End Formation Research Articles

Antioxidation and rheological modification of polylactide by gallic acid at chain end and stereocomplex formation

Abstract This study offers a novel approach that enables both functionalization of degradable polymers and modification of polymer properties during processing and use. By utilizing degradable polylactide, it was copolymerized with polyethylene glycol with the aim to facilitate processing and blending by heating. Moreover, L,L- and D,D-lactide were employed for the possible stereocomplexation, with the aim to enhance physical properties during use after processing. Additionally, the gallic acid was introduced at both chainends, which exhibits antioxidant properties as functionalization.

Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism

We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3'-untranslated region (3'-UTR) of SPINK1 as the cause of severe infantile isolated exocrine pancreatic insufficiency. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here, we aimed to elucidate these mechanisms through a hypothesis-driven approach. Initially, we speculated that, owing to its particular location, Alu_Ins could independently disrupt mRNA 3' end formation and/or affect other post-transcriptional processes such as nuclear export and translation. However, employing a 3'-UTR luciferase reporter assay, Alu_Ins was found to result in only an ∼50% reduction in luciferase activity compared to wild type, which is insufficient to account for the severe pancreatic deficiency in the Alu_Ins homozygote. We then postulated that double-stranded RNA (dsRNA) structures formed between Alu elements, an upstream mechanism regulating gene expression, might be responsible. Using RepeatMasker, we identified two Alu elements within SPINK1's third intron, both oriented oppositely to Alu_Ins. Through RNAfold predictions and full-length gene expression assays, we investigated orientation-dependent interactions between these Alu repeats. We provide compelling evidence to link the detrimental effect of Alu_Ins to extensive dsRNA structures formed between Alu_Ins and pre-existing intronic Alu sequences, including the restoration of SPINK1 mRNA expression by aligning all three Alu elements in the same orientation. Given the widespread presence of Alu elements in the human genome and the potential for new Alu insertions at almost any locus, our findings have important implications for detecting and interpreting Alu insertions in disease genes.

Isoform balance of the long noncoding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts cell migration

The long noncoding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) is involved in a variety of human cancers. Two overlapping NEAT1 isoforms, NEAT1_1 and NEAT1_2, are produced through mutually exclusive alternative 3' end formation. Previous studies extensively investigated NEAT1 dysregulation in tumors, but often failed to achieve distinct quantification of the two NEAT1 isoforms. Moreover, molecular mechanisms governing the biogenesis of NEAT1 isoforms and the functional impacts of their dysregulation in tumorigenesis remain poorly understood. In this study, we employed an isoform-specific quantification assay and found differential dysregulation of NEAT1 isoforms in patient-derived glioblastoma multiforme cells. We further showed usage of the NEAT1 proximal polyadenylation site (PAS) is a critical mechanism that controls glioma NEAT1 isoform production. CRISPR-Cas9-mediated PAS deletion reduced NEAT1_1 and reciprocally increased NEAT1_2, which enhanced nuclear paraspeckle formation in human glioma cells. Moreover, the utilization of the NEAT1 PAS is facilitated by the RNA-binding protein quaking (QKI), which binds to the proximal QKI recognition elements. Functionally, we identified transcriptomic changes and altered biological pathways caused by NEAT1 isoform imbalance in glioma cells, including the pathway for the regulation of cell migration. Finally, we demonstrated the forced increase of NEAT1_2 upon NEAT1 PAS deletion is responsible for driving glioma cell migration and promoting the expression of genes implicated in the regulation of cell migration. Together, our studies uncovered a novel mechanism that regulates NEAT1 isoforms and their functional impacts on the glioma transcriptome, which affects pathological pathways of glioma, represented by migration.

Proto-oncogene cSrc-mediated RBM10 phosphorylation arbitrates anti-hypertrophy gene program in the heart and controls cardiac hypertrophy

AimsRBM10 is a well-known RNA binding protein that regulates alternative splicing in various disease states. We have shown a splicing-independent function of RBM10 that regulates heart failure. This study aims to unravel a new biological function of RBM10 phosphorylation by proto-oncogene cSrc that enables anti-hypertrophy gene program and controls cardiac hypertrophy. Materials and methodsWe employ in vitro and in vivo approaches to characterise RBM10 phosphorylation at three-tyrosine residues (Y81, Y500, and Y971) by cSrc and target mRNA regulation. We also use isoproterenol induced rat heart and cellular hypertrophy model to determine role of cSrc-mediated RBM10 phosphorylation. Key findingsWe show that RBM10 phosphorylation is induced in cellular and animal heart model of cardiac hypertrophy and regulates target mRNA expression and 3′-end formation. Inhibition of cSrc kinase or mutation of the three-tyrosine phosphorylation sites to phenylalanine accentuates myocyte hypertrophy, and results in advancement and an early attainment of hypertrophy in the heart. RBM10 is down regulated in the hypertrophic myocyte and that its re-expression reverses cellular and molecular changes in the myocyte. However, in the absence of phosphorylation (cSrc inhibition or phospho-deficient mutation), restoration of endogenous RBM10 level in the hypertrophic heart or ectopic re-expression in vitro failed to reverse cardiomyocyte hypertrophy. Mechanistically, loss of RBM10 phosphorylation inhibits nuclear localisation and interaction with Star-PAP compromising anti-hypertrophy gene expression. SignificanceOur study establishes that cSrc-mediated RBM10 phosphorylation arbitrates anti-hypertrophy gene program. We also report a new functional regulation of RBM10 by phosphorylation that is poised to control heart failure.

Geochemical characteristics of shale gas hydraulic fracturing flowback/produced water in Zheng’an block, northern Guizhou Province, China

Guizhou Province of China is rich in shale gas resources. In recent years, important progress has been made in the exploration and development of shale gas in the Upper Ordovician Wufeng Formation-Lower Silurian Longmaxi Formation in Zheng'an block in northern Guizhou, adjacent to Sichuan Basin. Due to the complex geological conditions and fragile ecological environment in the shale gas distribution area, serious environmental pollution risks may exist in shale gas exploitation. Therefore, this paper conducted element, hydrogen and oxygen isotope analyses for shale gas fracturing flowback/produced water of Well AY7-4 in Zheng'an block. The results showed that the contents of K, Na, Ca, Mg and NH4+ in the flowback/produced water of Well AY7-4 were very high, with an average of 118 mg/L, 7616 mg/L, 266 mg/L, 47 mg/L and 76 mg/L, respectively. The content of Na, Ca and Mg is similar to that of shale gas flowback/produced water in Weiyuan, but lower than that in Changning and Fuling. NH4+ content was similar to that in Changning, but much higher than that in Weiyuan. The average Cl content was 11605 mg/L, which was similar to that in Weiyuan, but lower than that in Changning and Fuling. The average Br content is 48 mg/L, slightly lower than that of Weiyuan, and about half of that of Changning and Fuling. Correspondingly, the Br/Cl value of Well AY7-4 is the lowest, reflecting its relatively low Br content. The average content of Li, B and Sr is 17 mg/L, 10 mg/L and 45 mg/L, respectively, which is similar to that of the Weiyuan, Changning and Fuling shale gas fields. The distribution model of Li and Sr is similar to that of Cl, Br and Na, but the B content and B/Cl value of Well AY7-4 are the lowest. The linear relationship between Br and Cl contents and between δD and δ18O of flowback/produced water of Well AY7-4, freshwater used for hydraulic fracturing and hydraulic fracturing injected fluid indicates that flowback/produced water of Well AY7-4 is mainly the mixed product between low salinity injected fracturing fluid and high salinity brine retained in shale formation. The hydrogen and oxygen isotopic compositions gradually become heavier over time, indicating that the proportion of high salt end formation brine in flowback/produced water is increasing. The contents of Cl, Br, Na and NH4+ in the flowback/produced water of Well AY7-4 are far higher than the allowable discharge value, which is a potential environmental pollution risk and cannot be discharged directly.

Neuronal RNA processing: cross-talk between transcriptional regulation and RNA-binding proteins.

In the nervous system, alternative RNA processing is particularly prevalent, which results in the expression of thousands of transcript variants found in no other tissue. Neuron-specific RNA-binding proteins co-transcriptionally regulate alternative splicing, alternative polyadenylation, and RNA editing, thereby shaping the RNA identity of nervous system cells. Recent evidence suggests that interactions between RNA-binding proteins and cis-regulatory elements such as promoters and enhancers play a role in the determination of neuron-specific expression profiles. Here, we discuss possible mechanisms through which transcription and RNA processing cross-talk to generate the uniquely complex neuronal transcriptome, with a focus on alternative 3'-end formation.

High–level production of a novel alginate lyase (FsAly7) from Flammeovirga sp. for efficient production of low viscosity soluble dietary fiber from sodium alginate

Sodium alginate is one of the most abundant sustainable gum source for dietary fiber production. However, the preparation efficiencies of low viscosity soluble dietary fiber from sodium alginate remain low. Here, a novel alginate lyase gene (FsAly7) from Flammeovirga sp. was identified and high–level expressed in Pichia pastoris for low viscosity soluble dietary fiber production. The highest enzyme production of 3050 U mL−1 was achieved, which is by far the highest yield ever reported. FsAly7 was used for low viscosity soluble dietary fiber production from sodium alginate, and the highest degradation rate of 85.5 % was achieved under a high substrate content of 20 % (w/v). The molecular weight of obtained soluble dietary fiber converged to 10.75 kDa. FsAly7 catalyzed the cleavage of glycosidic bonds in alginate chains with formation of unsaturated non-reducing ends simultaneously in the degradation process, thus altered the chemical structures of hydrolysates. The soluble dietary fiber exhibited excellent properties, including low viscosity, high oil adsorption capacity activity (2.20 ± 0.03 g g−1) and high emulsifying activity (60.05 ± 2.96 mL/100 mL). This investigation may provide a novel alginate lyase catalyst as well as a solution for the efficient production of low viscosity soluble dietary fiber from sodium alginate.

Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation.

Small nuclear RNAs (snRNAs) are structural and functional cores of the spliceosome. In metazoan genomes, each snRNA has multiple copies/variants, up to hundreds in mammals. However, the expressions and functions of each copy/variant in one organism have not been systematically studied. Focus on U1 snRNA genes, we investigated all five copies in Drosophila melanogaster using two series of constructed strains. Analyses of transgenic flies that each have a U1 promoter-driven gfp revealed that U1:21D is the major and ubiquitously expressed copy, and the other four copies have specificities in developmental stages and tissues. Mutant strains that each have a precisely deleted copy of U1-gene exhibited various extents of defects in fly morphology or mobility, especially deletion of U1:82Eb. Interestingly, splicing was changed at limited levels in the deletion strains, while large amounts of differentially-expressed genes and alternative polyadenylation events were identified, showing preferences in the down-regulation of genes with 1-2 introns and selection of proximal sites for 3'-end polyadenylation. In vitro assays suggested that Drosophila U1 variants pulled down fewer SmD2 proteins compared to the canonical U1. This study demonstrates that all five U1-genes in Drosophila have physiological functions in development and play regulatory roles in transcription and 3'-end formation.

Shifted PAMs generate DNA overhangs and enhance SpCas9 post-catalytic complex dissociation

Using Sanger sequencing and high-throughput genome sequencing of DNA cleavage reactions, we find that the Streptococcus pyogenes SpCas9 complex responds to internal mechanical strain by robustly generating a distribution of overhanging, rather than blunt, DNA ends. Internal mechanical strain is generated by shifting (increasing or decreasing) the spacing between the RNA-DNA hybrid and the downstream canonical PAM. Up to 2-base 3′ overhangs can be robustly generated via a 2-base increase in the distance between hybrid and PAM. We also use single-molecule experiments to reconstruct the full course of the CRISPR–SpCas9 reaction in real-time, structurally and kinetically monitoring and quantifying R-loop formation, the first and second DNA-incision events, and dissociation of the post-catalytic complex. Complex dissociation and release of broken DNA ends is a rate-limiting step of the reaction, and shifted SpCas9 is sufficiently destabilized so as to rapidly dissociate after formation of broken DNA ends.

The impact of pulpotomy on the long-term prognosis and survival of young permanent teeth

This review explores the impact of pulpotomies on the long-term prognosis and survival of primary and young permanent teeth. Pulpotomy is a vital pulp therapy procedure aiming to preserve pulp health and functions. The review covers various vital pulp therapy techniques, including indirect pulp treatment, direct pulp treatment, partial pulpotomy, and full pulpotomy. Apexogenesis, a procedure promoting root end formation, is also discussed. Long-term success in endodontic therapy requires an effective coronal seal to prevent microleakage and bacterial ingress into root canals. The study's methodology involved a comprehensive literature search to gather information on pulpotomy's effects on tooth prognosis and survival. Factors influencing the success of vital pulp therapy, such as the size of the exposure, the state of the pulp, and the choice of capping material, are analyzed. Bacterial contamination is identified as a crucial factor affecting the therapy's prognosis. Strategies to improve pulp healing and treatment outcomes are explored, offering insights into clinical decision-making for pulpotomy procedures.

Reinvestigating the concurring reactions in early-stage cellulose pyrolysis by solution state NMR spectroscopy

Low temperature pre-treatments increase the char yield during cellulose carbonization. Although this effect is mostly understood on a kinetic basis, the formed chemical structures leave room for scrutiny. In ongoing ambitions to enhance the char yield of bioderived precursors, the thereby occurring chemistry was reinvestigated. A set of isothermal heating protocols ranging from 150° to 250°C was applied to man-made Ioncell® cellulose fibers and to Avicel® PH-101 microcrystalline cellulose. The prepared cellulosic samples were examined by solution state NMR using a tetra-n-butyl phosphonium acetate ([P4444][OAc]): DMSO-d6 (1:4 wt%) electrolyte as dissolving medium. Complementary, IR spectroscopy, size-exclusion chromatography (SEC) and thermogravimetric analysis coupled with mass spectroscopy (TGA-MS) measurements were performed. The NMR spectra evidenced the formation of levoglucosan end capped moieties as being the first and major occurring reaction during low temperature pre-treatments. In contrast to other mechanistic proposals, no signs for carbonyl or alkene functionalities were discernible in the cellulosic material soluble in the NMR electrolyte, even after treatment at 250 °C for several hours. Thermal cross-linking was observed in SEC already at temperatures not known to significantly influence the overall char yield. In the solution state analytics only partial solubility was observed, owing to the formation of a reluctant fraction previously described as “thermostable condensed phase”. This resulted in analytical blind spots and led to discrepancies between NMR results and FTIR spectra in which carbonyl and alkene vibrations were clearly discernible. Those discrepancies might also imply the co-existence of different fractions in the early stages of cellulose pyrolysis.

What causes the formation of discs and end of bursty star formation?

ABSTRACT As they grow, galaxies can transition from irregular/spheroidal with ‘bursty’ star formation histories (SFHs), to discy with smooth SFHs. But even in simulations, the direct physical cause of such transitions remains unclear. We therefore explore this in a large suite of numerical experiments re-running portions of cosmological simulations with widely varied physics, further validated with existing FIRE simulations. We show that gas supply, cooling/thermodynamics, star formation model, Toomre scale, galaxy dynamical times, and feedback properties do not have a direct causal effect on these transitions. Rather, both the formation of discs and cessation of bursty star formation are driven by the gravitational potential, but in different ways. Disc formation is promoted when the mass profile becomes sufficiently centrally concentrated in shape (relative to circularization radii): we show that this provides a well-defined dynamical centre, ceases to support the global ‘breathing modes’ that can persist indefinitely in less-concentrated profiles and efficiently destroy discs, promotes orbit mixing to form a coherent angular momentum, and stabilizes the disc. Smooth SF is promoted by the potential or escape velocity Vesc (not circular velocity Vc) becoming sufficiently large at the radii of star formation that cool, mass-loaded (momentum-conserving) outflows are trapped/confined near the galaxy, as opposed to escaping after bursts. We discuss the detailed physics, how these conditions arise in cosmological contexts, their relation to other correlated phenomena (e.g. inner halo virialization, vertical disc ‘settling’), and observations.

Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73.

Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.

Interplay of endonucleolytic and exonucleolytic processing in the 3'-end formation of a mitochondrial nad2 RNA precursor in Arabidopsis.

Initiation and termination of plant mitochondrial transcription are poorly controlled steps. Precursor transcripts are thus often longer than necessary, and 3'-end processing as well as control of RNA stability are essential to produce mature mRNAs in plant mitochondria. Plant mitochondrial 3' ends are determined by 3'-to-5' exonucleolytic trimming until the progression of mitochondrial exonucleases along transcripts is stopped by stable RNA structures or RNA binding proteins. In this analysis, we investigated the function of the endonucleolytic mitochondrial stability factor 1 (EMS1) pentatricopeptide repeat (PPR) protein and showed that it is essential for the production and the stabilization of the mature form of the nad2 exons 1-2 precursor transcript, whose 3' end corresponds to the 5' half of the nad2 trans-intron 2. The accumulation of an extended rather than a truncated form of this transcript in ems1 mutant plants suggests that the role of EMS1 in 3' end formation is not strictly limited to blocking the passage of 3'-5' exonucleolytic activity, but that 3' end formation of the nad2 exons 1-2 transcript involves an EMS1-dependent endonucleolytic cleavage. This study demonstrates that the formation of the 3' end of mitochondrial transcripts may involve an interplay of endonucleolytic and exonucleolytic processing mediated by PPR proteins.

Condition-specific 3′ mRNA isoform half-lives and stability elements in yeast

Alternative polyadenylation generates numerous 3' mRNA isoforms that can differ in their stability, structure, and function. These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3' untranslated regions (3'UTRs). Here, we examine how environmental conditions affect 3' mRNA isoform turnover and structure in yeast cells on a transcriptome scale. Isoform stability broadly increases when cells grow more slowly, with relative half-lives of most isoforms being well correlated across multiple conditions. Surprisingly, dimethyl sulfate probing reveals that individual 3' isoforms have similar structures across different conditions, in contrast to the extensive structural differences that can exist between closely related isoforms in an individual condition. Unexpectedly, most mRNA stabilizing and destabilizing elements function only in a single growth condition. The genes associated with some classes of condition-specific stability elements are enriched for different functional categories, suggesting that regulated mRNA stability might contribute to adaptation to different growth environments. Condition-specific stability elements do not result in corresponding condition-specific changes in steady-state mRNA isoform levels. This observation is consistent with a compensatory mechanism between polyadenylation and stability, and it suggests that condition-specific mRNA stability elements might largely reflect condition-specific regulation of mRNA 3' end formation.

The dynamics of the nickel foam formation and its effect on the catalytic properties toward hydrogen evolution reaction

Porous nickel deposits were obtained by electrodeposition via dynamic hydrogen bubble template in a galvanostatic mode at a current density of 0.3, 0.6, 0.9 and 1.2 A·cm−2. Change of nickel foam morphology (dendrite particles, pore number and their sizes) with the applied current density was analyzed. It was found that at low hydrogen evolution rate, a gradual formation of a porous structure occurs, while at high ones, the formation of the template structure ends in the first minutes of electrolysis. It is shown that the log-normal distribution can be used to describe the formation of a hydrogen template as a system of nickel foam macropores. The catalytic activity of nickel foams toward hydrogen evolution was analyzed in an alkali solution. The Tafel slope for the obtained foams is in the range of 126-107 mV·dec−1. Nickel foams obtained at 1.2 A·cm−2 are the best candidates for hydrogen evolution electrodes due to their stable structure, providing maximum access of reacting particles to the inner surface of the electrode.

Sequential Polyadenylation to Enable Alternative mRNA 3' End Formation.

In eukaryotic cells, a key RNA processing step to generate mature mRNA is the coupled reaction for cleavage and polyadenylation (CPA) at the 3' end of individual transcripts. Many transcripts are alternatively polyadenylated (APA) to produce mRNAs with different 3' ends that may either alter protein coding sequence (CDS-APA) or create different lengths of 3'UTR (tandem-APA). As the CPA reaction is intimately associated with transcriptional termination, it has been widely assumed that APA is regulated cotranscriptionally. Isoforms terminated at different regions may have distinct RNA stability under different conditions, thus altering the ratio of APA isoforms. Such differential impacts on different isoforms have been considered as post-transcriptional APA, but strictly speaking, this can only be considered "apparent" APA, as the choice is not made during the CPA reaction. Interestingly, a recent study reveals sequential APA as a new mechanism for post-transcriptional APA. This minireview will focus on this new mechanism to provide insights into various documented regulatory paradigms.

The MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4) is essential for the accumulation of dicistronic rpl5-cob mRNAs in Arabidopsis thaliana.

The Arabidopsis thaliana genome harbors more than 450 nuclear genes encoding pentatricopeptide repeat (PPR) proteins that operate in the RNA metabolism of mitochondria and/or plastids. To date, the molecular function of many PPR proteins is still unknown. Here we analyzed the nucleus-encoded gene At4g19440 coding for a P-type PPR protein. Knockout of this gene interferes with normal embryo development and seed maturation. Two experimental approaches were applied to overcome lethality and to investigate the outcome of At4g19440 knockout in adult plants. These studies revealed changes in the abundance of several mitochondria-encoded transcripts. In particular, steady-state levels of dicistronic rpl5-cob RNAs were markedly reduced, whereas levels of mature ccmC and rpl2-mttB transcripts were clearly increased. Predictions according to the one repeat to one nucleotide code for PPR proteins indicate binding of the At4g19440 protein to a previously detected small RNA at the 3' termini of the dicistronic rpl5-cob transcripts. This potential interaction indicates a function of this protein in 3' end formation and stabilization of these RNA species, whereas the increase in the levels of the ccmC mRNA along with other mitochondria-encoded RNAs seems to be a secondary effect of At4g19440 knockout. Since the inactivation of At4g19440 influences the stability of several mitochondrial RNAs we call this gene MITOCHONDRIAL TRANSCRIPT STABILITY FACTOR 4 (MTSF4). This factor will be an interesting subject to study opposing effects of a single nucleus-encoded protein on mitochondrial transcript levels.

Mutation of the polyadenylation complex subunit CstF77 reveals that mRNA 3' end formation and HSP101 levels are critical for a robust heat stress response.

Heat shock protein 101 (HSP101) in plants, and bacterial and yeast orthologs, is essential for thermotolerance. To investigate thermotolerance mechanisms involving HSP101, we performed a suppressor screen in Arabidopsis thaliana of a missense HSP101 allele (hot1-4). hot1-4 plants are sensitive to acclimation heat treatments that are otherwise permissive for HSP101 null mutants, indicating that the hot1-4 protein is toxic. We report one suppressor (shot2, suppressor of hot1-4 2) has a missense mutation of a conserved residue in CLEAVAGE STIMULATION FACTOR77 (CstF77), a subunit of the polyadenylation complex critical for mRNA 3' end maturation. We performed ribosomal RNA depletion RNA-Seq and captured transcriptional readthrough with a custom bioinformatics pipeline. Acclimation heat treatment caused transcriptional readthrough in hot1-4 shot2, with more readthrough in heat-induced genes, reducing the levels of toxic hot1-4 protein and suppressing hot1-4 heat sensitivity. Although shot2 mutants develop like the wild type in the absence of stress and survive mild heat stress, reduction of heat-induced genes and decreased HSP accumulation makes shot2 in HSP101 null and wild-type backgrounds sensitive to severe heat stress. Our study reveals the critical function of CstF77 for 3' end formation of mRNA and the dominant role of HSP101 in dictating the outcome of severe heat stress.

Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis.

3' end formation of most eukaryotic mRNAs is dependent on the assembly of a ~1.5 MDa multiprotein complex, that catalyzes the coupled reaction of pre-mRNA cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) constitutes the core of the 3' end processing machinery onto which the remaining factors, including cleavage stimulation factor (CstF) and poly(A) polymerase (PAP), assemble. These interactions are mediated by Fip1, a CPSF subunit characterized by high degree of intrinsic disorder. Here, we report two crystal structures revealing the interactions of human Fip1 (hFip1) with CPSF30 and CstF77. We demonstrate that CPSF contains two copies of hFip1, each binding to the zinc finger (ZF) domains 4 and 5 of CPSF30. Using polyadenylation assays we show that the two hFip1 copies are functionally redundant in recruiting one copy of PAP, thereby increasing the processivity of RNA polyadenylation. We further show that the interaction between hFip1 and CstF77 is mediated via a short motif in the N-terminal 'acidic' region of hFip1. In turn, CstF77 competitively inhibits CPSF-dependent PAP recruitment and 3' polyadenylation. Taken together, these results provide a structural basis for the multivalent scaffolding and regulatory functions of hFip1 in 3' end processing.