Biology subjects

Ni, J. Z.

Publications and source records attributed to Ni, J. Z..

8 recordsLinked to original sources

bioRxiv2026

The nuclear Argonaute HRDE-1 broadly interacts with euchromatin via an RGG domain to enable transgenerational epigenetic silencing

Small RNA(sRNA)-guided transcriptional repression, a process termed as nuclear RNAi, safeguards genome integrity and germline development. Central to this pathway are the highly conserved Argonaute (AGO) proteins, which are guided by sRNAs to mediate transcriptional silencing and heterochromatin formation at the target locus. The mechanism of how nuclear AGO proteins engage chromatin remains poorly understood. By studying C. elegans nuclear AGO HRDE-1, we found that an intrinsically disordered arginine-glycine-glycine (RGG) domain in HRDE-1 is essential for siRNA-guided transgenerational epigenetic silencing and germline immortality. The function of RGG occurs in the downstream of siRNA loading and nuclear localization. Mutant HRDE-1 that lacks the RGG domain is defective in binding to the chromatin of the siRNA targets. Strikingly, ChIP-seq analysis reveals that HRDE-1 interacts with hundreds of highly transcribed euchromatic protein-coding genes in the germ cells, which is unexpected for an epigenetic silencing protein. The HRDE-1-euchromatin interaction is not mediated by siRNAs but requires the RGG domain. The interaction appears to be necessary but not sufficient to cause gene silencing. We propose that the initial siRNA-independent, RGG-dependent HRDE-1-chromatin interaction enables HRDE-1 to enter the transcribing chromatin compartment, a likely prerequisite for the subsequent siRNA-pre-mRNA interaction. Given the prevalence of the RGG domain in eukaryotic proteins, we constructed chimera HRDE-1 proteins and found that RGGs from other proteins, including human hnRNP U, can substitute for the HRDE-1 RGG to restore chromatin binding and transgenerational silencing. Our findings suggest an evolutionarily conserved role for RGG-rich intrinsically disordered regions in coupling AGOs and other RNA-binding proteins to active chromatin as a mechanism to target nascent pre-mRNA.

molecular biology↗

bioRxiv2025

Hypoxia-induced metastatic heterogeneity in pancreatic cancer

In most solid tumors, hypoxia constitutes a defining microenvironmental feature that reprograms malignant cells into a highly metastatic state by driving cellular plasticity and exacerbating chromosomal instability (CIN). However, the mechanisms by which cancer cells concurrently co-opt these elements of hypoxic adaptation to promote metastasis remains poorly understood. Here, we report that hypoxia promotes metastasis by suppressing the JmjC-containing histone lysine demethylase Kdm8. CRISPR/Cas9-mediated targeting of Kdm8 in a Kras;Trp53-driven mouse model of pancreatic ductal adenocarcinoma (PDA) robustly rewires the malignant cell transcriptomic programs, leading to a profound loss of the epithelial morphology and widespread metastatic disease. In PDA patients, a high KDM8-induced gene signature is associated with reduced metastatic burden and better survival in advanced disease. Notably, Kdm8 suppression in normoxia recapitulates key aspects of the global epigenetic and transcriptomic rewiring, mitotic spindle defects, and CIN induced by hypoxia. Moreover, disruption of Kdm8s demethylase activity phenocopies Kdm8 loss, whereas expression of hypermorphic Kdm8 variants resistant to hypoxic suppression markedly reduces metastasis beyond the levels achieved by the wildtype protein. Through the suppression of Kdm8 demethylase function, hypoxia unleashes a potent metastatic program by simultaneously advancing cellular plasticity and CIN.

cell biology↗

bioRxiv2025

CHD7 binds distinct regions in the Sox11 locus to regulate neuronal differentiation

The chromodomain helicase DNA binding protein 7 (CHD7) is a nucleosome repositioner implicated in multiple cellular processes, including neuronal differentiation. We identified CHD7 genome-wide binding sites that regulate neuronal differentiation in an otic stem cell line. We identified CHD7 enrichment at the Sox11 promoter and 3 untranslated region (UTR). Sox11 is a transcription factor essential for neuronal differentiation. CRISPRi of Sox11 promoter or 3UTR displayed decreased neurite lengths and reduced neuronal marker expression TUBB3 expression. We showed that the Sox11 locus resides at TAD boundaries, and CTCF marks the 3UTR. We propose that CHD7 modulates chromatin accessibility of the Sox11 promoter and CTCF-marked insulators in the 3UTR to facilitate neuronal differentiation. CRISPRi of the insulator site alters 3D chromatin organization, affects gene expression and ultimately perturbs cellular processes. Our results implicate a general mechanism of CHD7 in facilitating neuronal differentiation and provide insight into CHD7 dysfunction in CHARGE syndrome, a congenital disorder associated with hearing loss.

molecular biology↗

bioRxiv2025

CHD7 binds to insulators during neuronal differentiation

Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in neuronal differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrated that CHD7 knockdown impaired neuronal differentiation. Genome-wide analysis revealed CHD7 binding at diverse cis-regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including Mir9-2. Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR-9 transcription, irrespective of the method. Blocking the CHD7 and CTCF marked sites suggested that the elements function as insulators to regulate gene expression. The study highlights CHD7 activity at insulators and underscores an unreported mechanism for promoting neuronal differentiation.

molecular biology↗

bioRxiv2024

Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance in Caenorhabditis elegans

Nuclear RNAi in C. elegans induces a set of transgenerationally heritable marks of H3K9me3, H3K23me3, and H3K27me3 at the target genes. The function of H3K23me3 in the nuclear RNAi pathway is largely unknown due to the limited knowledge of H3K23 histone methyltransferase (HMT). In this study we identified SET-21 as a novel H3K23 HMT. By taking combined genetic, biochemical, imaging, and genomic approaches, we found that SET-21 functions synergistically with a previously reported H3K23 HMT SET-32 to deposit H3K23me3 at the native targets of germline nuclear RNAi. We identified a subset of native nuclear RNAi targets that are transcriptionally activated in the set-21;set-32 double mutant. SET-21 and SET-32 are also required for robust transgenerational gene silencing induced by exogenous dsRNA. The set-21;set-32 double mutant strain exhibits an enhanced temperature-sensitive mortal germline phenotype compared to the set-32 single mutant, while the set-21 single mutant animals are fertile. We also found that HRDE-1 and SET-32 are required for cosuppression, a transgene-induced gene silencing phenomenon, in C. elegans germline. Together, these results support a model in which H3K23 HMTs SET-21 and SET-32 function cooperatively to ensure the robustness of germline nuclear RNAi and promotes the germline immortality under the heat stress.

molecular biology↗

bioRxiv2024

Chromatin remodeling protein CHD4 regulates axon guidance of spiral ganglion neurons in developing cochlea

Spiral ganglion neurons (SGNs) are the primary afferent neurons that convey auditory information from the cochlea to the central nervous system. Pathogenic variants of human chromodomain helicase DNA-binding protein 4 (CHD4) cause Sifrim-Hitz-Weiss (SIHIWES) syndrome, a neurodevelopmental disorder associated with hearing loss. Here, we identified expression of CHD4, an ATP-dependent chromatin remodeler, in developing SGNs and proceeded to delete Chd4 in mice. Auditory brainstem recordings showed that animals lacking Chd4 in SGNs exhibit hearing loss. SGNs are classified as type I and type II neurons, which display distinct peripheral innervation patterns. Notably, loss of CHD4 resulted in abnormal fasciculation of type I neurons and improper pathfinding of type II fibers. To uncover the underlying molecular mechanisms, we mapped genome-wide CHD4 chromatin occupancy in immortalized multipotent otic progenitor (iMOP)-derived neurons. Gene ontology analysis of CHD4 target genes revealed pathways governing axon guidance, axonal fasciculation, and ephrin receptor signaling. In vivo, we observed upregulation of specific Eph/ephrin genes in SGNs from Chd4-conditional knockout cochleae. Together, these results demonstrate that CHD4 modulates chromatin at cis-regulatory elements to repress a subset of axon guidance molecules during development. The coordinated regulation of multiple guidance cues is essential for establishing precise neural circuitry in the cochlea. Our findings reveal a critical role for CHD4-dependent epigenetic regulation in neural circuit wiring and offer a translational framework for strategies to regenerate SGNs.

neuroscience↗

bioRxiv2018

Developmentally regulated transcription and silencing cycle of nuclear RNAi-targeted LTR retrotransposons in Caenorhabditis elegans

Small RNA-guided chromatin silencing, also referred to as nuclear RNAi, plays an essential role in genome surveillance in eukaryotes and provides a unique paradigm to explore the complexity in RNA-mediated chromatin regulation and transgenerational epigenetics. A well-recognized paradox in this research area is that transcription of the target loci is necessary for the initiation and maintenance of the silencing at the same loci. How the two opposing activities (transcriptional activation and repression) are coordinated during animal development is poorly understood. To resolve this gap, we took single-molecule RNA imaging, deep-sequencing, and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two exemplary endogenous germline nuclear RNAi targets in C. elegans, Cer3 and Cer8 LTR retrotransposons. By examining the wild type and a collection of mutant strains, we found that transcription and silencing cycle of Cer3 and Cer8 is tightly coupled with the early embryogenesis and germline mitotic and meiotic cell cycles. Strikingly, Cer3 and Cer8 transcripts are exclusively localized in the nuclei of germ cells in both wild type and germline nuclear RNAi-defective mutant animals. RNA-sequencing analysis found that this nuclear enrichment feature is a general feature for the endogenous targets of the germline nuclear RNAi pathway. In addition, the germline and somatic repressions of Cer3 have different genetic requirement for the three H3K9 histone methyltransferases, MET-2, SET-25, and SET-32, in conjunction with the nuclear Argonaute protein WAGO-9/HRDE-1. These results provide a first comprehensive cellular and developmental characterization of the nuclear RNAi-targeted endogenous targets throughout animal reproductive cycle. Altogether, these results support a model in which (1) both the transcriptional activation and repression steps of the germline nuclear RNAi pathway are tightly coupled with animal development, (2) the endogenous targets exhibit a hallmark of nuclear enrichment of their transcripts, and (3) different heterochromatin enzymes play distinct roles in somatic and germline silencing of the endogenous targets.

developmental biology↗

bioRxiv2017

spe-43 is required for sperm activation in C. elegans

Successful fertilization requires that sperm are activated prior to contacting an oocyte. In C. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization of spe-43, a new component of the spe-8 pathway, which is required for spermiogenesis in hermaphrodites; spe-43 hermaphrodites are self-sterile, while spe-43 males show wild-type fertility. When exposed to Pronase to activate sperm in vitro, spe-43 spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed. Using a combination of recombinant and deletion mapping and whole genome sequencing, we identified F09E8.1 as spe-43. SPE-43 is predicted to exist in two isoforms; one isoform appears to be a single-pass transmembrane protein while the other is predicted to be a secreted protein. SPE-43 can bind to other known sperm proteins, including SPE-4 and SPE-29, which are known to impact spermiogenesis. In summary, we have identified a membrane protein that is present in C. elegans sperm and is required for sperm activation via the hermaphrodite activation signal.

developmental biology↗