Publications by authors named "Radek Malik"
Article Synopsis
- Adar null mutant mouse embryos experience death due to abnormal activation of the interferon response driven by double-stranded RNA (dsRNA), while eliminating this response in Adar Mavs double mutants leads to early postnatal death.
- In Adar Mavs mice, Protein kinase R (PKR) becomes mistakenly activated in the intestines, causing intestinal cell death and loss of villi, but adding an Eifak2 (Pkr) mutation restores these defects and enables survival.
- Research shows that ADAR1 directly interacts with PKR to inhibit its activity, and while ADAR1 binding to dsRNA is necessary for this inhibition, changes in specific binding regions disrupt ADAR1's ability to control PKR,
Article Synopsis
- Canonical RNA interference (RNAi) is a process where small interfering RNAs (siRNAs) guide the breakdown of specific mRNAs, playing roles in gene regulation and defense mechanisms.
- In mammals, RNAi is typically limited due to Dicer producing microRNAs instead, but a specific variant (ΔHEL1) allows for RNAi in mouse oocytes, and mutations to this variant can lead to severe developmental issues.
- Research on Dicer mice shows they can exhibit increased siRNA levels without significant changes to their microRNA profiles, suggesting the possibility of using these mice to study the overall impacts and potential of RNAi in living organisms.
Article Synopsis
- Gene evolution is complex, with simpler genes like lncRNAs emerging de novo from non-genic sequences; however, protein-coding genes usually have ties to ancestral sequences.* -
- The study focuses on the evolution of the D6Ertd527e gene in rodents, which likely started as an lncRNA due to a retrotransposon insertion, eventually acquiring protein-coding abilities in some species.* -
- Although the D6Ertd527e gene shows limited function in lab mice, its evolutionary journey in rodents over the past ~40 million years illustrates key processes in gene formation and evolution.*
Article Synopsis
- Dicer endonucleases produce small RNAs for microRNA (miRNA) and RNA interference (RNAi) pathways, playing a crucial role in gene regulation.
- The DExD/H helicase domain of Dicer is vital for high-fidelity miRNA biogenesis, with its complete absence being lethal and its ATPase function being dispensable.
- Structural studies show that the DExD/H domain helps lock Dicer in a closed state for miRNA precursor selection, while mutations can lead to reduced selectivity and activation of the RNAi pathway.
Article Synopsis
- PIWI-interacting RNAs (piRNAs) play a crucial role in suppressing retrotransposons in germline cells, traditionally viewed as more essential for male fertility than female fertility in mammals like mice.
- Research on golden hamsters reveals that the piRNA pathway functions differently across sexes, with female hamsters becoming sterile due to the loss of the Mov10l1 RNA helicase, which is vital for piRNA biogenesis.
- Male hamsters also show significant reproductive issues, including problems with spermatogonia development and a rise in retrotransposon expression, highlighting that the piRNA pathway is crucial for fertility in both sexes and adapts to manage genomic threats.
Article Synopsis
- RNA interference (RNAi) involves the targeted degradation of mRNA by small RNAs derived from long double-stranded RNA, primarily mediated by the enzyme Dicer.
- In mammals, RNAi is largely inactive, except in mouse oocytes, where a specific shortened version of Dicer is more efficient at processing dsRNA.
- The study explored CRISPR-based techniques to reactivate the Dicer gene in mouse embryonic stem cells, successfully restoring its expression but finding it insufficient for a strong RNAi response.
Article Synopsis
- * As oocytes grow, miRNAs do not accumulate at the same rate as mRNAs, leading to a significant dilution effect and lower overall concentrations of miRNAs in fully grown oocytes.
- * This low abundance of miRNAs is seen across various mammalian species, indicating that miRNA inactivity is a common trait in oocytes rather than being specific to mice.
Article Synopsis
- Tens of thousands of long non-coding RNA (lncRNA) genes exist, but only a few have established functions, especially in mouse oocytes where the role of lncRNAs like Sirena1 was previously unknown.
- Sirena1, the most expressed lncRNA in mouse oocytes, has evolved functions in RNA interference and is involved in regulating maternal mRNA through unique mechanisms, despite not affecting fertility directly.
- Knock-out studies show that while Sirena1 alters the maternal transcriptome and affects mitochondrial organization, it highlights the complex evolutionary role of lncRNAs which may not translate to significant laboratory impacts.
Article Synopsis
- The study investigates how the germline genome defends against retrotransposons, focusing on two small RNA pathways: the piRNA pathway and RNA interference (RNAi).
- Mice lacking the piRNA pathway are sterile males but fertile females, leading researchers to explore whether RNAi can compensate for this loss.
- The findings indicate that while the two pathways target different retrotransposon families, neither pathway alone is essential for ovarian development, and another mechanism likely prevents the mobilization of certain retrotransposons like LINE-1.
Main constraints for RNAi induced by expressed long dsRNA in mouse cells.
Life Sci Alliance
February 2019
Article Synopsis
- RNA interference (RNAi) involves the degradation of specific mRNA molecules guided by small interfering RNAs (siRNAs) created from long double-stranded RNA (dsRNA) by the enzyme Dicer.
- A study found that the main obstacle to effective RNAi in mammals is producing effective siRNAs, influenced by Dicer's activity and the structure of dsRNA.
- Unexpectedly, enhancing certain Dicer cofactors was shown to decrease RNAi efficiency, while the removal of the protein kinase R had little impact, indicating a complex interaction between RNAi and microRNA pathways in mammalian cells.
Article Synopsis
- The removal of the poly(A) tail from mRNA is a crucial process for regulating mRNA stability in eukaryotic cells, primarily carried out by the CCR4-NOT complex.
- In mammalian systems, the CCR4 component is essential for proper maternal function in mouse, hamster, and bovine oocytes, significantly affecting litter size and embryo development.
- Deletion of the CNOT6L gene in females leads to delays and issues in embryo development, indicating its vital role in the transition from oocyte to embryo, with distinct mRNA targeting by decapping and deadenylation processes.
Article Synopsis
- Researchers conducted a high-throughput screening (HTS) of 12,816 chemical compounds to identify potential miRNA inhibitors using human HeLa and mouse NIH 3T3 cell lines with luciferase reporters influenced by specific miRNAs.
- The study identified 163 potential miRNA inhibitors but noted that many identified compounds were non-specific and emphasized the need for effective negative controls and improved validation methods in future research on miRNA-targeted therapies.
Article Synopsis
- * A study found that LTRs from the ERVL retrotransposon class significantly influence gene expression during the oocyte-to-embryo transition in various species, including mice and humans, by activating transcription and altering gene sequences.
- * The research highlights that ERVL LTRs can recycle genetic material, such as pseudogenes into functional RNAs, and even contribute to the evolution of new genes, demonstrating their vast potential for reshaping genome expression and evolution.
Article Synopsis
- Fully grown mammalian oocytes rely on RNA transcripts made earlier in development for their functions, regulated by RNA localization and translation mechanisms.
- In mouse oocytes, three cap-dependent translational repressors (4E-BP1, 4E-BP2, and 4E-BP3) are produced at the mRNA level, but only 4E-BP1 is active as a protein, promoting translation after nuclear envelope breakdown through phosphorylation.
- Key regulators of 4E-BP1 phosphorylation during meiosis are mTOR and CDK1 kinases, with evidence suggesting that this regulatory pathway is also present and likely functions similarly in human oocytes.
Article Synopsis
- The initial stages of embryo development are regulated by parental influences, primarily through maternal proteins and transcripts present in the zygote.
- As the embryo grows, these parental factors are systematically cleared, allowing the embryo to take control over its own development and reprogram gene expression.
- The chapter highlights the mechanisms involved in this transition, such as the removal of maternal RNAs and proteins, modifications to the chromatin from both parents, and processes like yolk consumption and disposal of paternal mitochondria.
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.
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- - The study investigates how Aurora kinase A affects the phosphorylation of CPEB1, which is essential for regulating mRNA translation during the maturation of oocytes in mammals.
- - Researchers inhibited Aurora kinase A using a specific inhibitor, MLN8237, while observing porcine oocytes' meiotic maturation.
- - Results indicate that inhibiting Aurora kinase A does not impact the polyadenylation of cyclin B1 mRNA or its translation, suggesting this kinase is not crucial for CPEB1 activation.
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.
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- Double-stranded RNA (dsRNA) can influence gene expression in mammals through various mechanisms, but long hairpin dsRNA had minimal effects on mammalian somatic cells in this study.
- Despite having negligible processing into small interfering RNAs (siRNAs) and not activating the interferon response, dsRNA expression was observed to reduce reporter expression in co-transfection experiments.
- The study reveals that dsRNA from transiently transfected plasmids can strongly inhibit co-transfected reporter plasmids in a concentration-dependent manner, suggesting a need for caution when interpreting results from these types of experiments due to the involvement of protein kinase R in this inhibition.
Article Synopsis
- * Dicer(O) has a modified structure that enhances its ability to process long double-stranded RNAs into small RNAs, making it more effective than the standard Dicer found in somatic cells (Dicer(S)).
- * The expression of Dicer(O) is regulated by a specific retrotransposon promoter, and its absence leads to infertility in females, highlighting its importance in reproductive biology and the evolutionary adaptability of RNA-silencing mechanisms.
Article Synopsis
- C/EBPβ is crucial for promoting oncogene-induced senescence (OIS), while C/EBPγ, its partner, appears to inhibit senescence and support cell growth.
- Cebpg(-/-) mouse embryonic fibroblasts show poor proliferation and early senescence, largely due to high C/EBPβ homodimer levels, which can activate senescence-associated secretory phenotype (SASP) genes.
- The study reveals that C/EBPγ counters the effects of C/EBPβ by forming heterodimers with it, which helps to maintain cell proliferation and might have implications for cancer prognosis.
Article Synopsis
- RNA interference (RNAi) is a method used to specifically silence genes through the degradation of mRNA using double-stranded RNA (dsRNA), with long dsRNA commonly used in plants and invertebrates.
- In mammals, short RNA molecules are preferred to avoid an immune response triggered by long dsRNA, although mammalian oocytes can effectively use long dsRNA for RNAi without this response.
- The paper reviews the development of a vector for oocyte-specific expression of dsRNA, detailing the advantages and challenges faced by researchers utilizing this transgenic RNAi system in studying gene function in mouse oocytes.
Article Synopsis
- - Transient plasmid transfection is frequently used in mammalian cell studies, and researchers analyzed the transcriptional landscape of these plasmids using deep sequencing techniques.
- - The study revealed that entire plasmid sequences are transcribed at varying levels, and spurious transcription can negatively impact gene expression, particularly when multiple plasmids are co-transfected.
- - A specific case showed that a Kan/Neo resistance cassette led to the creation of small RNAs that influenced luciferase reporter expression, highlighting the need for careful experimental controls due to the complexities of plasmid expression.
Article Synopsis
- Double-stranded RNA (dsRNA) can initiate different cellular pathways in mammals, including RNA interference (RNAi) and the interferon response.
- In a study using transgenic mice, researchers found that the expression of dsRNA did not lead to developmental issues or an interferon response unless at very high levels.
- The results showed that while dsRNA poorly produced siRNAs in somatic cells, it effectively triggered RNAi in oocytes, suggesting that somatic cells lack the necessary factors for efficient siRNA production.
Article Synopsis
- * In transformed cells, a specific part of its mRNA (3'UTR) inhibits C/EBPβ's activation by Ras, affecting its ability to bind DNA and promote genes that foster cancer progression.
- * This inhibition and compartmentalization of Cebpb mRNA prevent C/EBPβ from being activated in immortalized cells, thus allowing cancer-promoting processes to take over, unlike in primary fibroblasts, where Ras can trigger its anti-cancer functions. *