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

Enwerem, Isioma I.; Elrod, Nathan D.; Chang, Chung Te; Ai, Lin; Ji, Ping; Bohn, Jennifer; Levdansky, Yevgen; Wagner, Eric J.; Valkov, Eugene; Goldstrohm, Aaron C.

doi:10.1101/2020.11.17.387456

Cited by 10 publications

(13 citation statements)

References 95 publications

(255 reference statements)

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“…In undifferentiated ESCs, eIF4A2 may sequester Pum1 through their physical association and restrict its functions to prevent ESC differentiation, which warrants future investigation. Moreover, as Ddx6 and Pum1 can also be involved in microRNA (miRNA)–mediated repression ( 56 , 57 ), we do not exclude the possibility that eIF4A2 may also be involved, indirectly, in the repression of certain mRNAs via miRNA-related functions in ESCs.…”

Section: Discussionmentioning

confidence: 99%

eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency

Yang

Huang

et al. 2022

Sci. Adv.

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Translational control has emerged as a fundamental regulatory layer of proteome complexity that governs cellular identity and functions. As initiation is the rate-limiting step of translation, we carried out an RNA interference screen for key translation initiation factors required to maintain embryonic stem cell (ESC) identity. We identified eukaryotic translation initiation factor 4A2 (eIF4A2) and defined its mechanistic action through ribosomal protein S26–independent and –dependent ribosomes in translation initiation activation of messenger RNAs (mRNAs) encoding pluripotency factors and the histone variant H3.3 with demonstrated roles in maintaining stem cell pluripotency. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent two-cell transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Accordingly, knockdown of eIF4A2 disrupts ESC proteome, causing the loss of ESC identity. Collectively, we establish a translational paradigm of the protein synthesis of pluripotency transcription factors and epigenetic regulators imposed on their established roles in controlling pluripotency.

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Section: Discussionmentioning

confidence: 99%

eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency

Yang

Huang

et al. 2022

Sci. Adv.

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“…The second class are RNA-binding proteins that, like miRNAs, occupy specific binding sites in 3’ UTRs. Well-characterized examples include tristetraprolin (Brooks and Blackshear, 2013; Bulbrook et al, 2018; Fabian et al, 2013; Webster et al, 2019), Pumilio (Enwerem et al, 2021; Goldstrohm et al, 2018; Webster et al, 2019; Wickens et al, 2002) and Roquin (Leppek et al, 2013; Sgromo et al, 2017), all of which interact directly with the CCR4-NOT complex.…”

Section: Introductionmentioning

confidence: 99%

RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system

Pekovic

Rammelt

Kubíková

et al. 2022

Preprint

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Posttranscriptional regulation of the maternal nanos mRNA is essential for the development of the anterior – posterior axis of the Drosophila embryo. The nanos RNA is regulated by the protein Smaug. Binding to Smaug recognition elements (SREs) in the nanos 3’-UTR, Smaug nucleates the assembly of a larger repressor complex including the eIF4E-T paralog Cup and five additional proteins. The Smaug-dependent complex represses translation of nanos and induces its deadenylation by the CCR4-NOT deadenylase. Here we report an in vitro reconstitution of the Drosophila CCR4-NOT complex and Smaug-dependent deadenylation. We find that Smaug by itself is sufficient to cause deadenylation by the Drosophila or human CCR4-NOT complexes in an SRE-dependent manner. CCR4-NOT subunits NOT10 and NOT11 are dispensable, but the NOT module, consisting of NOT2, NOT3 and the C-terminal part of NOT1, is required. Smaug interacts with the C-terminal domain of NOT3. Both catalytic subunits of CCR4-NOT contribute to Smaug-dependent deadenylation. Whereas the CCR4-NOT complex itself acts distributively, Smaug induces a processive behavior. The cytoplasmic poly(A) binding protein (PABPC) has but a minor effect on Smaug-dependent deadenylation. Among the additional constituents of the Smaug-dependent repressor complex, Cup also facilitates CCR4-NOT-dependent deadenylation, both independently and in cooperation with Smaug.

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“…Thereby it is central in mRNA turnover and translational repression (34,35). It is generally active for post-translational mRNA decay, but can also be tethered to mRNAs by RNA binding proteins or the microRNA machinery (36)(37)(38)(39). Ccr4-Not can also inhibit translation independently of deadenylation (40) or activate decapping (41).…”

Section: Introductionmentioning

confidence: 99%

Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

Allen

Weiss

Panasenko

et al. 2022

Preprint

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Background: The Ccr4-Not complex is most well known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics have been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts. In this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impact mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion. Our results reveal that mRNA solubility defines dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus.

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

Cited by 10 publications

References 95 publications

eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency

eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency

RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system

Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

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