Qi Dai

BMP signaling acts as an instructive cue in various developmental processes such as tissue patterning, stem cell proliferation, and differentiation. However, it is not fully understood how this signaling pathway generates different cell-specific outputs. Here, we have identified PRDM16 as a key co-factor for BMP signaling in the mouse brain. PRDM16 contributes to a repressive role of BMP signaling on neural stem cell (NSC) proliferation. We demonstrate that PRDM16 regulates the genomic distribution of BMP pathway transcription factors, the SMAD4/pSMAD complex, preventing the activation of cell proliferation genes. When Prdm16 is lost, the SMAD complex relocates to nearby genomic regions, leading to abnormal upregulation of BMP target genes. This function of PRDM16 is also required for the specification of choroid plexus (ChP) epithelial cells. Through a single-cell resolution fluorescent in situ approach, we have observed that genes co-repressed by SMAD and PRDM16, such as Wnt7b and several cell cycle regulators, become overexpressed in Prdm16 mutant ChP. Our findings elucidate a mechanism through which SMAD4 and pSMAD1/5/8 repress gene expression. Moreover, our study suggests a regulatory circuit composed of BMP and Wnt signaling, along with PRDM16, in controlling stem cell behaviors.

Epithelial tissue fusion requires coordinated molecular events at the ends of two epithelial structures. Regulatory mechanisms controlling these events remain largely elusive. In the Drosophila reproductive system (RS), this fusion unites the gonad and the genital disc-derived tissues, into a continuous tube. This study unveils the pivotal role of Hamlet (Ham), a Drosophila PR domain containing transcription factor, in orchestrating epithelial tissue fusion in the RS. Loss of ham leads to sterility and disconnection between the testes and seminal vesicles. Systematic analysis of Ham downstream genes reveals cytoskeletal, metabolic regulators and signaling pathway components. Ham activates genes for epithelial differentiation and remodeling, while repressing genes required for tissue growth and patterning. Using multiplexed in situ hybridization, we demonstrate spatial–temporal gene expression dynamics in contacting epithelia. Key Ham downstream effectors include E-Cadherin (E-Cad), Toll (Tl), and Wnt2 signaling pathways, regulating tissue interaction and fusion. Our findings present a comprehensive gene network crucial for heterotypic epithelial tissue fusion. Mammalian Ham orthologs PRDM3 and PRDM16 are highly expressed in epithelial tissues, suggesting a conserved role across species.

BMP signalling acts as an instructive cue in various developmental processes such as tissue patterning, stem cell proliferation, and differentiation. However, it is not fully understood how this signalling pathway generates different cell-specific outputs. Here we have identified PRDM16 as a key co-factor for BMP signalling. PRDM16 contributes to a repressive role of BMP signalling on neural stem cell (NSC) proliferation. We demonstrate that PRDM16 regulates the genomic distribution of BMP pathway transcription factors, the SMAD4/pSMAD complex, preventing the activation of cell proliferation genes. When Prdm16 is lost, the SMAD complex relocates to nearby genomic regions, leading to abnormal upregulation of BMP target genes. This function of PRDM16 is also required for the specification of choroid plexus (ChP) epithelial cells. Through a single-cell resolution fluorescent in situ approach, we have observed that genes co-repressed by SMAD and PRDM16, such as Wnt7b and several cell cycle regulators, become overexpressed in Prdm16 mutant ChP. Our findings elucidate a mechanism through which SMAD4 and pSMAD1/5/8 repress gene expression. Moreover, our study suggests a regulatory circuit composed of BMP and Wnt signaling, along with PRDM16, in controlling stem cell behaviors.

Epithelial tissue fusion requires coordinated molecular events at the ends of two epithelial structures. Regulatory mechanisms controlling these events remain largely elusive. In the Drosophila reproductive system (RS), this fusion unites the gonad and the genital disc-derived tissues, into a continuous tube. This study unveils the pivotal role of Hamlet (Ham), a Drosophila PR-domain containing transcription factor, in orchestrating epithelial tissue fusion in the RS. Loss of ham leads to sterility and disconnection between the testes (TE) and seminal vesicles (SV). Systematic analysis of Ham-downstream genes reveals cytoskeletal, metabolic regulators and signaling pathway components. Ham activates genes for epithelial differentiation and remodeling, while repressing genes required for tissue growth and patterning. Using multiplexed in situ hybridization, we demonstrate spatial-temporal gene expression dynamics in contacting epithelia. Key Ham downstream effectors include E-Cadherin (E-Cad), Toll (Tl) and Wnt2 signaling pathways, regulating tissue interaction and fusion. Our findings present a comprehensive gene network crucial for heterotypic epithelial tissue fusion. Mammalian Ham orthologs PRDM3 and PRDM16 are highly expressed in epithelial tissues, suggesting a conserved role across species.

Tunable and reversible regulation of exogenous and endogenous gene expression would be useful for improving the safety and efficacy of gene therapy. Current chemically inducible systems are limited by the rapid diffusion and extended metabolism of small molecules, and associated side effects. Here we develop a photoactivatable RNA adenosine base editor (PA-rABE) by harnessing a compact Cas13 variant and a split ADAR2 deaminase fused with the Magnets system, which is activated through blue-light-induced dimerization. PA-rABE achieves highly efficient editing on endogenous RNA with minimal bystander editing and off-target effects. By editing a phosphorylation site of the endogenous CTNNB1 gene, PA-rABE stabilizes the β-catenin protein and activates Wnt signaling in vivo. Using adeno-associated virus vectors to deliver PA-rABE along with an hF9 variant containing a premature termination codon, we show amelioration of clotting defects in hemophilia B mice upon illumination. In summary, PA-rABE offers a controlled RNA base-editing technology for diverse biomedical applications, enabling reversible and spatiotemporally specific modulation.

Epithelial tissue fusion requires coordinated molecular events at the ends of two epithelial structures. Regulatory mechanisms controlling these events remain largely elusive. In the Drosophila reproductive system (RS), this fusion unites the gonad and the genital disc-derived tissues, into a continuous tube. This study unveils the pivotal role of Hamlet (Ham), a Drosophila PR-domain containing transcription factor, in orchestrating epithelial tissue fusion in the RS. Loss of ham leads to sterility and disconnection between the testes (TE) and seminal vesicles (SV). Systematic analysis of Ham-downstream genes reveals cytoskeletal, metabolic regulators and signaling pathway components. Ham activates genes for epithelial differentiation and remodeling, while repressing genes required for tissue growth and patterning. Using multiplexed in situ hybridization, we demonstrate spatial-temporal gene expression dynamics in contacting epithelia. Key Ham downstream effectors include E-Cadherin (E-Cad), Toll (Tl) and Wnt2 signaling pathways, regulating tissue interaction and fusion. Our findings present a comprehensive gene network crucial for heterotypic epithelial tissue fusion. Mammalian Ham orthologs PRDM3 and PRDM16 are highly expressed in epithelial tissues, suggesting a conserved role across species.

An unexpected interaction between a long non-coding RNA locus and a genetic insulator called Fub-1 has an important role in gene regulation during development in Drosophila.

BMP signalling acts as an instructive cue in various developmental processes such as tissue patterning, stem cell proliferation, and differentiation. However, it is not fully understood how this signalling pathway generates different cell-specific outputs. Here we have identified PRDM16 as a key co-factor for BMP signalling. PRDM16 contributes to a repressive role of BMP signalling on neural stem cell (NSC) proliferation. We demonstrate that PRDM16 regulates the genomic distribution of BMP pathway transcription factors, the SMAD4/pSMAD complex, preventing the activation of cell proliferation genes. When Prdm16 is lost, the SMAD complex relocates to nearby genomic regions, leading to abnormal upregulation of BMP target genes. This function of PRDM16 is also required for the specification of choroid plexus (ChP) epithelial cells. Through a single-cell resolution fluorescent in situ approach, we have observed that genes co-repressed by SMAD and PRDM16, such as Wnt7b and several cell cycle regulators, become overexpressed in Prdm16 mutant ChP. Our findings elucidate a mechanism through which SMAD4 and pSMAD1/5/8 repress gene expression. Moreover, our study suggests a regulatory circuit composed of BMP and Wnt signaling, along with PRDM16, in controlling stem cell behaviors.

The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known forDrosophilafactors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. We conducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.

Radial glia (RG) in the neocortex sequentially generate distinct subtypes of projection neurons, accounting for the diversity and complex assembly of cortical neural circuits. Mechanisms that drive the rapid and precise temporal progression of RG are beginning to be elucidated. Here, we reveal that the RG-specific transcriptional regulator PRDM16 promotes the transition of early to late phase of neurogenesis in the mouse neocortex. Loss of Prdm16 delays the timely progression of RG, leading to defective cortical laminar organization. Our genomic analyses demonstrate that PRDM16 regulates a subset of genes that are dynamically expressed between early and late neurogenesis. We show that PRDM16 suppresses target gene expression through limiting chromatin accessibility of permissive enhancers. We further confirm that crucial target genes regulated by PRDM16 are neuronal specification genes, cell cycle regulators and molecules required for neuronal migration. These findings provide evidence to support the finding that neural progenitors temporally shift the gene expression program to achieve neural cell diversity.