Zhou X et al. (2021) J Cell Biol "The HSPG syndecan is a core organizer of cholinergic synapses."

Zhou X, VACHON C, Cizeron M, Romatif O, Bessereau JL, Bulow HE, Jospin M

[J Cell Biol, 2021]

The extracellular matrix has emerged as an active component of chemical synapses regulating synaptic formation, maintenance, and homeostasis. The heparan sulfate proteoglycan (HSPG) syndecans are known to regulate cellular and axonal migration in the brain. They are also enriched at synapses, but their synaptic functions remain more elusive. Here, we show that SDN-1, the sole orthologue of syndecan in C. elegans, is absolutely required for the synaptic clustering of homomeric 7-like acetylcholine receptors (AChRs) and regulates the synaptic content of heteromeric AChRs. SDN-1 is concentrated at neuromuscular junctions (NMJs) by the neurally secreted synaptic organizer Ce-Punctin/MADD-4, which also activates the transmembrane netrin receptor DCC. Those cooperatively recruit the FARP and CASK orthologues that localize 7-like-AChRs at cholinergic NMJs through physical interactions. Therefore, SDN-1 stands at the core of the cholinergic synapse organization by bridging the extracellular synaptic determinants to the intracellular synaptic scaffold that controls the postsynaptic receptor content.

Zhou X et al. (2019) Front Mol Neurosci "Molecular Architecture of Genetically-Tractable GABA Synapses in C. elegans."

Zhou X, Bessereau JL

[Front Mol Neurosci, 2019]

Inhibitory synapses represent a minority of the total chemical synapses in the mammalian brain, yet proper tuning of inhibition is fundamental to shape neuronal network properties. The neurotransmitter -aminobutyric acid (GABA) mediates rapid synaptic inhibition by the activation of the type A GABA receptor (GABA_AR), a pentameric chloride channel that governs major inhibitory neuronal transduction in the nervous system. Impaired GABA transmission leads to a variety of neuropsychiatric diseases, including schizophrenia, autism, epilepsy or anxiety. From an evolutionary perspective, GABA_AR shows remarkable conservations, and are found in all eukaryotic clades and even in bacteria and archaea. Specifically, <i>bona fide</i> GABA_ARs are found in the nematode <i>Caenorhabditis elegans</i>. Because of the anatomical simplicity of the nervous system and its amenability to genetic manipulations, <i>C. elegans</i> provide a powerful system to investigate the molecular and cellular biology of GABA synapses. In this mini review article, we will introduce the structure of the <i>C. elegans</i> GABAergic system and describe recent advances that have identified novel proteins controlling the localization of GABA_ARs at synapses. In particular, Ce-Punctin/MADD-4 is an evolutionarily-conserved extracellular matrix protein that behaves as an anterograde synaptic organizer to instruct the excitatory or inhibitory identity of postsynaptic domains.

Zhou X et al. (2007) PLoS Comput Biol "Characterization and identification of microRNA core promoters in four model species."

Zhang W, Ruan J, Zhou X, Wang G

[PLoS Comput Biol, 2007]

MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote), which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.

Zhou X et al. (2017) RNA Biol "A new layer of rRNA regulation by small interference RNAs and the nuclear RNAi pathway."

Wang Y, Zhou X, Feng X, Guang S, Chen X

[RNA Biol, 2017]

Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process remain poorly understood. For a long time, small ribosomal RNA sequences have been widely treated as non-specific degradation products and neglected as garbage sequences. Recently, we identified a new class of antisense ribosomal siRNAs (risiRNAs) that downregulate pre-rRNA through the nuclear RNAi pathway in C. elegans. risiRNAs exhibit sequence characteristics similar to 22G RNA while complement to 18S and 26S rRNA. risiRNAs elicit the translocation of the nuclear Argonaute protein NRDE-3 from the cytoplasm to nucleus and nucleolus, in which the risiRNA/NRDE complex binds to pre-rRNA and silences rRNA expression. Interestingly, when C. elegans is exposed to environmental stimuli, such as cold shock and ultraviolet illumination, risiRNAs accumulate and further turn on the nuclear RNAi-mediated gene silencing pathway. risiRNA may act in a quality control mechanism of rRNA homeostasis. When the exoribonuclease SUSI-1(ceDis3L2) is mutated, risiRNAs are dramatically increased. In this Point of View article, we will summarize our understanding of the small antisense ribosomal siRNAs in a variety of organisms, especially C. elegans, and their possible roles in the quality control mechanism of rRNA homeostasis.

Zhou X et al. (2014) Genetics "Nuclear RNAi contributes to the silencing of off-target genes and repetitive sequences in Caenorhabditis elegans."

Xu F, Meng Y, Feng X, Zhou X, Guang S, Ji J, Mao H

[Genetics, 2014]

Small RNAs recognize, bind, and regulate other complementary cellular RNAs. The introduction of small RNAs to eukaryotic cells frequently results in unintended silencing of related, but not identical, RNAs: a process termed off-target gene silencing. Off-target gene silencing is one of the major concerns during the application of small RNA-based technologies for gene discovery and the treatment of human disease. Off-target gene silencing is commonly thought to be due to inherent biochemical limitations of the RNAi machinery. Here we show that following the introduction of exogenous sources of double-stranded RNA, the nuclear RNAi pathway, but not its cytoplasmic counterparts, is the primary source of off-target silencing in Caenorhabditis elegans. In addition, we show that during the normal course of growth and development the nuclear RNAi pathway regulates repetitive gene families. Therefore, we speculate that RNAi off-target effects might not be &quot;mistakes&quot; but rather an intentional and genetically programmed aspect of small RNA-mediated gene silencing, which might allow small RNAs to silence rapidly evolving parasitic nucleic acids. Finally, reducing off-target effects by manipulating the nuclear RNAi pathway in vivo might improve the efficacy of small RNA-based technologies.

Zhou X et al. (2016) FEBS Lett "A novel bipartite UNC-101/AP-1 1 binding signal mediates KVS-4/Kv2.1 somatodendritic distribution in Caenorhabditis elegans."

Zeng J, Yang Z, Zhou X, Yu M, Shen K, Luo Q, Ouyang C, Shi A, Wang H

[FEBS Lett, 2016]

Potassium channels such as Kv2.1 are targeted to specific subcellular compartments to fulfill various functions. However, the mechanisms for their localization are poorly understood. Here, we show that KVS-4/Kv2.1 somatodendritic localization in Caenorhabditis elegansDA9 neuron requires UNC-101(AP-1 subunit). We define a bipartite sorting signal within KVS-4 consisting of a C-terminal EQMIL and N-terminal WNIIE motifs. The bipartite signal is sufficient to target nonpolarized transmembrane protein MIG-13 into DA9 somatodendritic compartments. Furthermore, we found that AP-1 interacts with the bipartite signal through UNC-101/AP-1 N-terminal predicted Longin-like domain. Our results provide new insight into the mechanisms of Kv2.1 post-Golgi sorting and targeting.

Zhou X et al. (2020) Nat Commun "The netrin receptor UNC-40/DCC assembles a postsynaptic scaffold and sets the synaptic content of GABAA receptors."

JI T, Pinan-Lucarre B, Valfort A, Bessereau JL, Jospin M, Gueydan M, Zhou X

[Nat Commun, 2020]

Increasing evidence indicates that guidance molecules used during development for cellular and axonal navigation also play roles in synapse maturation and homeostasis. In C. elegans the netrin receptor UNC-40/DCC controls the growth of dendritic-like muscle cell extensions towards motoneurons and is required to recruit type A GABA receptors (GABA_ARs) at inhibitory neuromuscular junctions. Here we show that activation of UNC-40 assembles an intracellular synaptic scaffold by physically interacting with FRM-3, a FERM protein orthologous to FARP1/2. FRM-3 then recruits LIN-2, the ortholog of CASK, that binds the synaptic adhesion molecule NLG-1/Neuroligin and physically connects GABA_ARs to prepositioned NLG-1 clusters. These processes are orchestrated by the synaptic organizer CePunctin/MADD-4, which controls the localization of GABA_ARs by positioning NLG-1/neuroligin at synapses and regulates the synaptic content of GABA_ARs through the UNC-40-dependent intracellular scaffold. Since DCC is detected at GABA synapses in mammals, DCC might also tune inhibitory neurotransmission in the mammalian brain.

Zhou X et al. (2017) Nat Struct Mol Biol "RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway."

Guang S, Zhou X, Mao H, Hu K, Feng X, Xu F, Li M

[Nat Struct Mol Biol, 2017]

Expression of rRNA affects cell growth and proliferation, but mechanisms that modulate rRNA levels are poorly understood. We conducted a genetic screen for factors that negatively regulate generation of endogenous short interfering RNA (endo-siRNA) in Caenorhabditis elegans and identified a suppressor of siRNA (susi-1) and antisense ribosomal siRNAs (risiRNAs). risiRNAs show sequence complementary to 18S and 26S rRNAs and require RNA-dependent RNA polymerases (RdRPs) for their production. They act through the nuclear RNA interference (RNAi) pathway to downregulate pre-rRNA. Stress stimuli, including low temperature and UV irradiation, induced the accumulation of risiRNAs. SUSI-1 is a homolog of the human DIS3L2 exonuclease involved in 3'-5' degradation of oligouridylated RNAs. In susi-1 mutant and in low temperature-treated animals, 3'-tail oligouridylated 26S rRNA accumulated. The injection of oligouridylated rRNA elicited nuclear accumulation of NRDE-3. Our findings identify a new subset of 22G-RNAs that regulate pre-rRNA expression and a mechanism to maintain rRNA homeostasis.

Zhou X et al. (2021) Comp Biochem Physiol C Toxicol Pharmacol "Bisphenol S promotes fat storage in multiple generations of Caenorhabditis elegans in a daf-16/nhr-49 dependent manner."

Li J, Zhang J, Bai J, Zhang C, Zhao Y, Zhou X, Xiao X, Zhu Y, Zhang X

[Comp Biochem Physiol C Toxicol Pharmacol, 2021]

Bisphenol S (BPS) has been gradually used in all kinds of productions. Our previous study has demonstrated that BPS increases the obesogenic effects of a high-glucose diet through regulating lipid metabolism in Caenorhabditis elegans (C. elegans). Whether the effects pass on to the next generations remains uncovered. In the present study, C. elegans was selected as the model organism to investigate the effects of BPS on lipid metabolism in multiple generations. Oil Red O staining and triglyceride assays showed that multi-generational exposure to BPS in C. elegans significantly increased the fat accumulation in wild type worms, while not in the daf-16 gene-deficient worms. In addition, BPS affected the expressions of fat-7 and acs-2 in four generations of C. elegans. Furthermore, BPS promotes fat storage in C. elegans of multiple generations by the daf-16/nhr-49-mediated signaling pathway.

Savini M et al. (2019) Cell "Does Autophagy Promote Longevity? It Depends."

Wang MC, Savini M

[Cell, 2019]

Zhou etal. challenge the well-known beneficial effect of autophagy in promoting longevity. Evidence presented demonstrate that autophagy induction coupled with increased mitochondrial permeability is detrimental to organismal health in both the nematode Caenorhabditis elegans and mammals.