes in floral alkene biosynthesis involved in reproductive isolation among Ophrys species.

In plants, the extraordinary floral diversity has been suggested to be a consequence of divergent adaptation. However, the genetic basis of this process is poorly understood. In this study, we take advantage of the high specificity of plant-pollinator interactions in the sexually deceptive orchid genus Ophrys. We leverage the available, ample evidence showing that floral odors, especially alkenes, are the key factor for specific pollinator attraction in certain species of these orchids. Further, we investigate the genetic basis of pollinator adaptation. By applying an inter-disciplinary approach, including chemical ecology, gene expression analysis, population genetics, and pollinator-behavioral tests, we show that genetic changes in different copies of a biosynthetic gene are associated with the production of different floral scents and with pollinator adaptation in these orchid species. Moreover, we found that both cis- and trans-regulatory factors are likely involved in controlling gene expression of these biosynthetic gene copies. These findings support the hypothesis that adaptation is mediated by very few genetic changes with large phenotypic effects, rather than requiring a large number of co-adapted genes.

Nucleolar localization of a netrin-1 isoform enhances tumor cell proliferation

Netrin-1 displays proto-oncogenic activity in several cancers, which is thought to be due to the ability of this secreted cue to stimulate survival when bound to its receptors. We showed that in contrast to full-length, secreted netrin-1, some cancer cells produced a truncated intranuclear form of netrin-1 (ΔN-netrin-1) through an alternative internal promoter. Because of a nucleolar localization signal located in its carboxyl terminus, ΔN-netrin-1 was targeted to the nucleolus, where it interacted with nucleolar proteins, affected nucleolar ultrastructure, and interacted with the promoters of ribosomal genes. Moreover, ΔN-netrin-1 stimulated cell proliferation in vitro and tumor growth in vivo. Thus, some cancer cells produce not only a full-length, secreted form of netrin-1 that promotes cell survival but also a truncated netrin-1 that stimulates cell proliferation, potentially by enhancing ribosome biogenesis.

The AbrB2 autorepressor, expressed from an atypical promoter, represses the hydrogenase operon to regulate hydrogen production in Synechocystis strain PCC6803

We have thoroughly investigated the abrB2 gene (sll0822) encoding an AbrB-like regulator in the wild-type strain of the model cyanobacterium Synechocystis strain PCC6803. We report that abrB2 is expressed from an active but atypical promoter that possesses an extended -10 element (TGTAATAT) that compensates for the absence of a -35 box. Strengthening the biological significance of these data, we found that the occurrence of an extended -10 promoter box and the absence of a -35 element are two well-conserved features in abrB2 genes from other cyanobacteria. We also show that AbrB2 is an autorepressor that is dispensable to cell growth under standard laboratory conditions. Furthermore, we demonstrate that AbrB2 also represses the hox operon, which encodes the Ni-Fe hydrogenase of biotechnological interest, and that the hox operon is weakly expressed even though it possesses the two sequences resembling canonical -10 and -35 promoter boxes. In both the AbrB2-repressed promoters of the abrB2 gene and the hox operon, we found a repeated DNA motif [TT-(N(5))-AAC], which could be involved in AbrB2 repression. Supporting this hypothesis, we found that a TT-to-GG mutation of one of these elements increased the activity of the abrB2 promoter. We think that our abrB2-deleted mutant with increased expression of the hox operon and hydrogenase activity, together with the reporter plasmids we constructed to analyze the abrB2 gene and the hox operon, will serve as useful tools to decipher the function and the regulation of hydrogen production in Synechocystis.

ARF-TSS: an alternative method for identification of transcription start site in bacteria

Current methods for identifying transcription start sites (TSSs) of specific genes in bacteria usually require adaptors or radioactive labeling. These approaches can be technically demanding and environmentally unfriendly. Here we present a method for identifying TSS called ARF-TSS, which is based on cDNA generation, circularization, PCR amplification, and DNA sequencing to determine the 5'-end of transcripts, thus circumventing the need for adaptors and radioactive labeling. We validated the method using the gene lasI from the bacterial pathogen Pseudomonas aeruginosa. Our results show that ARF-TSS could be a good alternative to traditional methods for bacterial TSS analysis.

Discovery and genomic characterization of noroviruses from a gastroenteritis outbreak in domestic cats in the US

Norovirus (NoV) RNA was detected in the stools of 6 out 14 (42.8%) 8–12-week-old cats with enteritis from a feline shelter, in New York State. Upon sequence analysis of the complete capsid, the six NoVs were found to be identical, suggesting the spread of a unique NoV strain in the shelter. The full-length genomic sequence (7839 nt) of one feline NoV, CU081210E/2010/US, was determined. In the capsid protein VP1 region, the virus displayed the highest amino acid identity to animal genogroup IV genotype 2 (GIV.2) NoVs: lion/Pistoia-387/06/IT (97.9%) and dog/Bari-170/07/IT (90.4%). These findings document the discovery of a novel feline calicivirus, different from vesiviruses, and extend the spectrum of NoV host range. Epidemiological studies using feline NoV-specific diagnostic tools and experimental infection of cats are required to understand whether NoVs have a pathogenic role in this species.

A transcriptional-switch model for Slr1738-controlled gene expression in the cyanobacterium Synechocystis

BACKGROUND

Protein-DNA interactions play a crucial role in the life of biological organisms in controlling transcription, regulation, as well as DNA recombination and repair. The deep understanding of these processes, which requires the atomic description of the interactions occurring between the proteins and their DNA partners is often limited by the absence of a 3D structure of such complexes.

RESULTS

In this study, using a method combining sequence homology, structural analogy modeling and biochemical data, we first build the 3D structure of the complex between the poorly-characterized PerR-like regulator Slr1738 and its target DNA, which controls the defences against metal and oxidative stresses in Synechocystis. In a second step, we propose an expanded version of the Slr1738-DNA structure, which accommodates the DNA binding of Slr1738 multimers, a feature likely operating in the complex Slr1738-mediated regulation of stress responses. Finally, in agreement with experimental data we present a 3D-structure of the Slr1738-DNA complex resulting from the binding of multimers of the FUR-like regulator onto its target DNA that possesses internal repeats.

CONCLUSION

Using a combination of different types of data, we build and validate a relevant model of the tridimensional structure of a biologically important protein-DNA complex. Then, based on published observations, we propose more elaborated multimeric models that may be biologically important to understand molecular mechanisms.

Isolation of the 5'-end of plant genes from genomic DNA by TATA-box-based degenerate primers

We report a rapid and simple method for isolating the 5'-end of plant genes from genomic DNA by polymerase chain reaction (PCR) with TATA-box-based degenerate primers (TDPs). The TDPs were specially designed according to the TATA box, which is conserved in the promoter region of most plant genes. The unknown 5'-ends of several genes in different plants were isolated by PCR with gene-specific primers of the known core fragment and the TDPs. Our method does not require the arduous RNA manipulations and expensive enzyme treatments of the popular rapid amplification of cDNA ends (RACE) and its variants, and so could be a cheap practical alternative.

Rapid amplification of cDNA ends (RACE)

Rapid Amplification of cDNA ends (RACE) provides an inexpensive and powerful tool to quickly obtain full-length cDNA when the sequence is only partially known. Starting with an mRNA mixture, gene-specific primers generated from the known regions of the gene and non-specific anchors, full-length sequences can be identified in as little as 3 days. RACE can also be used to identify alternative transcripts of a gene when the partial or complete sequence of only one transcript is known. In the following sections, we outline details for rapid amplification of 5(') and 3(') cDNA ends using the "new RACE" technique.

Target validation of plant microRNAs

microRNAs (miRNAs) regulate gene expression through sequence-specific interactions with cognate mRNAs that result in translational inhibition, mRNA decay, or slicing within the region of complementarity. miRNA processing activity on complementary target mRNAs generates 3' end cleavage products that contain -ligation-competent, 5'-monophosphates. Precise mapping of miRNA-directed cleavage sites within target transcripts is, therefore, possible using RNA ligase-mediated 5' amplification of cDNA ends (RLM-RACE). Here, we provide a comprehensive RLM-RACE-based protocol for the amplification of 5' ends derived from cleaved transcripts resulting from miRNA-guided cleavage events. Novel strategies for high-throughput analysis of miRNA cleavage products have emerged as powerful tools for the novo identification of miRNA targets in a genomic perspective. In this work, we also describe a novel methodology for genome-wide identification of miRNA targets that exploits RLM-RACE for non-sequence-specific enrichment of cleaved transcripts, T7 RNA polymerase-mediated amplification of target products, and microarray hybridization.

Mechanism of transcriptional activation by Pseudomonas aeruginosa ExsA

ExsA is a transcriptional activator of the Pseudomonas aeruginosa type III secretion system (T3SS). The T3SS consists of >40 genes organized within 10 transcriptional units, each of which is controlled by the transcriptional activator ExsA. ExsA-dependent promoters contain two adjacent ExsA binding sites that when occupied protect the -30 to -70 region from DNase I cleavage. The promoters also possess regions bearing strong resemblance to the consensus -10 and -35 regions of sigma(70)-dependent promoters. The spacing distance between the putative -10 and -35 regions of ExsA-dependent promoters, however, is increased by 4 to 5 bp compared to that in typical sigma(70)-dependent promoters. In the present study, we demonstrate that ExsA-dependent transcriptional activation requires a 21- or 22-bp spacer length between the -10 and -35 regions. Despite the atypical spacing in this region, in vitro transcription assays using sigma(70)-saturated RNA polymerase holoenzyme (RNAP-sigma(70)) confirm that ExsA-dependent promoters are indeed sigma(70) dependent. Potassium permanganate footprinting experiments indicate that ExsA facilitates an early step in transcriptional initiation. Although RNAP-sigma(70) binds to the promoters with low affinity in the absence of ExsA, the activator stimulates transcription by enhancing recruitment of RNAP-sigma(70) to the P(exsC) and P(exsD) promoters. Abortive initiation assays confirm that ExsA enhances the equilibrium binding constant for RNAP while having only a modest effect on the isomerization rate constant.

Identification of alternative transcripts using rapid amplification of cDNA ends (RACE)

Many organisms, including humans, have many more proteins than are actually coded for by their genes. This discrepancy is partially explained by the existence of alternative transcripts produced by the same gene. Multiple isoforms of the same gene sometimes perform completely different functions, and as such, knowing the sequence of one of the transcripts is not enough. Rapid Amplification of cDNA Ends (RACE) provides an inexpensive and powerful tool to quickly identify alternative transcripts of a gene when the partial or complete sequence of only one transcript is known. In the following sections, we outline details for rapid amplification of 5' and 3' cDNA ends using the "New Race" technique.

Analysis of RNA polymerase-promoter complex formation

Bacterial promoter identification and characterization is not as straightforward as one might presume. Promoters vary widely in their similarity to the consensus recognition element sequences, in their activities, and in their utilization of transcription factors, and multiple approaches often must be used to provide a framework for understanding promoter regulation. Characterization of RNA polymerase-promoter complex formation in the absence of additional regulatory factors (basal promoter function) can provide a basis for understanding the steps in transcription initiation that are ultimately targeted by nutritional or environmental factors. Promoters can be localized using genetic approaches in vivo, but the detailed properties of the RNAP-promoter complex are studied most productively in vitro. We first describe approaches for identification of bacterial promoters and transcription start sites in vivo, including promoter-reporter fusions and primer-extension. We then describe a number of methods for characterization of RNAP-promoter complexes in vitro, including in vitro transcription, gel mobility shift assays, footprinting, and filter binding. Utilization of these methods can result in determination of not only basal promoter strength but also the rates of transcription initiation complex formation and decay.

Sensitive detection of mRNA decay products by use of reverse-ligation-mediated PCR (RL-PCR)

Ligation-mediated PCR allows the detection and mapping of cleavage products of specific nucleic acid molecules out of complex nucleic acid mixtures. It can be applied to the detection of either degradation products of exogenously added nucleases in footprinting applications or natural decay products or reaction intermediates. We have developed various ligation-mediated PCR approaches to analyze mRNAs, all relying on RNA ligation, followed by reverse-transcription and PCR amplification. We have termed these approaches reverse-ligation-mediated PCR (RL-PCR). The ligation event involves either an RNA linker added to the 5'-end of cleaved RNA or RNA circularization, allowing, respectively, the mapping and quantification of the cleavage points or the simultaneous analysis of the presence or absence of the 5'-cap structure and the length of the poly(A) tail. These methods enabled us to develop a very efficient 5'-RACE procedure to map mRNA 5'-ends, to footprint in permeabilized cells the interaction of regulatory proteins with RNA, to detect the products of cellular ribozyme action and to analyze cellular decay pathways that involve deadenylation and/or decapping. I review herein the methodologic aspects and protocols of the various RL-PCR procedures we have developed.

5' end cDNA amplification using classic RACE

The 5' ends of transcripts provide important information about transcription initiation sites and the approximate locations of local cis-acting enhancer elements; it is therefore important to establish the 5' ends with some precision. RACE (rapid amplification of cDNA ends) PCR is useful for quickly obtaining full length cDNAs for mRNAs for which only part of the sequence is known and to identify alternative 5' or 3' ends of fully sequenced genes. The method consists of using PCR to amplify, from complex mixtures of cellular mRNA, the regions between the known parts of the sequence and non-specific tags appended to the ends of the cDNA. Whereas the poly(A) tail serves to provide such a tag at the 3' end of the mRNA, an artificial one needs to be generated at the 5' end, and various approaches have been described to address this step. The classical scheme for 5' RACE described here is simple, suffices in many instances in which RACE is needed and can be performed in 1-3 days.

3' end cDNA amplification using classic RACE

Having knowledge of the entire 3' sequence of a cDNA is often important because the non-coding terminal region can contain signals that regulate the stability or subcellular localization of the mRNA. Also, some messages use alternative genomic sites for cleavage and polyadenylation that can alter the above properties, or change the encoded protein. Full-length cDNAs can be obtained from complex mixtures of cellular mRNA using rapid amplification of cDNA ends (RACE) PCR as long as part of the mRNA sequence is known; adding non-specific tags to the ends of the cDNA allows the regions between the known parts of the sequence and the ends to be amplified. In 3' RACE, the poly(A) tail functions as a non-specific tag at the 3' end of the mRNA. cDNA ends can be obtained in 1-3 days using this protocol.