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Yamada, T.

Publications and source records attributed to Yamada, T..

At least 55 records · Page 3Linked to original sources

Enteropathway: the metabolic pathway database for the human gut microbiota

The human gut microbiota produces diverse, extensive metabolites which have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3,121 compounds, 3,460 reactions, and 837 modules that were obtained from 835 manually curated scientific literature. Notably, 757 modules of these modules are new entries and cannot be found in any other databases. The database is accessible from a web application (https://enteropathway.org) that offers a metabolic diagram for graphical visualization of metabolic pathways, a customization interface, and an enrichment analysis feature for highlighting enriched modules on the metabolic diagram. Overall, Enteropathway is a comprehensive reference database and a tool for visual and statistical analysis in human gut microbiota studies and was designed to help researchers pinpoint new insights into the complex interplay between microbiota and host metabolism.

bioinformatics↗

Insulin Effectiveness, a Measure Consisting of Insulin Sensitivity, Secretion, and Clearance, Captures Differences Between Diabetic and Nondiabetic States

ContextInsulin clearance is implicated in regulation of glucose homeostasis independently of insulin sensitivity and insulin secretion. ObjectiveTo understand the relation between blood glucose and insulin sensitivity, secretion, and clearance. MethodsWe performed a hyperglycemic clamp, a hyperinsulinemic-euglycemic clamp, and an oral glucose tolerance test (OGTT) in 47, 16, and 49 subjects with normal glucose tolerance (NGT), impaired glucose tolerance (IGT), and type 2 diabetes mellitus (T2DM), respectively. Mathematical analyses were retrospectively performed on this dataset. ResultsThe disposition index (DI), defined as the product of insulin sensitivity and secretion, showed a weak correlation with blood glucose levels, especially in IGT (r = 0.04; 95% CI, -0.63- 0.44). However, an equation relating DI, insulin clearance, and blood glucose levels was well conserved regardless of the extent of glucose intolerance. As a measure of the effect of insulin, we developed an index, designated "DI/cle," that is based on this equation and corresponds to DI divided by the square of insulin clearance. DI/cle was not impaired in IGT compared with NGT, possibly as a result of a decrease in insulin clearance in response to a reduction in DI, whereas it was impaired in T2DM relative to IGT. Moreover, DI/cle estimated from a hyperinsulinemic-euglycemic clamp, OGTT, or a fasting blood test were significantly correlated with that estimated from two clamp tests (r = 0.52; 95% CI, 0.37- 0.64, r = 0.43; 95% CI, 0.24- 0.58, and r = 0.54; 95% CI, 0.38- 0.68, respectively). ConclusionsDI/cle can serve as a new indicator for the trajectory of changes in glucose tolerance.

systems biology↗

Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography

Gum arabic (GA) is widely used as an emulsion stabilizer and edible coating, and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidic chains of GA and modify their properties are valuable tools for structural analysis and industrial application. Cryogenic X-ray crystal structure of GA-specific L-rhamnose--1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1), belonging to the polysaccharide lyase (PL) family 42, has been previously reported. To determine the specific reaction mechanism based on its hydrogen-containing enzyme structure, we performed joint X-ray/neutron crystallography of FoRham1. Large crystals were grown in the presence of L-rhamnose (a reaction product), and neutron and X-ray diffraction datasets were collected at room temperature up to 1.80 and 1.25 [A] resolutions, respectively. The active site contained L-rhamnose and acetate, the latter being a partial analog of glucuronate. Incomplete H/D exchange between Arg166 and acetate suggested that a strong salt-bridge interaction was maintained. Doubly deuteronated His105 and deuteronated Tyr150 supported this interaction. The unusually hydrogen-rich environment functions as a charge neutralizer for glucuronate and stabilizes the oxyanion intermediate. The NE2 atom of His85 was deprotonated and formed a hydrogen bond with the deuterated O1 hydroxy of L-rhamnose, indicating the function of His85 as the base/acid catalyst for bond cleavage via {beta}-elimination. Asp83 functions as a pivot between the two catalytic histidine residues by bridging them, and this His-His-Asp structural motif is conserved in the three PL families. Significance StatementAlthough hydrogen transfer plays an important role in enzymatic reactions, hydrogen atoms are generally invisible in macromolecular X-ray crystallography. In the reaction of polysaccharide lyases, substrate activation by negative charge stabilization of uronic acid and base/acid-catalyzed {beta}-elimination reaction have been postulated. Here, we report the neutron crystallography of polysaccharide lyase. Joint X-ray/neutron crystallography of L-rhamnose--1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1) complexed with L-rhamnose was performed, and the hydrogen and deuterium atoms were visualized at a high resolution. FoRham1 catalyzes the specific cleavage of the cap structure of gum arabic, which is useful for various applications in the food, cosmetic, and pharmaceutical industries. A detailed catalytic mechanism for FoRham1 was proposed based on the key structural features of its active site.

biophysics↗

Structure of a LRRC8 chimera with physiologically relevant properties reveals heptameric assembly and pore-blocking lipids

Volume-regulated anion channels (VRACs) mediate Cl- and organic solute efflux from vertebrate cells and are essential for cell volume homeostasis. VRACs are heteromeric assemblies of LRRC8A-E proteins with unknown stoichiometries. Homomeric LRRC8A and LRRC8D channels have a hexameric structure. However, these channels are either non-functional or exhibit abnormal functional properties limiting their utility for structure-function analyses. We circumvented these limitations by developing novel homomeric LRRC8 chimeric channels with physiologically relevant functional properties. We demonstrate here that the LRRC8C-LRRC8A(IL125) chimera comprising LRRC8C and 25 amino acids unique to the first intracellular loop (IL1) of LRRC8A has a heptameric structure like that of homologous pannexin channels. Membrane lipids are a key structural element of the channel and are located between subunits and occluding the channel pore. Our results suggest that native VRAC/LRRC8 channels are heptamers and that associated lipids are likely essential for normal channel gating and regulation.

biophysics↗

Relationship between salmon egg subsidy and the distribution of an avian predator

As a spatial subsidy, which is the phenomenon of transferring resources from a donor system to a recipient system, anadromous salmonids contribute to the supply of marine-derived nutrients to freshwater and terrestrial systems. Live salmon and salmon carcasses and eggs are utilized by various organisms and affect their abundance and distribution. However, the evaluation of the effect of salmon subsidies on the abundance and distribution of terrestrial animals is biased towards predators or scavengers that utilize spawning adults and carcasses, and few studies have focused on the effect of salmon eggs as a subsidy. To avoid underestimating the function of salmon subsidies, the response to the availability of salmon eggs in various systems should be investigated. Here, we investigated the abundance and feeding behaviour of the brown dipper Cinclus pallasii, as salmon egg a consumer, based on the hypothesis that the availability of salmon eggs affects the diet composition and stream distribution of this small predator. In addition, to test whether changes in the abundance of brown dippers are determined by salmon spawning, their abundance was compared upstream and downstream of the dam. Brown dippers used salmon eggs during the spawning season (53.7% of diet composition), and their abundance increased as the number of spawning redds increased. In contrast, this pattern was not observed upstream of the dam. These results suggested that the abundance and stream distribution of brown dippers vary according to the variation in the spatiotemporal availability of salmon eggs.

ecology↗

A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set

It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G x E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. Here we developed a data-driven approach termed Environmental Covariate Search Affecting Genetic Correlations (ECGC) to identify environmental stimuli and genes responsible for the G x E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (Glycine max) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G x E interactions in six traits including yield, flowering time, and protein content and when they were involved. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G x E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G x E interactions observed in fields. Key messageThe proposed method is able to identify environmental stimuli and genes responsible for the G x E interactions observed in multi-environmental trials. The method is based on similarity search between genetic correlation and environmental stimuli among environments.

plant biology↗

Inhibition of immunoglobulin class-switching prevents pemphigus onset in desmoglein 3-specific B cell receptor knock-in mouse

Although immunoglobulin class-switching is essential for humoral immunity, its role in B-cell immune tolerance remains unclear. Pemphigus vulgaris is an autoimmune blistering disease caused by IgG targeting desmoglein 3, an adhesion molecule of keratinocytes. In this study, we generated knock-in mice that express anti-Dsg3 AK23 autoantibodies. Knock-in B cells developed normally in vivo and showed Ca2+ influx upon IgM cross-linking in vitro. The mice predominantly produced circulating AK23 IgM but little IgG antibodies. Although no IgG deposition or blister formation was observed in Dsg3-bearing tissues, Dsg3 immunization forced to induce pemphigus phenotype after class-switching to IgG in vivo. Transcriptomic analysis revealed that FCGR2B and Fc{gamma}RIIB-related genes were downregulated in B cells from peripheral blood of pemphigus patients. Indeed, in AK23 knock-in mice, Fcgr2b deficiency or haploinsufficiency spontaneously led to class-switching, AK23 IgG production, and pemphigus phenotype development. Thus, inhibition of pathogenic class-switching is a crucial tolerogenic process to prevent pemphigus onset, where attenuated Fc{gamma}RIIB signaling is one of the key predispositions to break this tolerogenic state.

immunology↗

Oxicam-type NSAIDs enhance Agrobacterium-mediated transformation in plants

Agrobacterium-mediated transformation represents a key innovation for plant breeding and is routinely used in research and applied biology. However, for several species, the efficacy of transformation is limited. In this study, we discovered that oxicam-type nonsteroidal anti-inflammatory drugs (NSAIDs), including tenoxicam (TNX), enhance the efficiency of Agrobacterium-mediated transient transformation in the model species Arabidopsis thaliana via leaf infiltration and can be successfully applied in analyses of the subcellular localisation of fluorescent fusion proteins. TNX acts as an inhibitor of plant immune responses and lacks similar transient transformation efficiency in a dde2/ein2/pad4/sid2 quadruple mutant background, thereby indicating that TNX increases the efficiency of Agrobacterium infection via a transient shutdown of the immune system mediated by jasmonic acid, ethylene, and salicylic acid signalling. In addition, we found that TNX enhances the efficiency of stable transformation in crops of agricultural and economic importance, such as Jatropha and maize, indicating that TNX can enhance the integration of exogenous DNA into the plant genome via an increased introduction of DNA into plant cells. Given that treatment with oxicam compounds is simple, cost effective, and has broad utility, we anticipate that this discovery will contribute to accelerating genome-editing technologies in plants.

plant biology↗

Visual perceptual learning of a primitive feature in human V1/V2 as a result of unconscious processing, revealed by Decoded fMRI Neurofeedback (DecNef)

While numerous studies have shown that visual perceptual learning (VPL) occurs as a result of exposure to a visual feature in a task-irrelevant manner, the underlying neural mechanism is poorly understood. In a previous psychophysical study, subjects were repeatedly exposed to a task-irrelevant global motion display that induced the perception of not only the local motions but also a global motion moving in the direction of the spatiotemporal average of the local motion vectors. As a result, subjects enhanced their sensitivity only to the local moving directions, suggesting that early visual areas (V1/V2) that process local motions are involved in task-irrelevant VPL. However, this hypothesis has never been examined by directly examining the involvement of early visual areas (V1/V2). Here, we employed a decoded neurofeedback technique (DecNef) using functional magnetic resonance imaging. During the DecNef training, subjects were trained to induce the activity patterns in V1/V2 that were similar to those evoked by the actual presentation of the global motion display. The DecNef training was conducted with neither the actual presentation of the display nor the subjects awareness of the purpose of the experiment. As a result, subjects increased the sensitivity to the local motion directions but not specifically to the global motion direction. The training effect was strictly confined to V1/V2. Moreover, subjects reported that they neither perceived nor imagined any motion during the DecNef training. These results together suggest that that V1/V2 are sufficient for exposure-based task-irrelevant VPL to occur unconsciously. Significance StatementWhile numerous studies have shown that visual perceptual learning (VPL) occurs as a result of exposure to a visual feature in a task-irrelevant manner, the underlying neural mechanism is poorly understood. Previous psychophysical experiments suggest that early visual areas (V1/V2) are involved in task-irrelevant VPL. However, this hypothesis has never been examined by directly examining the involvement of early visual areas (V1/V2). Here, using decoded fMRI neurofeedback, the activity patterns similar to those evoked by the presentation of a complex motion display were repeatedly induced only in early visual areas. The training sensitized only the local motion directions and not the global motion direction, suggesting that V1/V2 are involved in task-irrelevant VPL.

neuroscience↗

Manage flowering time in Miscanthus and sugarcane to facilitate intra- and intergeneric crosses

Miscanthus is a close relative of Saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between Miscanthus and Saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of Saccharum and Miscanthus genotypes. We found that day length was an important factor influencing when Miscanthus and Saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 Miscanthus genotypes, including 28 M. sinensis, 2 M. floridulus, and 3 M. xgiganteus collected from 20.9{degrees} S to 44.9{degrees} N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis, short days typically hastened floral induction, consistent with the expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis, days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas that the latter needs day lengths <12.5 h.

plant biology↗

Common brain networks between major depressive disorder and symptoms of depression that are validated for independent cohorts

Many studies have highlighted the difficulty inherent to the clinical application of fundamental neuroscience knowledge based on machine learning techniques. It is difficult to generalize machine learning brain markers to the data acquired from independent imaging sites, mainly due to large site differences in functional magnetic resonance imaging. We address the difficulty of finding a generalizable major depressive disorder (MDD) brain network markers which would distinguish patients from healthy controls (a classifier) or would predict symptom severity (a prediction model) based on resting state functional connectivity patterns. For the discovery dataset with 713 participants from 4 imaging sites, we removed site differences using our recently developed harmonization method and developed a machine learning MDD brain network markers. The classifier achieved 70% generalization accuracy, and the prediction model moderately well predicted symptom severity for an independent validation dataset with 449 participants from 4 different imaging sites. Finally, we found common 2 functional connections between those related to MDD diagnosis and those related to depression symptoms. The successful generalization to the perfectly independent dataset acquired from multiple imaging sites is novel and ensures scientific reproducibility and clinical applicability.

neuroscience↗

Metabolic labeling of RNA using multiple ribonucleoside analogs enables simultaneous evaluation of transcription and degradation rates

Gene expression is one of the factors determining cellular conditions, and its level is determined by the balance between transcription and RNA degradation. However, it has been not well elucidated how transcription and degradation are related to each other. To elucidate the relationship of them, methods enabling simultaneous measurement of transcription and degradation are required. Here, we report the development of "Dyrec-seq" to evaluate transcription and RNA degradation rates simultaneously, by using 4-thiouridine and 5-bromouridine. Using Dyrec-seq, we quantified the transcription and degradation rates of 4,702 genes in HeLa cells. Functional enrichment analysis showed that the transcription and degradation rates of genes are actually determined by the genes biological functions. Comparison of theoretical and experimental analysis results revealed that the amount of RNA was determined by the ratio of transcription to degradation rates, while the rapidity of responses to external stimuli was determined only by the degradation rate. This study emphasizes that degradation as well as transcription is important in determining the behavior of RNA.

systems biology↗

Distinct transcriptional programs of SOX2 in different types of small cell lung cancers

SOX2 is an oncogene in human small cell lung cancer (SCLC), an aggressive neuroendocrine (NE) tumor. However, the roles of SOX2 in SCLC remain unclear, and strategies to selectively target SOX2 in SCLC cells have not yet been established. We herein demonstrated that SOX2 is involved in NE differentiation and tumorigenesis in cooperation with ASCL1, a lineage-specific transcriptional factor, in the classical subtype of SCLC cell lines. ASCL1 recruits SOX2, which promotes INSM1 expression. Precursor SCLC lesions were established in Trp53 (-/-); CCSPrtTA; tetOCre; floxedRb1; floxedHes1 mice, and the NE neoplasms induced were positive for Ascl1, Sox2, and Insm1. In contrast to the ASCL1-SOX2 signaling axis to control the SCLC phenotype in classical subtype SCLC, SOX2 targeted distinct genes, such as those related to the Hippo pathway, in ASCL1-negative, variant subtype SCLC. The present results support the importance of the ASCL1-SOX2 axis as a main subtype of SCLC, and suggest the therapeutic potential of targeting the ASCL1-SOX2 signaling axis and the clinical utility of SOX2 as a biological marker in the classical subtype of SCLC.

cancer biology↗

A space-saving visual screening method, Glycine max FAST, for generating transgenic soybean

Soybean is an important crop plant for food and biofuel production, and there have been considerable efforts to develop transgenic soybean lines with higher seed oil contents and/or seed yields. However, the process of screening transgenic lines is laborious and requires a large amount of space. Here, we describe a powerful screening method, Glycine max Fluorescence-Accumulating Seed Technology (GmFAST), which is based on a seed-specific fluorescent marker. The marker is composed of a soybean seed-specific promoter coupled to the OLE1-GFP gene, which encodes GFP fused to the oil-body membrane protein OLEOSIN1 of Arabidopsis thaliana. We introduced the marker gene into cotyledonary nodes of G. max Kariyutaka via Agrobacterium-mediated transformation and regenerated heterozygous transgenic plants. OLE1-GFP-expressing soybean seeds can be selected nondestructively using a fluorescence stereomicroscope. Among T2 seeds, the most strongly fluorescent seeds were homozygous. GmFAST uses one-tenth of the growing space required for the conventional method. This space-saving method will contribute to facilitating transformation of soybean. OLE1-GFP was localized specifically to oil bodies in the cotyledon cells of seeds, but it did not affect oil content per seed, the size and density of the oil bodies, or oil composition. One of the homozygous lines (line #8) showed a 44% increase in the seed pod number, which resulted in 41% and 30% increases in seed yield and total oil production, respectively, compared with the wild type. In line #8, OLE1-GFP was inserted into the intron of Glyma13g30950, causing its overexpression. An increase in seed pod number was confirmed in Arabidopsis thaliana plants that overexpressed the Arabidopsis ortholog of Glyma13g30950, E6L1. These results suggest that line #8 is a valuable resource for agricultural and industrial applications. Taken together, GmFAST provides a space-saving visual and non-destructive screening method for soybean transformation, thereby increasing the chance of developing useful soybean lines.

plant biology↗

Translocational unfolding in clostridial binary iota toxin complex

Protein translocation across the membrane is critical for microbial pathogenesis and various cellular functions. Bacterial binary toxins such as anthrax toxin are composed of enzyme components and a translocation channel, which catalyses substrate unfolding and translocation. Here we report the structures of the clostridial binary toxin (iota toxin) translocation channel Ib-pore and its complex with ADP-ribosyltransferase Ia. The Ib-pore structure at atomic resolution provides a similar structural framework as observed for the catalytic {phi}-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure showed a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia N-terminal domain interacts with Ib via two other Ib-pore bottlenecks with multiple weak interactions. Furthermore, Ib-binding induces Ia N-terminal -helix tilting and partial unfolding, whereupon the unfolded N-terminus continues to the {phi}-clamp gate. This study reveals the novel mechanism of N-terminal unfolding, which is crucial for protein translocation.

biophysics↗

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis

The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases (IBDs); however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin not only establishes a first-line barrier against pathogens, but also serves as a niche for microbial growth. We hypothesized that dysbiosis may cause abnormal mucin utilization and microbial metabolic dysfunction. To test this hypothesis, we analyzed short-chain fatty acids (SCFAs) and mucin components in the stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohns disease (CD) patients from Japan. The levels of n-butyrate were significantly lower in the stools of both the CD and UC patients than in those of the healthy subjects. Correlation analysis identified 7 bacterial species positively correlated with n-butyrate levels, among which the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans act as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt+Treg cells and IgA-producing cells in the colonic lamina propria. Importantly, the availability of mucin-associated O-glycans to the microbiota was significantly reduced in n-butyrate-deficient UC patients. Taken together, our findings highlight the biological significance of the symbiosynthesis pathway in the production of n-butyrate, which maintains gut immune homeostasis.

microbiology↗

Harmonization of resting-state functional MRI data across multiple imaging sites via the separation of site differences into sampling bias and measurement bias

When collecting large neuroimaging data associated with psychiatric disorders, images must be acquired from multiple sites because of the limited capacity of a single site. However, site differences represent the greatest barrier when acquiring multi-site neuroimaging data. We utilized a traveling-subject dataset in conjunction with a multi-site, multi-disorder dataset to demonstrate that site differences are composed of biological sampling bias and engineering measurement bias. Effects on resting-state functional MRI connectivity because of both bias types were greater than or equal to those because of psychiatric disorders. Furthermore, our findings indicated that each site can sample only from among a subpopulation of participants. This result suggests that it is essential to collect large neuroimaging data from as many sites as possible to appropriately estimate the distribution of the grand population. Finally, we developed a novel harmonization method that removed only the measurement bias by using traveling-subject dataset and achieved the reduction of the measurement bias by 29% and the improvement of the signal to noise ratios by 40%.

neuroscience↗

Identification of Functional Targets Reveals that the Suppression of Pumilio mediated mRNA Decay Increases Cell Resistance to DNA Damage in Human Cells

RNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts; however, the identification of degradation targets of RBPs remains difficult. Here, we identified 48 target mRNAs of human Pumilio 1 (PUM1), an evolutionally conserved RBP, by combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs to PUM1. Here, we developed an approach to identify mRNA targets of Pumilio 1 (PUM1), an evolutionally conserved RBP. By combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs to PUM1, we identified 48 mRNAs that both bound to PUM1 and exhibited PUM1-dependent degradation. Analysis of changes in the abundance of PUM1 and its targets in RNA-seq data indicated that DNA-damaging agents negatively regulated PUM1-mediated mRNA decay. Cells exposed to cisplatin had reduced PUM1 abundance and increased PCNA and UBE2A mRNAs, encoding proteins involved in DNA repair by translesion synthesis (TLS). Cells overexpressing PUM1 exhibited impaired DNA synthesis and TLS and increased sensitivity to the cytotoxic effect of cisplatin. Thus, our method identified targets of PUM1-mediated decay and revealed that cells respond to DNA damage by inhibiting PUM1-mediated mRNA decay to activate TLS.

molecular biology↗