Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome.

Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required for stable interaction with PUM1&2 and to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad coregulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved amino-terminal region that confers the predominant repressive activity via direct interaction with CNOT. In addition, we show that the mRNA decapping enzyme, DCP2, has an important role in repression by PUM1&2 amino-terminal regions. Our results support a molecular model of repression by human PUM1&2 via direct recruitment of CNOT deadenylation machinery in a decapping-dependent mRNA decay pathway.

A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing.

CCR4-NOT is a major effector complex in miRNA-mediated gene silencing. It is recruited to miRNA targets through interactions with tryptophan (W)-containing motifs in TNRC6/GW182 proteins and is required for both translational repression and degradation of miRNA targets. Here, we elucidate the structural basis for the repressive activity of CCR4-NOT and its interaction with TNRC6/GW182s. We show that the conserved CNOT9 subunit attaches to a domain of unknown function (DUF3819) in the CNOT1 scaffold. The resulting complex provides binding sites for TNRC6/GW182, and its crystal structure reveals tandem W-binding pockets located in CNOT9. We further show that the CNOT1 MIF4G domain interacts with the C-terminal RecA domain of DDX6, a translational repressor and decapping activator. The crystal structure of this complex demonstrates striking similarity to the eIF4G-eIF4A complex. Together, our data provide the missing physical links in a molecular pathway that connects miRNA target recognition with translational repression, deadenylation, and decapping.

Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs.

Pumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility and neurological functions in Drosophila. We sought to identify the mechanism of Pumilio-mediated repression and find that it accelerates degradation of target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique to Pumilio orthologs. We show that the repressive activities of the Pumilio RDs depend on specific subunits of the Ccr4-Not (CNOT) deadenylase complex. Depletion of Pop2, Not1, Not2, or Not3 subunits alleviates Pumilio RD-mediated repression of protein expression and mRNA decay, whereas depletion of other CNOT components had little or no effect. Moreover, the catalytic activity of Pop2 deadenylase is important for Pumilio RD activity. Further, we show that the Pumilio RDs directly bind to the CNOT complex. We also report that the decapping enzyme, Dcp2, participates in repression by the N-terminus of Pumilio. These results support a model wherein Pumilio utilizes CNOT deadenylase and decapping complexes to accelerate destruction of target mRNAs. Because the N-terminal RDs are conserved in mammalian Pumilio orthologs, the results of this work broadly enhance our understanding of Pumilio function and roles in diseases including cancer, neurodegeneration and epilepsy.

A low-complexity region in human XRN1 directly recruits deadenylation and decapping factors in 5'-3' messenger RNA decay.

XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5'-3' mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Here, we reveal a direct interaction between XRN1 and the CCR4-NOT deadenylase complex mediated by a low-complexity region in XRN1, which we term the 'C-terminal interacting region' or CIR. The CIR represses reporter mRNA deadenylation in human cells when overexpressed and inhibits CCR4-NOT and isolated CAF1 deadenylase activity in vitro. Through complementation studies in an XRN1-null cell line, we dissect the specific contributions of XRN1 domains and regions toward decay of an mRNA reporter. We observe that XRN1 binding to the decapping activator EDC4 counteracts the dominant negative effect of CIR overexpression on decay. Another decapping activator PatL1 directly interacts with CIR and alleviates the CIR-mediated inhibition of CCR4-NOT activity in vitro. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. Our findings reveal an additional layer of direct interactions in a tightly integrated network of factors mediating deadenylation, decapping and 5'-3' exonucleolytic decay.

Assessment of MODIS-derived indices (2001-2013) to drought across Taiwan's forests.

Tropical and subtropical ecosystems, the largest terrestrial carbon pools, are very susceptible to the variability of seasonal precipitation. However, the assessment of drought conditions in these regions is often overlooked due to the preconceived notion of the presence of high humidity. Drought indices derived from remotely sensed imagery have been commonly used for large-scale monitoring, but feasibility of drought assessment may vary across regions due to climate regimes and local biophysical conditions. Therefore, this study aims to evaluate the feasibility of 11 commonly used MODIS-derived vegetation/drought index in the forest regions of Taiwan through comparison with the station-based standardized precipitation index with a 3-month time scale (SPI3). The drought indices were further transformed (standardized anomaly, SA) to make them better delineate the spatiotemporal variations of drought conditions. The results showed that the Normalized Difference Infrared Index utilizing the near-infrared and shortwave infrared bands (NDII6) may be more superior to other indices in delineating drought patterns. Overall, the NDII6 SA-SPI3 pair yielded the highest correlation (mean r ± standard deviation = 0.31 ± 0.13) and was most significant in central and south Taiwan (r = 0.50-0.90) during the cold, dry season (January and April). This study illustrated that the NDII6 is suitable to delineate drought conditions in a relatively humid region. The results suggested the better performance of the NDII6 SA-SPI3 across the high climate gradient, especially in the regions with dramatic interannual amplifications of rainfall. This synthesis was conducted across a wide bioclimatic gradient, and the findings could be further generalized to a much broader geographical extent.

Chtop is a component of the dynamic TREX mRNA export complex.

The TREX complex couples nuclear pre-mRNA processing with mRNA export and contains multiple protein components, including Uap56, Alyref, Cip29 and the multi-subunit THO complex. Here, we have identified Chtop as a novel TREX component. We show that both Chtop and Alyref activate the ATPase and RNA helicase activities of Uap56 and that Uap56 functions to recruit both Alyref and Chtop onto mRNA. As observed with the THO complex subunit Thoc5, Chtop binds to the NTF2-like domain of Nxf1, and this interaction requires arginine methylation of Chtop. Using RNAi, we show that co-knockdown of Alyref and Chtop results in a potent mRNA export block. Chtop binds to Uap56 in a mutually exclusive manner with Alyref, and Chtop binds to Nxf1 in a mutually exclusive manner with Thoc5. However, Chtop, Thoc5 and Nxf1 exist in a single complex in vivo. Together, our data indicate that TREX and Nxf1 undergo dynamic remodelling, driven by the ATPase cycle of Uap56 and post-translational modifications of Chtop.

The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1.

The removal of the 5'-cap structure by the decapping enzyme DCP2 and its coactivator DCP1 shuts down translation and exposes the mRNA to 5'-to-3' exonucleolytic degradation by XRN1. Although yeast DCP1 and DCP2 directly interact, an additional factor, EDC4, promotes DCP1-DCP2 association in metazoan. Here, we elucidate how the human proteins interact to assemble an active decapping complex and how decapped mRNAs are handed over to XRN1. We show that EDC4 serves as a scaffold for complex assembly, providing binding sites for DCP1, DCP2 and XRN1. DCP2 and XRN1 bind simultaneously to the EDC4 C-terminal domain through short linear motifs (SLiMs). Additionally, DCP1 and DCP2 form direct but weak interactions that are facilitated by EDC4. Mutational and functional studies indicate that the docking of DCP1 and DCP2 on the EDC4 scaffold is a critical step for mRNA decapping in vivo. They also revealed a crucial role for a conserved asparagine-arginine containing loop (the NR-loop) in the DCP1 EVH1 domain in DCP2 activation. Our data indicate that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5'-to-3' mRNA degradation by XRN1 in human cells.

Human DDX6 regulates translation and decay of inefficiently translated mRNAs.

Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.

Wet depositions of cations in forests across NADP, EMEP, and EANET monitoring networks over the last two decades.

Studies focused on emissions and acid deposition of sulfur (S) and nitrogen (N) and the consequent precipitation acidity have a long history. However, atmospheric depositions of cations play a critical role in buffering precipitation acidity, and providing cationic nutrients for vegetation growth lacks sufficient studies equally. The spatiotemporal patterns of cation depositions and their neutralization potential across broad scales remain unclear. Through synthesizing the long-term data in forest sites (n = 128) derived from three monitoring networks (NADP in Northern America, EMEP in Europe, and EANET in East Asia) on wet deposition of cations (Na+, NH4-N, K+, Mg2+, and Ca2+), this study assesses the temporal changes and spatial patterns of cation depositions and their neutralization potential over the last two decades. The results showed that the depositions of cationic nutrients were considerably higher in EANET compared to NADP and EMEP. The depositions of sea salt-associated sodium exhibited a significant transition from marine (> 15 kg ha-1 year-1) to inland (< 3.0 kg ha-1 year-1) forest sites attributable to the precipitation quantity and influences of sea spray. The higher emissions of NH3 and particulate matter in East Asia explained the higher cation depositions in EANET than NADP and EMEP. The annual trends of cations revealed that only 20-30% of the forest sites showed significant changing trends and the sites widely spread across the three networks. Possibly, base cation (BC) deposition has reached a low and stable condition in NADP and EMEP, while it has high spatial heterogeneity in the temporal change in EANET. The difference in BC deposition among the three networks reflects their distinct development of economy. Our synthesis indicates that the annual trends of neutralization factor (NF) in NADP can be explained by the declining of acid potential (AP), not by neutralization potential (NP) as BC deposition has been stably low over the past two decades. Whereas, the concurrent decreases of AP and NP in EMEP or plateau period of both AP and NP in EANET have come to a standstill of acid neutralizing capacity.

The Contribution of Epigenetics to Evolutionary Adaptation in Zingiber kawagoii Hayata (Zingiberaceae) Endemic to Taiwan.

We epigenotyped 211 individuals from 17 Zingiber kawagoii populations using methylation-sensitive amplification polymorphism (MSAP) and investigated the associations of methylated (mMSAP) and unmethylated (uMSAP) loci with 16 environmental variables. Data regarding genetic variation based on amplified fragment length polymorphism (AFLP) were obtained from an earlier study. We found a significant positive correlation between genetic and epigenetic variation. Significantly higher mean mMSAP and uMSAP uHE (unbiased expected heterozygosity: 0.223 and 0.131, respectively, p < 0.001) per locus than that estimated based on AFLP (uHE = 0.104) were found. Genome scans detected 10 mMSAP and 9 uMSAP FST outliers associated with various environmental variables. A significant linear fit for 11 and 12 environmental variables with outlier mMSAP and uMSAP ordination, respectively, generated using full model redundancy analysis (RDA) was found. When conditioned on geography, partial RDA revealed that five and six environmental variables, respectively, were the most important variables influencing outlier mMSAP and uMSAP variation. We found higher genetic (average FST = 0.298) than epigenetic (mMSAP and uMSAP average FST = 0.044 and 0.106, respectively) differentiation and higher genetic isolation-by-distance (IBD) than epigenetic IBD. Strong epigenetic isolation-by-environment (IBE) was found, particularly based on the outlier data, controlling either for geography (mMSAP and uMSAP ßE = 0.128 and 0.132, respectively, p = 0.001) or for genetic structure (mMSAP and uMSAP ßE = 0.105 and 0.136, respectively, p = 0.001). Our results suggest that epigenetic variants can be substrates for natural selection linked to environmental variables and complement genetic changes in the adaptive evolution of Z. kawagoii populations.

Fog and rain water chemistry in a tea plantation of northern Taiwan.

Tea plantations are expanding globally and many are in mountainous areas with frequent fog but few studies have examined fog chemistry in these areas. We examined chemical composition of fog and rain water at a tea plantation in northern Taiwan. Fog water was collected using a Kroneis passive cylindrical fog-water collector and rain water was collected using a 20-cm-diameter funnel. The most abundant ions were Cl- and Na+ in both fog and rain waters due to the proximity of the site to the coast. The order of abundance of other ions was NO3- > Mg2+ > SO42- > Ca2+ > NH4+ > K+ > H+ in fog water and SO42- > K+ > NO3- > NH4+ > Ca2+ > Mg2+ > H+ in rain water. The concentration enrichment ratio (fog to rain) ranged between 2.2 (K+) and 22 (Mg2+) lying between sites near major emission sources and sites in remote areas, possibly because the immediate surrounding landscape is covered with secondary forests although it is near large cities. Factor analysis highlights the influences of sea-salt aerosols on the variation of fog and rain water chemistry. Sea-salt corrections using Na+ as the sea salt tracer led to negative concentrations of Cl- and Mg2+ suggesting that assumptions involved in sea-salt corrections were not satisfied. Agriculture influence is identified as a unique factor for explaining variance of K+, NH4+, and dissolved organic nitrogen (DON) concentrations in fog water but not rain water. Ion concentrations in fog and rain water were generally higher in the weekly samples associated with air trajectories passing through the continental East Asia than those associated with oceanic trajectories pointing to the role of regional pollution sources in affecting local fog and rain water chemistry. Our study highlights greater effects of tea agriculture on fog than rain water chemistry.

Sequential isolation of metabolites and lipids from a single sample to achieve multiomics by using TRIzol reagent.

Simultaneous extraction of various types of biomolecule from a single sample can be beneficial for multiomics studies of unique specimens. An efficient and convenient sample preparation approach must be developed that can comprehensively isolate and extract biomolecules from one sample. TRIzol reagent is widely used in biological studies for DNA, RNA, and protein isolation. This study evaluated the feasibility of using TRIzol reagent for the simultaneous isolation of not only DNA, RNA, and proteins but also metabolites and lipids from a single sample. Through the comparison of known metabolites and lipids obtained using the conventional methanol (MeOH) and methyl-tert-butyl ether (MTBE) extraction methods, we determined the presence of metabolites and lipids in the supernatant during TRIzol sequential isolation. Finally, we performed untargeted metabolomics and lipidomics to examine metabolite and lipid alterations associated with the jhp0417 mutation in Helicobacter pylori by using the TRIzol sequential isolation protocol and MeOH and MTBE extraction methods. Metabolites and lipids with significant differences isolated using the TRIzol sequential isolation protocol were consistent with those obtained using the conventional MeOH and MTBE extraction methods. These results indicated that TRIzol reagent can be used to simultaneously isolate metabolites and lipids from a single sample. Thus, TRIzol reagent can be used in biological and clinical research, especially in multiomics studies.

Adaptive Divergence without Distinct Species Relationships Indicate Early Stage Ecological Speciation in Species of the Rhododendronpseudochrysanthum Complex Endemic to Taiwan.

The testing association of environmental variables with genetic and epigenetic variation could be crucial to deciphering the effects of environmental factors playing roles as selective drivers in ecological speciation. Although ecological speciation may occur in closely related species, species boundaries may not be established over a short evolutionary timescale. Here, we investigated the genetic and epigenetic variations using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP), respectively, and tested their associations with environmental variables in populations of four closely related species in the R. pseudochrysanthum complex. No distinctive species relationships were found using genetic clustering analyses, neighbor-joining tree, and neighbor-net tree based on the total AFLP variation, which is suggestive of the incomplete lineage sorting of ancestral variation. Nonetheless, strong isolation-by-environment and adaptive divergence were revealed, despite the significant isolation-by-distance. Annual mean temperature, elevation, normalized difference vegetation index, and annual total potential evapotranspiration were found to be the most important environmental variables explaining outlier genetic and epigenetic variations. Our results suggest that the four closely related species of the R. pseudochrysanthum complex share the polymorphism of their ancestor, but reproductive isolation due to ecological speciation can occur if local environmental divergence persists over time.

Air pollutant removal by four sidewalk tree species in the largest city in Taiwan.

Air pollutants pose risks to human health, especially in densely populated cities. We compared the interception of suspended particles and metal elements by four sidewalk tree species with different leaf surface wettability (based on contact angle), leaf area, and phenology in Taipei, Taiwan. Suspended particles were enriched 2.0-2.5 times in throughfall relative to rainfall due to wash-off of suspended particles deposited on leaf surfaces during rainless periods. The enrichment in throughfall was greater in tree species with larger leaf areas. Despite greater concentrations of suspended particles in rainfall during the low-leaf-area period, enrichment was greater in the high-leaf-area period, indicating that leaf area was a key factor affecting canopy interception of pollutants. Throughfall enrichment of suspended particles positively correlated with water quantity, indicating that air pollutants intercepted by tree canopies were not fully washed off by rainfall. Annually, ∼830 g of suspended particles were intercepted and washed off from one tree canopy, with a crown area of 42 m2 . Scaling up, a rough estimate of 72.7 Mg of suspended particles were intercepted annually by the 90,000 sidewalk trees in Taipei City. Copper, chromium, and aluminum were enriched in throughfall compared with rainfall. However, lead was depleted in throughfall, indicating greater interception than wash-off. Based on our results, leaf area and length of foliated period are key characteristics affecting canopy interception of particulate matter and associated metal elements, whereas leaf surface wettability is of secondary importance.

Pattern of Adaptive Divergence in Zingiber kawagoii Hayata (Zingiberaceae) along a Narrow Latitudinal Range.

Ecological and evolutionary processes linking adaptation to environment are related to species' range shifts. In this study, we employed amplified-fragment-length-polymorphism-based genome scan methods to identify candidate loci among Zingiber kawagoii populations inhabiting varying environments distributed at low to middle elevations (143-1488 m) in a narrow latitudinal range (between 21.90 and 25.30° N). Here, we show evidence of selection driving the divergence of Z. kawagoii. Twenty-six FST outliers were detected, which were significantly correlated with various environmental variables. The allele frequencies of nine FST outliers were either positively or negatively correlated with the population mean FST. Using several independent approaches, we found environmental variables act in a combinatorial fashion, best explaining outlier genetic variation. Nonetheless, we found that adaptive divergence was affected mostly by annual temperature range, and it is significantly positively correlated with latitude and significantly negatively correlated with the population mean FST. This study addresses a latitudinal pattern of changes in annual temperature range (which ranged from 13.8 °C in the Lanyu population to 18.5 °C in the Wulai population) and emphasizes the pattern of latitudinal population divergence closely linked to the allele frequencies of adaptive loci, acting in a narrow latitudinal range. Our results also indicate environmentally dependent local adaptation for both leading- and trailing-edge populations.

Changes of precipitation acidity related to sulfur and nitrogen deposition in forests across three continents in north hemisphere over last two decades.

Through synthesizing bulk precipitation chemistry in forest sites (n = 128) from three monitoring networks, (NADP in Northern America, EMEP in Europe, and EANET in East Asia), this study quantifies the temporal changes of precipitation acidity and its dominant acidifying agents over the last two decades. Results show distinct declines of sulfate and nitrate depositions and increases of precipitation pH in northeast America and central and east Europe, but not in Asia during 1999 and 2018. The decreases of sulfate and nitrate depositions likely reflect the long-term effort of pollutant emission controls. The temporal pattern of sulfate (SO42-)/nitrate (NO3-) and ammonium nitrogen (NH4-N)/nitrate nitrogen (NO3-N) equivalent ratios indicate that acid rain in the NADP and EMEP have transitioned from sulfate-dominated to nitrate-dominated, and the DIN deposition has shifted from nitrate-dominated to ammonium-dominated in recent years, owing to reductions of sulfur dioxides (SO2) and nitrogen oxides (NOx) emissions. In contrast, sulfate still plays a dominant role on the acidity of precipitation than nitrate in Asia, and NH4-N deposition also has a significant contribution in N flux due to increasing trends of ammonia emissions in Southeast Asia.

Tropical Cyclone Ecology: A Scale-Link Perspective.

Tropical cyclones are increasing in intensity and size and, thus, are poised to increase in importance as disturbance agents. Our understanding of cyclone ecology is biased towards the North Atlantic Basin, because cyclone effects do differ across oceanic basins. Cyclones have both short and long-term effects across the levels of biological organization, but we lack a scale-perspective of cyclone ecology. Effects on individual trees, such as defoliation or branch stripping and uprooting, are mechanistically linked to effects at the community and ecosystem levels, including forest productivity and stand regeneration time. Forest dwarfing via the gradual removal of taller trees by cyclones over many generations illustrates that cyclones shape forest structure through the accumulation of short-term effects over longer timescales.

Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar (Calocedrus formosana).

Population diversification can be shaped by a combination of environmental factors as well as geographic isolation interacting with gene flow. We surveyed genetic variation of 243 samples from 12 populations of Calocedrus formosana using amplified fragment length polymorphism (AFLP) and scored a total of 437 AFLP fragments using 11 selective amplification primer pairs. The AFLP variation was used to assess the role of gene flow on the pattern of genetic diversity and to test environments in driving population adaptive evolution. This study found the relatively lower level of genetic diversity and the higher level of population differentiation in C. formosana compared with those estimated in previous studies of conifers including Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides occurring in Taiwan. BAYESCAN detected 26 F ST outlier loci that were found to be associated strongly with various environmental variables using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression. We found several environmentally dependent adaptive loci with high frequencies in low- or high-elevation populations, suggesting their involvement in local adaptation. Ecological factors, including relative humidity and sunshine hours, that are generally not altitude related could have been the most important selective drivers for population divergent evolution in C. formosana. The present study provides fundamental information in relation to adaptive evolution and can be useful for assisted migration program of C. formosana in the future conservation of this species.

Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae).

Demographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R2 index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.

Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation.

CCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails of messenger RNA or deadenylation. Here, we reconstitute a complete, recombinant human CCR4-NOT complex. Our reconstitution strategy permits strict compositional control to test mechanistic hypotheses with purified component variants. CCR4-NOT is more active and selective for poly(A) than the isolated exonucleases, CCR4a and CAF1, which have distinct deadenylation profiles in vitro. The exonucleases require at least two out of three conserved non-enzymatic modules (CAF40, NOT10:NOT11 or NOT) for full activity in CCR4-NOT. CAF40 and the NOT10:NOT11 module both bind RNA directly and stimulate deadenylation in a partially redundant manner. Linear motifs from different RNA-binding factors that recruit CCR4-NOT to specific mRNAs via protein-protein interactions with CAF40 can inhibit bulk deadenylation. We reveal an additional layer of regulatory complexity to the human deadenylation machinery, which may prime it either for general or target-specific degradation.