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1.
EMBO Rep ; 2024 May 20.
Article in English | MEDLINE | ID: mdl-38769420

ABSTRACT

Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made by RNase III Dicer from long double-stranded RNA (dsRNA). RNAi roles include gene regulation, antiviral immunity or defense against transposable elements. In mammals, RNAi is constrained by Dicer's adaptation to produce another small RNA class-microRNAs. However, a truncated Dicer isoform (ΔHEL1) supporting RNAi exists in mouse oocytes. A homozygous mutation to express only the truncated ΔHEL1 variant causes dysregulation of microRNAs and perinatal lethality in mice. Here, we report the phenotype and canonical RNAi activity in DicerΔHEL1/wt mice, which are viable, show minimal miRNome changes, but their endogenous siRNA levels are an order of magnitude higher. We show that siRNA production in vivo is limited by available dsRNA, but not by Protein kinase R, a dsRNA sensor of innate immunity. dsRNA expression from a transgene yields sufficient siRNA levels to induce efficient RNAi in heart and muscle. DicerΔHEL1/wt mice with enhanced canonical RNAi offer a platform for examining potential and limits of mammalian RNAi in vivo.

2.
BMC Biol ; 20(1): 272, 2022 12 08.
Article in English | MEDLINE | ID: mdl-36482406

ABSTRACT

BACKGROUND: Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g., long non-coding RNA (lncRNA) expressing genes) readily emerge de novo from non-genic sequences and have high evolutionary turnover. Genesis of a gene may be facilitated by adoption of functional genic sequences from retrotransposon insertions. However, protein-coding sequences in extant genomes rarely lack any connection to an ancestral protein-coding sequence. RESULTS: We describe remarkable evolution of the murine gene D6Ertd527e and its orthologs in the rodent Muroidea superfamily. The D6Ertd527e emerged in a common ancestor of mice and hamsters most likely as a lncRNA-expressing gene. A major contributing factor was a long terminal repeat (LTR) retrotransposon insertion carrying an oocyte-specific promoter and a 5' terminal exon of the gene. The gene survived as an oocyte-specific lncRNA in several extant rodents while in some others the gene or its expression were lost. In the ancestral lineage of Mus musculus, the gene acquired protein-coding capacity where the bulk of the coding sequence formed through CAG (AGC) trinucleotide repeat expansion and duplications. These events generated a cytoplasmic serine-rich maternal protein. Knock-out of D6Ertd527e in mice has a small but detectable effect on fertility and the maternal transcriptome. CONCLUSIONS: While this evolving gene is not showing a clear function in laboratory mice, its documented evolutionary history in Muroidea during the last ~ 40 million years provides a textbook example of how a several common mutation events can support de novo gene formation, evolution of protein-coding capacity, as well as gene's demise.


Subject(s)
Muridae , RNA, Long Noncoding , Animals , RNA, Long Noncoding/genetics
3.
Mol Cell ; 82(21): 4064-4079.e13, 2022 11 03.
Article in English | MEDLINE | ID: mdl-36332606

ABSTRACT

MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer's DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer•-miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.


Subject(s)
MicroRNAs , Ribonuclease III , Mice , Animals , Ribonuclease III/metabolism , RNA Interference , MicroRNAs/genetics , MicroRNAs/metabolism , Carrier Proteins/metabolism , Mammals/metabolism
4.
Nat Cell Biol ; 23(9): 992-1001, 2021 09.
Article in English | MEDLINE | ID: mdl-34489573

ABSTRACT

PIWI-interacting RNAs (piRNAs) support the germline by suppressing retrotransposons. Studies of the pathway in mice have strongly shaped the view that mammalian piRNAs are essential for male but not for female fertility. Here, we report that the role of the piRNA pathway substantially differs in golden hamsters (Mesocricetus auratus), the piRNA pathway setup of which more closely resembles that of other mammals, including humans. The loss of the Mov10l1 RNA helicase-an essential piRNA biogenesis factor-leads to striking phenotypes in both sexes. In contrast to mice, female Mov10l1-/- hamsters are sterile because their oocytes do not sustain zygotic development. Furthermore, Mov10l1-/- male hamsters have impaired establishment of spermatogonia accompanied by transcriptome dysregulation and an expression surge of a young retrotransposon subfamily. Our results show that the mammalian piRNA pathway has essential roles in both sexes and its adaptive nature allows it to manage emerging genomic threats and acquire new critical roles in the germline.


Subject(s)
Oocytes/metabolism , RNA, Small Interfering/genetics , Spermatogenesis/physiology , Spermatogonia/pathology , Animals , Cricetinae , Gene Silencing/physiology , Male , Mesocricetus/metabolism , Oocytes/pathology , RNA Helicases/genetics , Retroelements/physiology , Spermatogenesis/genetics , Spermatogonia/metabolism , Testis/metabolism
5.
Genes (Basel) ; 12(4)2021 04 08.
Article in English | MEDLINE | ID: mdl-33918028

ABSTRACT

RNA interference (RNAi) designates sequence-specific mRNA degradation mediated by small RNAs generated from long double-stranded RNA (dsRNA) by RNase III Dicer. RNAi appears inactive in mammalian cells except for mouse oocytes, where high RNAi activity exists because of an N-terminally truncated Dicer isoform, denoted DicerO. DicerO processes dsRNA into small RNAs more efficiently than the full-length Dicer expressed in somatic cells. DicerO is expressed from an oocyte-specific promoter of retrotransposon origin, which is silenced in other cell types. In this work, we evaluated CRISPR-based strategies for epigenetic targeting of the endogenous Dicer gene to restore DicerO expression and, consequently, RNAi. We show that reactivation of DicerO expression can be achieved in mouse embryonic stem cells, but it is not sufficient to establish a robust canonical RNAi response.


Subject(s)
Clustered Regularly Interspaced Short Palindromic Repeats , DEAD-box RNA Helicases/genetics , Embryonic Stem Cells/metabolism , Promoter Regions, Genetic , RNA, Small Interfering/genetics , Ribonuclease III/genetics , 3T3 Cells , Animals , DEAD-box RNA Helicases/antagonists & inhibitors , Embryonic Stem Cells/cytology , Mice , RNA Interference , Ribonuclease III/antagonists & inhibitors
6.
Nucleic Acids Res ; 48(14): 8050-8062, 2020 08 20.
Article in English | MEDLINE | ID: mdl-32609824

ABSTRACT

MicroRNAs (miRNAs) are ubiquitous small RNAs guiding post-transcriptional gene repression in countless biological processes. However, the miRNA pathway in mouse oocytes appears inactive and dispensable for development. We propose that marginalization of the miRNA pathway activity stems from the constraints and adaptations of RNA metabolism elicited by the diluting effects of oocyte growth. We report that miRNAs do not accumulate like mRNAs during the oocyte growth because miRNA turnover has not adapted to it. The most abundant miRNAs total tens of thousands of molecules in growing (∅ 40 µm) and fully grown (∅ 80 µm) oocytes, a number similar to that observed in much smaller fibroblasts. The lack of miRNA accumulation results in a 100-fold lower miRNA concentration in fully grown oocytes than in somatic cells. This brings a knock-down-like effect, where diluted miRNAs engage targets but are not abundant enough for significant repression. Low-miRNA concentrations were observed in rat, hamster, porcine and bovine oocytes, arguing that miRNA inactivity is not mouse-specific but a common mammalian oocyte feature. Injection of 250,000 miRNA molecules was sufficient to restore reporter repression in mouse and porcine oocytes, suggesting that miRNA inactivity comes from low-miRNA abundance and not from some suppressor of the pathway.


Subject(s)
MicroRNAs/genetics , Oocytes/metabolism , Oogenesis , 3T3 Cells , Animals , Cattle , Cells, Cultured , Cricetinae , Female , Gene Expression Regulation, Developmental , Mice , Mice, Inbred C57BL , MicroRNAs/metabolism , Models, Theoretical , Oocytes/cytology , RNA, Messenger/genetics , RNA, Messenger/metabolism , Rats , Species Specificity , Swine
7.
Nucleic Acids Res ; 48(6): 3211-3227, 2020 04 06.
Article in English | MEDLINE | ID: mdl-31956907

ABSTRACT

Tens of thousands of rapidly evolving long non-coding RNA (lncRNA) genes have been identified, but functions were assigned to relatively few of them. The lncRNA contribution to the mouse oocyte physiology remains unknown. We report the evolutionary history and functional analysis of Sirena1, the most expressed lncRNA and the 10th most abundant poly(A) transcript in mouse oocytes. Sirena1 appeared in the common ancestor of mouse and rat and became engaged in two different post-transcriptional regulations. First, antisense oriented Elob pseudogene insertion into Sirena1 exon 1 is a source of small RNAs targeting Elob mRNA via RNA interference. Second, Sirena1 evolved functional cytoplasmic polyadenylation elements, an unexpected feature borrowed from translation control of specific maternal mRNAs. Sirena1 knock-out does not affect fertility, but causes minor dysregulation of the maternal transcriptome. This includes increased levels of Elob and mitochondrial mRNAs. Mitochondria in Sirena1-/- oocytes disperse from the perinuclear compartment, but do not change in number or ultrastructure. Taken together, Sirena1 contributes to RNA interference and mitochondrial aggregation in mouse oocytes. Sirena1 exemplifies how lncRNAs stochastically engage or even repurpose molecular mechanisms during evolution. Simultaneously, Sirena1 expression levels and unique functional features contrast with the lack of functional importance assessed under laboratory conditions.


Subject(s)
Mitochondria/genetics , Oocytes/metabolism , RNA, Long Noncoding/genetics , RNA, Messenger/genetics , RNA, Mitochondrial/genetics , Animals , Gene Knockout Techniques , Mice , Mitochondria/ultrastructure , Oocytes/growth & development , Oocytes/ultrastructure , Polyadenylation/genetics , Rats , Transcriptome/genetics
8.
PLoS Genet ; 15(12): e1008261, 2019 12.
Article in English | MEDLINE | ID: mdl-31860668

ABSTRACT

Germline genome defense evolves to recognize and suppress retrotransposons. One of defensive mechanisms is the PIWI-associated RNA (piRNA) pathway, which employs small RNAs for sequence-specific repression. The loss of the piRNA pathway in mice causes male sterility while females remain fertile. Unlike spermatogenic cells, mouse oocytes posses also RNA interference (RNAi), another small RNA pathway capable of retrotransposon suppression. To examine whether RNAi compensates the loss of the piRNA pathway, we produced a new RNAi pathway mutant DicerSOM and crossed it with a catalytically-dead mutant of Mili, an essential piRNA gene. Normal follicular and oocyte development in double mutants showed that RNAi does not suppress a strong ovarian piRNA knock-out phenotype. However, we observed redundant and non-redundant targeting of specific retrotransposon families illustrating stochasticity of recognition and targeting of invading retrotransposons. Intracisternal A Particle retrotransposon was mainly targeted by the piRNA pathway, MaLR and RLTR10 retrotransposons were targeted mainly by RNAi. Double mutants showed accumulations of LINE-1 retrotransposon transcripts. However, we did not find strong evidence for transcriptional activation and mobilization of retrotransposition competent LINE-1 elements suggesting that while both defense pathways are simultaneously expendable for ovarian oocyte development, yet another transcriptional silencing mechanism prevents mobilization of LINE-1 elements.


Subject(s)
Oocytes/growth & development , RNA Interference , RNA, Small Interfering/genetics , Retroelements , Animals , Argonaute Proteins/genetics , DEAD-box RNA Helicases/genetics , Female , Mice , Mutation , Oocytes/chemistry , Ribonuclease III/genetics , Signal Transduction
9.
Life Sci Alliance ; 2(1)2019 02.
Article in English | MEDLINE | ID: mdl-30808654

ABSTRACT

RNAi is the sequence-specific mRNA degradation guided by siRNAs produced from long dsRNA by RNase Dicer. Proteins executing RNAi are present in mammalian cells but rather sustain the microRNA pathway. Aiming for a systematic analysis of mammalian RNAi, we report here that the main bottleneck for RNAi efficiency is the production of functional siRNAs, which integrates Dicer activity, dsRNA structure, and siRNA targeting efficiency. Unexpectedly, increased expression of Dicer cofactors TARBP2 or PACT reduces RNAi but not microRNA function. Elimination of protein kinase R, a key dsRNA sensor in the interferon response, had minimal positive effects on RNAi activity in fibroblasts. Without high Dicer activity, RNAi can still occur when the initial Dicer cleavage of the substrate yields an efficient siRNA. Efficient mammalian RNAi may use substrates with some features of microRNA precursors, merging both pathways even more than previously suggested. Although optimized endogenous Dicer substrates mimicking miRNA features could evolve for endogenous regulations, the same principles would make antiviral RNAi inefficient as viruses would adapt to avoid efficacy.


Subject(s)
RNA Interference/physiology , RNA, Double-Stranded/genetics , RNA, Double-Stranded/metabolism , Animals , Base Sequence/genetics , Carrier Proteins/metabolism , DEAD-box RNA Helicases/metabolism , Gene Knockout Techniques , Mice , MicroRNAs/metabolism , NIH 3T3 Cells , Plasmids/genetics , RNA, Small Interfering/metabolism , RNA-Binding Proteins/metabolism , Ribonuclease III/metabolism , Transfection , eIF-2 Kinase/genetics
10.
Life Sci Alliance ; 1(4): e201800084, 2018 Aug.
Article in English | MEDLINE | ID: mdl-30456367

ABSTRACT

Removal of poly(A) tail is an important mechanism controlling eukaryotic mRNA turnover. The major eukaryotic deadenylase complex CCR4-NOT contains two deadenylase components, CCR4 and CAF1, for which mammalian CCR4 is encoded by Cnot6 or Cnot6l paralogs. We show that Cnot6l apparently supplies the majority of CCR4 in the maternal CCR4-NOT in mouse, hamster, and bovine oocytes. Deletion of Cnot6l yielded viable mice, but Cnot6l -/- females exhibited ∼40% smaller litter size. The main onset of the phenotype was post-zygotic: fertilized Cnot6l -/- eggs developed slower and arrested more frequently than Cnot6l +/- eggs, suggesting that maternal CNOT6L is necessary for accurate oocyte-to-embryo transition. Transcriptome analysis revealed major transcriptome changes in Cnot6l -/- ovulated eggs and one-cell zygotes. In contrast, minimal transcriptome changes in preovulatory Cnot6l -/- oocytes were consistent with reported Cnot6l mRNA dormancy. A minimal overlap between transcripts sensitive to decapping inhibition and Cnot6l loss suggests that decapping and CNOT6L-mediated deadenylation selectively target distinct subsets of mRNAs during oocyte-to-embryo transition in mouse.

11.
Front Genet ; 9: 45, 2018.
Article in English | MEDLINE | ID: mdl-29535760

ABSTRACT

MicroRNAs (miRNAs) are small RNAs repressing gene expression. They contribute to many physiological processes and pathologies. Consequently, strategies for manipulation of the miRNA pathway are of interest as they could provide tools for experimental or therapeutic interventions. One of such tools could be small chemical compounds identified through high-throughput screening (HTS) with reporter assays. While a number of chemical compounds have been identified in such high-throughput screens, their application potential remains elusive. Here, we report our experience with cell-based HTS of a library of 12,816 chemical compounds to identify miRNA pathway modulators. We used human HeLa and mouse NIH 3T3 cell lines with stably integrated or transiently expressed luciferase reporters repressed by endogenous miR-30 and let-7 miRNAs and identified 163 putative miRNA inhibitors. We report that compounds relieving miRNA-mediated repression via stress induction are infrequent; we have found only two compounds that reproducibly induced stress granules and relieved miRNA-targeted reporter repression. However, we have found that this assay type readily yields non-specific (miRNA-independent) stimulators of luciferase reporter activity. Furthermore, our data provide partial support for previously published miRNA pathway modulators; the most notable intersections were found among anthracyclines, dopamine derivatives, flavones, and stilbenes. Altogether, our results underscore the importance of appropriate negative controls in development of small compound inhibitors of the miRNA pathway. This particularly concerns validation strategies, which would greatly profit from assays that fundamentally differ from the routinely employed miRNA-targeted reporter assays.

12.
Genome Res ; 27(8): 1384-1394, 2017 08.
Article in English | MEDLINE | ID: mdl-28522611

ABSTRACT

Retrotransposons are "copy-and-paste" insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified more than 800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons. The LTR-mediated gene remodeling also extends to hamster, human, and bovine oocytes. The LTRs function in a stage-specific manner during the oocyte-to-embryo transition by activating transcription, altering protein-coding sequences, producing noncoding RNAs, and even supporting evolution of new protein-coding genes. These functions result, for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles. The functional potential of the studied LTRs is even higher, because we show that dormant LTR promoter activity can rescue loss of an essential upstream promoter. We also report a novel protein-coding gene evolution-D6Ertd527e-in which an MT LTR provided a promoter and the 5' exon with a functional start codon while the bulk of the protein-coding sequence evolved through a CAG repeat expansion. Altogether, ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale. ERVL LTRs thus offer means for a comprehensive survey of the genome's expression potential, tightly intertwining with gene expression and evolution in the germline.


Subject(s)
Evolution, Molecular , Gene Expression Regulation , Oocytes/metabolism , Retroelements , Terminal Repeat Sequences , Zygote/metabolism , Animals , Cattle , Cricetinae , Endogenous Retroviruses , Humans , Mice , Oocytes/cytology , Promoter Regions, Genetic , Transcription, Genetic , Zygote/cytology
13.
Cell Cycle ; 16(10): 927-939, 2017 May 19.
Article in English | MEDLINE | ID: mdl-28272965

ABSTRACT

Fully grown mammalian oocytes utilize transcripts synthetized and stored during earlier development. RNA localization followed by a local translation is a mechanism responsible for the regulation of spatial and temporal gene expression. Here we show that the mouse oocyte contains 3 forms of cap-dependent translational repressor expressed on the mRNA level: 4E-BP1, 4E-BP2 and 4E-BP3. However, only 4E-BP1 is present as a protein in oocytes, it becomes inactivated by phosphorylation after nuclear envelope breakdown and as such it promotes cap-dependent translation after NEBD. Phosphorylation of 4E-BP1 can be seen in the oocytes after resumption of meiosis but it is not detected in the surrounding cumulus cells, indicating that 4E-BP1 promotes translation at a specific cell cycle stage. Our immunofluorescence analyses of 4E-BP1 in oocytes during meiosis I showed an even localization of global 4E-BP1, as well as of its 4E-BP1 (Thr37/46) phosphorylated form. On the other hand, 4E-BP1 phosphorylated on Ser65 is localized at the spindle poles, and 4E-BP1 phosphorylated on Thr70 localizes on the spindle. We further show that the main positive regulators of 4E-BP1 phosphorylation after NEBD are mTOR and CDK1 kinases, but not PLK1 kinase. CDK1 exerts its activity toward 4E-BP1 phosphorylation via phosphorylation and activation of mTOR. Moreover, both CDK1 and phosphorylated mTOR co-localize with 4E-BP1 phosphorylated on Thr70 on the spindle at the onset of meiotic resumption. Expression of the dominant negative 4E-BP1 mutant adversely affects translation and results in spindle abnormality. Taken together, our results show that the phosphorylation of 4E-BP1 promotes translation at the onset of meiosis to support the spindle assembly and suggest an important role of CDK1 and mTOR kinases in this process. We also show that the mTOR regulatory pathway is present in human oocytes and is likely to function in a similar way as in mouse oocytes.


Subject(s)
CDC2 Protein Kinase/genetics , Carrier Proteins/genetics , Oocytes/growth & development , Phosphoproteins/genetics , TOR Serine-Threonine Kinases/genetics , Adaptor Proteins, Signal Transducing , Animals , Carrier Proteins/metabolism , Cell Cycle/genetics , Cell Cycle Proteins , Eukaryotic Initiation Factors , Gene Expression Regulation, Developmental , Humans , Mice , Oocytes/metabolism , Phosphoproteins/metabolism , Phosphorylation , Protein Biosynthesis , Spindle Apparatus/genetics
14.
Adv Exp Med Biol ; 953: 489-535, 2017.
Article in English | MEDLINE | ID: mdl-27975278

ABSTRACT

The beginning of development is controlled parentally. For example, early zygotic proteosynthesis produces proteins encoded by the maternal transcriptome. As parental factors become replaced by factors synthesized in the embryo, parental developmental control is gradually passed to the embryo. This chapter focuses on the clearance of parental factors during oocyte-to-embryo transition in vertebrates. Coordinated removal of parental factors erases ancestral oocyte identity of the zygote and facilitates reprogramming of gene expression into a state that will support development of a new organism. Here, we will review functional and mechanistic aspects of clearance of selected parental factors from early embryos, including different types of maternal RNAs, proteins, erasure of chromatin features of maternal and paternal genomes, as well as consumption of yolk and elimination of paternal mitochondria.


Subject(s)
Embryo, Mammalian , Oocytes , Zygote , Animals , Chromatin , Gene Expression Regulation, Developmental , Transcriptome
15.
Nat Commun ; 6: 6078, 2015 Jan 28.
Article in English | MEDLINE | ID: mdl-25629602

ABSTRACT

The fully grown mammalian oocyte is transcriptionally quiescent and utilizes only transcripts synthesized and stored during early development. However, we find that an abundant RNA population is retained in the oocyte nucleus and contains specific mRNAs important for meiotic progression. Here we show that during the first meiotic division, shortly after nuclear envelope breakdown, translational hotspots develop in the chromosomal area and in a region that was previously surrounded the nucleus. These distinct translational hotspots are separated by endoplasmic reticulum and Lamin, and disappear following polar body extrusion. Chromosomal translational hotspots are controlled by the activity of the mTOR-eIF4F pathway. Here we reveal a mechanism that-following the resumption of meiosis-controls the temporal and spatial translation of a specific set of transcripts required for normal spindle assembly, chromosome alignment and segregation.


Subject(s)
Eukaryotic Initiation Factor-4F/metabolism , Mammals/metabolism , Oocytes/metabolism , Protein Biosynthesis , Signal Transduction , TOR Serine-Threonine Kinases/metabolism , Animals , Chromosomes, Mammalian/metabolism , Down-Regulation , Fertilization , Genomic Instability , Humans , Meiosis , Mice , Nuclear Envelope/metabolism , RNA Caps/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Time Factors
16.
PLoS One ; 9(7): e101222, 2014.
Article in English | MEDLINE | ID: mdl-24983972

ABSTRACT

Regulation of mRNA translation by cytoplasmic polyadenylation is known to be important for oocyte maturation and further development. This process is generally controlled by phosphorylation of cytoplasmic polyadenylation element binding protein 1 (CPEB1). The aim of this study is to determine the role of Aurora kinase A in CPEB1 phosphorylation and the consequent CPEB1-dependent polyadenylation of maternal mRNAs during mammalian oocyte meiosis. For this purpose, we specifically inhibited Aurora kinase A with MLN8237 during meiotic maturation of porcine oocytes. Using poly(A)-test PCR method, we monitored the effect of Aurora kinase A inhibition on poly(A)-tail extension of long and short cyclin B1 encoding mRNAs as markers of CPEB1-dependent cytoplasmic polyadenylation. Our results show that inhibition of Aurora kinase A activity impairs neither cyclin B1 mRNA polyadenylation nor its translation and that Aurora kinase A is unlikely to be involved in CPEB1 activating phosphorylation.


Subject(s)
Aurora Kinase A/metabolism , Cyclin B1/genetics , Meiosis , Oocytes/metabolism , RNA, Messenger/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism , Animals , Female , Oocytes/enzymology , Phosphorylation , Polyadenylation , Sus scrofa/metabolism , mRNA Cleavage and Polyadenylation Factors/chemistry
17.
Mol Cell Biol ; 34(16): 3041-52, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24912683

ABSTRACT

The main role of the translation initiation factor 3 (eIF3) is to orchestrate formation of 43S-48S preinitiation complexes (PICs). Until now, most of our knowledge on eIF3 functional contribution to regulation of gene expression comes from yeast studies. Hence, here we developed several novel in vivo assays to monitor the integrity of the 13-subunit human eIF3 complex, defects in assembly of 43S PICs, efficiency of mRNA recruitment, and postassembly events such as AUG recognition. We knocked down expression of the PCI domain-containing eIF3c and eIF3a subunits and of eIF3j in human HeLa and HEK293 cells and analyzed the functional consequences. Whereas eIF3j downregulation had barely any effect and eIF3a knockdown disintegrated the entire eIF3 complex, eIF3c knockdown produced a separate assembly of the a, b, g, and i subunits (closely resembling the yeast evolutionary conserved eIF3 core), which preserved relatively high 40S binding affinity and an ability to promote mRNA recruitment to 40S subunits and displayed defects in AUG recognition. Both eIF3c and eIF3a knockdowns also severely reduced protein but not mRNA levels of many other eIF3 subunits and indeed shut off translation. We propose that eIF3a and eIF3c control abundance and assembly of the entire eIF3 and thus represent its crucial scaffolding elements critically required for formation of PICs.


Subject(s)
Eukaryotic Initiation Factor-3/metabolism , Ribosomal Proteins/metabolism , Cell Line , Cell Proliferation , Eukaryotic Initiation Factor-3/genetics , Gene Expression Regulation , HEK293 Cells , HeLa Cells , Humans , Peptide Chain Initiation, Translational/genetics , Protein Binding/genetics , Protein Binding/physiology , RNA Interference , RNA, Ribosomal/genetics , RNA, Small Interfering , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Ribosomal Proteins/genetics
18.
PLoS One ; 9(1): e87517, 2014.
Article in English | MEDLINE | ID: mdl-24475301

ABSTRACT

In mammals, double-stranded RNA (dsRNA) can mediate sequence-specific RNA interference, activate sequence-independent interferon response, or undergo RNA editing by adenosine deaminases. We showed that long hairpin dsRNA expression had negligible effects on mammalian somatic cells--expressed dsRNA was slightly edited, poorly processed into siRNAs, and it did not activate the interferon response. At the same time, we noticed reduced reporter expression in transient co-transfections, which was presumably induced by expressed dsRNA. Since transient co-transfections are frequently used for studying gene function, we systematically explored the role of expressed dsRNA in this silencing phenomenon. We demonstrate that dsRNA expressed from transiently transfected plasmids strongly inhibits the expression of co-transfected reporter plasmids but not the expression of endogenous genes or reporters stably integrated in the genome. The inhibition is concentration-dependent, it is found in different cell types, and it is independent of transfection method and dsRNA sequence. The inhibition occurs at the level of translation and involves protein kinase R, which binds the expressed dsRNA. Thus, dsRNA expression represents a hidden danger in transient transfection experiments and must be taken into account during interpretation of experimental results.


Subject(s)
Gene Expression Regulation/genetics , Genes, Reporter/genetics , RNA, Double-Stranded/metabolism , 3T3 Cells , Animals , Blotting, Western , Flow Cytometry , HEK293 Cells , HeLa Cells , Humans , Immunoprecipitation , Mice , Plasmids/genetics , Protein Serine-Threonine Kinases/metabolism , RNA, Small Interfering/genetics , Transfection/methods
19.
Cell ; 155(4): 807-16, 2013 Nov 07.
Article in English | MEDLINE | ID: mdl-24209619

ABSTRACT

In mammals, a single Dicer participates in biogenesis of small RNAs in microRNA (miRNA) and RNAi pathways. In mice, endogenous RNAi is highly active in oocytes, but not in somatic cells, which we ascribe here to an oocyte-specific Dicer isoform (Dicer(O)). Dicer(O) lacks the N-terminal DExD helicase domain and has higher cleavage activity than the full-length Dicer in somatic cells (Dicer(S)). Unlike Dicer(S), Dicer(O) efficiently produces small RNAs from long double-stranded (dsRNA) substrates. Expression of the Dicer(O) isoform is driven by an intronic MT-C retrotransposon promoter, deletion of which causes loss of Dicer(O) and female sterility. Oocytes from females lacking the MT-C element show meiotic spindle defects and increased levels of endogenous small interfering RNA (endo-siRNA) targets, phenocopying the maternal Dicer null phenotype. The alternative Dicer isoform, whose phylogenetic origin demonstrates evolutionary plasticity of RNA-silencing pathways, is the main determinant of endogenous RNAi activity in the mouse female germline.


Subject(s)
DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Oocytes/metabolism , RNA, Small Interfering/metabolism , Retroelements , Ribonuclease III/genetics , Ribonuclease III/metabolism , Animals , Base Sequence , DEAD-box RNA Helicases/chemistry , Female , Gene Expression , Infertility, Female , Mice , Molecular Sequence Data , Phylogeny , Promoter Regions, Genetic , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA, Small Interfering/chemistry , Ribonuclease III/chemistry
20.
Mol Cell Biol ; 33(16): 3242-58, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23775115

ABSTRACT

C/EBPß is an important regulator of oncogene-induced senescence (OIS). Here, we show that C/EBPγ, a heterodimeric partner of C/EBPß whose biological functions are not well understood, inhibits cellular senescence. Cebpg(-/-) mouse embryonic fibroblasts (MEFs) proliferated poorly, entered senescence prematurely, and expressed a proinflammatory gene signature, including elevated levels of senescence-associated secretory phenotype (SASP) genes whose induction by oncogenic stress requires C/EBPß. The senescence-suppressing activity of C/EBPγ required its ability to heterodimerize with C/EBPß. Covalently linked C/EBPß homodimers (ß∼ß) inhibited the proliferation and tumorigenicity of Ras(V12)-transformed NIH 3T3 cells, activated SASP gene expression, and recruited the CBP coactivator in a Ras-dependent manner, whereas Î³âˆ¼ß heterodimers lacked these capabilities and efficiently rescued proliferation of Cebpg(-/-) MEFs. C/EBPß depletion partially restored growth of C/EBPγ-deficient cells, indicating that the increased levels of C/EBPß homodimers in Cebpg(-/-) MEFs inhibit proliferation. The proliferative functions of C/EBPγ are not restricted to fibroblasts, as hematopoietic progenitors from Cebpg(-/-) bone marrow also displayed impaired growth. Furthermore, high CEBPG expression correlated with poorer clinical prognoses in several human cancers, and C/EBPγ depletion decreased proliferation and induced senescence in lung tumor cells. Our findings demonstrate that C/EBPγ neutralizes the cytostatic activity of C/EBPß through heterodimerization, which prevents senescence and suppresses basal transcription of SASP genes.


Subject(s)
CCAAT-Enhancer-Binding Protein-beta/metabolism , CCAAT-Enhancer-Binding Proteins/metabolism , Cellular Senescence , Gene Expression Regulation , Neoplasms/genetics , Animals , CCAAT-Enhancer-Binding Proteins/genetics , Cell Cycle , Cell Line , Cell Line, Tumor , Cell Proliferation , Cells, Cultured , Fibroblasts/cytology , Fibroblasts/metabolism , Gene Deletion , Gene Expression Regulation, Neoplastic , Hematopoiesis , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Humans , Inflammation/genetics , Inflammation/metabolism , Mice , Mice, Inbred C57BL , NIH 3T3 Cells , Neoplasms/metabolism , Protein Multimerization
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