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PRC2 promotes canalisation during endodermal differentiation.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-30 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011584
Jurriaan Jochem Hölzenspies, Dipta Sengupta, Wendy Anne Bickmore, Joshua Mark Brickman, Robert Scott Illingworth

The genetic circuitry that encodes the developmental programme of mammals is regulated by transcription factors and chromatin modifiers. During early gestation, the three embryonic germ layers are established in a process termed gastrulation. The impact of deleterious mutations in chromatin modifiers such as the polycomb proteins manifests during gastrulation, leading to early developmental failure and lethality in mouse models. Embryonic stem cells have provided key insights into the molecular function of polycomb proteins, but it is impossible to fully appreciate the role of these epigenetic factors in development, or how development is perturbed due to their deficiency, in the steady-state. To address this, we have employed a tractable embryonic stem cell differentiation system to model primitive streak formation and early gastrulation. Using this approach, we find that loss of the repressive polycomb mark H3K27me3 is delayed relative to transcriptional activation, indicating a subordinate rather than instructive role in gene repression. Despite this, chemical inhibition of polycomb enhanced endodermal differentiation efficiency, but did so at the cost of lineage fidelity. These findings highlight the importance of the polycomb system in stabilising the developmental transcriptional response and, in so doing, in shoring up cellular specification.

{"title":"PRC2 promotes canalisation during endodermal differentiation.","authors":"Jurriaan Jochem Hölzenspies, Dipta Sengupta, Wendy Anne Bickmore, Joshua Mark Brickman, Robert Scott Illingworth","doi":"10.1371/journal.pgen.1011584","DOIUrl":"10.1371/journal.pgen.1011584","url":null,"abstract":"<p><p>The genetic circuitry that encodes the developmental programme of mammals is regulated by transcription factors and chromatin modifiers. During early gestation, the three embryonic germ layers are established in a process termed gastrulation. The impact of deleterious mutations in chromatin modifiers such as the polycomb proteins manifests during gastrulation, leading to early developmental failure and lethality in mouse models. Embryonic stem cells have provided key insights into the molecular function of polycomb proteins, but it is impossible to fully appreciate the role of these epigenetic factors in development, or how development is perturbed due to their deficiency, in the steady-state. To address this, we have employed a tractable embryonic stem cell differentiation system to model primitive streak formation and early gastrulation. Using this approach, we find that loss of the repressive polycomb mark H3K27me3 is delayed relative to transcriptional activation, indicating a subordinate rather than instructive role in gene repression. Despite this, chemical inhibition of polycomb enhanced endodermal differentiation efficiency, but did so at the cost of lineage fidelity. These findings highlight the importance of the polycomb system in stabilising the developmental transcriptional response and, in so doing, in shoring up cellular specification.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011584"},"PeriodicalIF":4.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11813121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sox2 interacts with Atoh1 and Huwe1 loci to regulate Atoh1 transcription and stability during hair cell differentiation. Sox2 与 Atoh1 和 Huwe1 Loci 相互作用,在毛细胞分化过程中调节 Atoh1 的转录和稳定性。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-30 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011573
Yen-Fu Cheng, Judith S Kempfle, Hao Chiang, Kohsuke Tani, Quan Wang, Sheng-Hong Chen, Danielle Lenz, Wei-Yi Chen, Wenjin Wu, Marco Petrillo, Albert S B Edge

Stem cell pluripotency gene Sox2 stimulates expression of proneural basic-helix-loop-helix transcription factor Atoh1. Sox2 is necessary for the development of cochlear hair cells and binds to the Atoh1 3' enhancer to stimulate Atoh1 expression. We show here that Sox2 deletion in late embryogenesis results in the formation of extra hair cells, in contrast to the absence of hair cell development obtained after Sox2 knockout early in gestation. Sox2 overexpression decreased the level of Atoh1 protein despite an increase in Atoh1 mRNA. Sox2 upregulated E3 ubiquitin ligase, Huwe1, by direct binding to the Huwe1 gene. By upregulating its cognate E3 ligase, Sox2 disrupts the positive feedback loop through which Atoh1 protein increases the expression of Atoh1. We conclude that Sox2 initiates expression, while also limiting continued activity of bHLH transcription factor, Atoh1, and this inhibition represents a new mechanism for regulating the activity of this powerful initiator of hair cell development.

{"title":"Sox2 interacts with Atoh1 and Huwe1 loci to regulate Atoh1 transcription and stability during hair cell differentiation.","authors":"Yen-Fu Cheng, Judith S Kempfle, Hao Chiang, Kohsuke Tani, Quan Wang, Sheng-Hong Chen, Danielle Lenz, Wei-Yi Chen, Wenjin Wu, Marco Petrillo, Albert S B Edge","doi":"10.1371/journal.pgen.1011573","DOIUrl":"10.1371/journal.pgen.1011573","url":null,"abstract":"<p><p>Stem cell pluripotency gene Sox2 stimulates expression of proneural basic-helix-loop-helix transcription factor Atoh1. Sox2 is necessary for the development of cochlear hair cells and binds to the Atoh1 3' enhancer to stimulate Atoh1 expression. We show here that Sox2 deletion in late embryogenesis results in the formation of extra hair cells, in contrast to the absence of hair cell development obtained after Sox2 knockout early in gestation. Sox2 overexpression decreased the level of Atoh1 protein despite an increase in Atoh1 mRNA. Sox2 upregulated E3 ubiquitin ligase, Huwe1, by direct binding to the Huwe1 gene. By upregulating its cognate E3 ligase, Sox2 disrupts the positive feedback loop through which Atoh1 protein increases the expression of Atoh1. We conclude that Sox2 initiates expression, while also limiting continued activity of bHLH transcription factor, Atoh1, and this inhibition represents a new mechanism for regulating the activity of this powerful initiator of hair cell development.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011573"},"PeriodicalIF":4.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11813075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Distinct checkpoint and homolog biorientation pathways regulate meiosis I in Drosophila oocytes.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-29 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011400
Joanatta G Shapiro, Neha Changela, Janet K Jang, Jay N Joshi, Kim S McKim

Mitosis and meiosis have two mechanisms for regulating the accuracy of chromosome segregation: error correction and the spindle assembly checkpoint (SAC). We have investigated the function of several checkpoint proteins in meiosis I of Drosophila oocytes. Increased localization of several SAC proteins was found upon depolymerization of microtubules by colchicine. However, unattached kinetochores or errors in biorientation of homologous chromosomes do not induce increased SAC protein localization. Furthermore, the metaphase I arrest does not depend on SAC genes, suggesting the APC is inhibited even if the SAC is not functional. Two SAC proteins, ROD of the ROD-ZW10-Zwilch (RZZ) complex and MPS1, are also required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Both proteins aid in preventing or correcting erroneous attachments and depend on SPC105R for localization to the kinetochore. We have defined a region of SPC105R, amino acids 123-473, that is required for ROD localization and biorientation of homologous chromosomes at meiosis I. Surprisingly, ROD removal from kinetochores and movement towards spindle poles, termed "streaming," is independent of the dynein adaptor Spindly and is not linked to the stabilization of end-on attachments. Instead, meiotic RZZ streaming appears to depend on cell cycle stage and may be regulated independently of kinetochore attachment or biorientation status. We also show that Spindly is required for biorientation at meiosis I, and surprisingly, the direction of RZZ streaming.

{"title":"Distinct checkpoint and homolog biorientation pathways regulate meiosis I in Drosophila oocytes.","authors":"Joanatta G Shapiro, Neha Changela, Janet K Jang, Jay N Joshi, Kim S McKim","doi":"10.1371/journal.pgen.1011400","DOIUrl":"10.1371/journal.pgen.1011400","url":null,"abstract":"<p><p>Mitosis and meiosis have two mechanisms for regulating the accuracy of chromosome segregation: error correction and the spindle assembly checkpoint (SAC). We have investigated the function of several checkpoint proteins in meiosis I of Drosophila oocytes. Increased localization of several SAC proteins was found upon depolymerization of microtubules by colchicine. However, unattached kinetochores or errors in biorientation of homologous chromosomes do not induce increased SAC protein localization. Furthermore, the metaphase I arrest does not depend on SAC genes, suggesting the APC is inhibited even if the SAC is not functional. Two SAC proteins, ROD of the ROD-ZW10-Zwilch (RZZ) complex and MPS1, are also required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Both proteins aid in preventing or correcting erroneous attachments and depend on SPC105R for localization to the kinetochore. We have defined a region of SPC105R, amino acids 123-473, that is required for ROD localization and biorientation of homologous chromosomes at meiosis I. Surprisingly, ROD removal from kinetochores and movement towards spindle poles, termed \"streaming,\" is independent of the dynein adaptor Spindly and is not linked to the stabilization of end-on attachments. Instead, meiotic RZZ streaming appears to depend on cell cycle stage and may be regulated independently of kinetochore attachment or biorientation status. We also show that Spindly is required for biorientation at meiosis I, and surprisingly, the direction of RZZ streaming.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011400"},"PeriodicalIF":4.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11809923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Coordinated neuron-glia regeneration through Notch signaling in planarians.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-27 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011577
M Lucila Scimone, Bryanna Isela-Inez Canales, Patrick Aoude, Kutay D Atabay, Peter W Reddien

Some animals can regenerate large missing regions of their nervous system, requiring mechanisms to restore the pattern, numbers, and wiring of diverse neuron classes. Because injuries are unpredictable, regeneration must be accomplished from an unlimited number of starting points. Coordinated regeneration of neuron-glia architecture is thus a major challenge and remains poorly understood. In planarians, neurons and glia are regenerated from distinct progenitors. We found that planarians first regenerate neurons expressing a Delta-encoding gene, delta-2, at key positions in the central and peripheral nervous systems. Planarian glia are specified later from dispersed Notch-1-expressing mesoderm-like phagocytic progenitors. Inhibition of delta-2 or notch-1 severely reduced glia in planarians, but did not affect the specification of other phagocytic cell types. Loss of several delta-2-expressing neuron classes prevented differentiation of the glia associated with them, whereas transplantation of delta-2-expressing photoreceptor neurons was sufficient for glia formation at an ectopic location. Our results suggest a model in which patterned delta-2-expressing neurons instruct phagocytic progenitors to locally differentiate into glia, presenting a mechanism for coordinated regeneration of numbers and pattern of cell types.

{"title":"Coordinated neuron-glia regeneration through Notch signaling in planarians.","authors":"M Lucila Scimone, Bryanna Isela-Inez Canales, Patrick Aoude, Kutay D Atabay, Peter W Reddien","doi":"10.1371/journal.pgen.1011577","DOIUrl":"10.1371/journal.pgen.1011577","url":null,"abstract":"<p><p>Some animals can regenerate large missing regions of their nervous system, requiring mechanisms to restore the pattern, numbers, and wiring of diverse neuron classes. Because injuries are unpredictable, regeneration must be accomplished from an unlimited number of starting points. Coordinated regeneration of neuron-glia architecture is thus a major challenge and remains poorly understood. In planarians, neurons and glia are regenerated from distinct progenitors. We found that planarians first regenerate neurons expressing a Delta-encoding gene, delta-2, at key positions in the central and peripheral nervous systems. Planarian glia are specified later from dispersed Notch-1-expressing mesoderm-like phagocytic progenitors. Inhibition of delta-2 or notch-1 severely reduced glia in planarians, but did not affect the specification of other phagocytic cell types. Loss of several delta-2-expressing neuron classes prevented differentiation of the glia associated with them, whereas transplantation of delta-2-expressing photoreceptor neurons was sufficient for glia formation at an ectopic location. Our results suggest a model in which patterned delta-2-expressing neurons instruct phagocytic progenitors to locally differentiate into glia, presenting a mechanism for coordinated regeneration of numbers and pattern of cell types.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011577"},"PeriodicalIF":4.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Minimization of the Bacillus subtilis divisome suggests FtsZ and SepF can form an active Z-ring, and reveals the amino acid transporter BraB as a new cell division influencing factor.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-27 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011567
Ilkay Celik Gulsoy, Terrens N V Saaki, Michaela Wenzel, Simon Syvertsson, Taku Morimoto, Tjalling K Siersma, Leendert W Hamoen

Bacterial cytokinesis begins with polymerization of the tubulin homologue FtsZ into a ring-like structure at midcell, the Z-ring, which recruits the late cell division proteins that synthesize the division septum. Assembly of FtsZ is carefully regulated and supported by a dozen conserved cell division proteins. Generally, these proteins are not essential, but removing more than one is in many cases lethal. Therefore, it is still not fully clear how the different protein components contribute to cell division, and whether there is a minimal set of proteins that can execute cell division. In this study, we tried to find the minimal set of proteins that is required to establish an active Z-ring in the model bacterium Bacillus subtilis. By making use of known suppressor mutations we were able to find a gene deletion route that eventually enabled us the remove eight conserved cell division proteins: ZapA, MinC, MinJ, UgtP, ClpX, Noc, EzrA and FtsA. Only FtsZ and its membrane anchor SepF appeared to be required for Z-ring formation. Interestingly, SepF is also the FtsZ anchor in archaea, and both proteins date back to the Last Universal Common Ancestor (LUCA). Viability of the multiple deletion mutant was not greatly affected, although the frequency of cell division was considerably reduced. Whole genome sequencing suggested that the construction of this minimal divisome strain was also possible due to the accumulation of suppressor mutations. After extensive phenotypic testing of these mutations, we found an unexpected cell division regulation function for the branched chain amino acid transporter BraB, which may be related to a change in fatty acid composition. The implications of these findings for the role of SepF, and the construction of a minimal cell division machinery are discussed.

{"title":"Minimization of the Bacillus subtilis divisome suggests FtsZ and SepF can form an active Z-ring, and reveals the amino acid transporter BraB as a new cell division influencing factor.","authors":"Ilkay Celik Gulsoy, Terrens N V Saaki, Michaela Wenzel, Simon Syvertsson, Taku Morimoto, Tjalling K Siersma, Leendert W Hamoen","doi":"10.1371/journal.pgen.1011567","DOIUrl":"10.1371/journal.pgen.1011567","url":null,"abstract":"<p><p>Bacterial cytokinesis begins with polymerization of the tubulin homologue FtsZ into a ring-like structure at midcell, the Z-ring, which recruits the late cell division proteins that synthesize the division septum. Assembly of FtsZ is carefully regulated and supported by a dozen conserved cell division proteins. Generally, these proteins are not essential, but removing more than one is in many cases lethal. Therefore, it is still not fully clear how the different protein components contribute to cell division, and whether there is a minimal set of proteins that can execute cell division. In this study, we tried to find the minimal set of proteins that is required to establish an active Z-ring in the model bacterium Bacillus subtilis. By making use of known suppressor mutations we were able to find a gene deletion route that eventually enabled us the remove eight conserved cell division proteins: ZapA, MinC, MinJ, UgtP, ClpX, Noc, EzrA and FtsA. Only FtsZ and its membrane anchor SepF appeared to be required for Z-ring formation. Interestingly, SepF is also the FtsZ anchor in archaea, and both proteins date back to the Last Universal Common Ancestor (LUCA). Viability of the multiple deletion mutant was not greatly affected, although the frequency of cell division was considerably reduced. Whole genome sequencing suggested that the construction of this minimal divisome strain was also possible due to the accumulation of suppressor mutations. After extensive phenotypic testing of these mutations, we found an unexpected cell division regulation function for the branched chain amino acid transporter BraB, which may be related to a change in fatty acid composition. The implications of these findings for the role of SepF, and the construction of a minimal cell division machinery are discussed.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011567"},"PeriodicalIF":4.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11790237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A mitochondria-to-nucleus regulation mediated by the nuclear-translocated mitochondrial lncRNAs.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-27 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011580
Jia Li, Ruoling Bai, Yulian Zhou, Xu Song, Ling Li

A bidirectional nucleus-mitochondria communication is essential for homeostasis and stress. By acting as critical molecules, the nuclear-encoded lncRNAs (nulncRNAs) have been implicated in the nucleus-to-mitochondria anterograde regulation. However, role of mitochondrial-derived lncRNAs (mtlncRNAs) in the mitochondria-to-nucleus retrograde regulation remains elusive. Here, we identify functional implication of the mtlncRNAs MDL1AS, lncND5 and lncCyt b in retrograde regulation. Mediated by HuR and PNPT1 proteins, the mtlncRNAs undergo a mitochondria-to-nucleus traveling and then regulate a network of nuclear genes. Moreover, as an example of the functional consequence, we showed that the nuclear-translocated lncCyt b cooperates with the splicing factor hnRNPA2B1 to influence several aspects of cell metabolism including glycolysis, possibly through their regulatory effect on the post-transcriptional processing of related nuclear genes. This study advances our knowledge in mitochondrial biology and provides new insights into the role of mtlncRNAs in mitochondria-nucleus communications.

{"title":"A mitochondria-to-nucleus regulation mediated by the nuclear-translocated mitochondrial lncRNAs.","authors":"Jia Li, Ruoling Bai, Yulian Zhou, Xu Song, Ling Li","doi":"10.1371/journal.pgen.1011580","DOIUrl":"10.1371/journal.pgen.1011580","url":null,"abstract":"<p><p>A bidirectional nucleus-mitochondria communication is essential for homeostasis and stress. By acting as critical molecules, the nuclear-encoded lncRNAs (nulncRNAs) have been implicated in the nucleus-to-mitochondria anterograde regulation. However, role of mitochondrial-derived lncRNAs (mtlncRNAs) in the mitochondria-to-nucleus retrograde regulation remains elusive. Here, we identify functional implication of the mtlncRNAs MDL1AS, lncND5 and lncCyt b in retrograde regulation. Mediated by HuR and PNPT1 proteins, the mtlncRNAs undergo a mitochondria-to-nucleus traveling and then regulate a network of nuclear genes. Moreover, as an example of the functional consequence, we showed that the nuclear-translocated lncCyt b cooperates with the splicing factor hnRNPA2B1 to influence several aspects of cell metabolism including glycolysis, possibly through their regulatory effect on the post-transcriptional processing of related nuclear genes. This study advances our knowledge in mitochondrial biology and provides new insights into the role of mtlncRNAs in mitochondria-nucleus communications.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011580"},"PeriodicalIF":4.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11801721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Wild-type bone marrow cells repopulate tissue resident macrophages and reverse the impacts of homozygous CSF1R mutation.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-27 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011525
Dylan Carter-Cusack, Stephen Huang, Sahar Keshvari, Omkar Patkar, Anuj Sehgal, Rachel Allavena, Robert A J Byrne, B Paul Morgan, Stephen J Bush, Kim M Summers, Katharine M Irvine, David A Hume

Adaptation to existence outside the womb is a key event in the life of a mammal. The absence of macrophages in rats with a homozygous mutation in the colony-stimulating factor 1 receptor (Csf1r) gene (Csf1rko) severely compromises pre-weaning somatic growth and maturation of organ function. Transfer of wild-type bone marrow cells (BMT) at weaning rescues tissue macrophage populations permitting normal development and long-term survival. To dissect the phenotype and function of macrophages in postnatal development, we generated transcriptomic profiles of all major organs of wild-type and Csf1rko rats at weaning and in selected organs following rescue by BMT. The transcriptomic profiles revealed subtle effects of macrophage deficiency on development of all major organs. Network analysis revealed a common signature of CSF1R-dependent resident tissue macrophages that includes the components of complement C1Q (C1qa/b/c genes). Circulating C1Q was almost undetectable in Csf1rko rats and rapidly restored to normal levels following BMT. Tissue-specific macrophage signatures were also identified, notably including sinus macrophage populations in the lymph nodes. Their loss in Csf1rko rats was confirmed by immunohistochemical localisation of CD209B (SIGNR1). By 6-12 weeks, Csf1rko rats succumb to emphysema-like pathology associated with the selective loss of interstitial macrophages and granulocytosis. This pathology was reversed by BMT. Along with physiological rescue, BMT precisely regenerated the abundance and expression profiles of resident macrophages. The exception was the brain, where BM-derived microglia-like cells had a distinct expression profile compared to resident microglia. In addition, the transferred BM failed to restore blood monocyte or CSF1R-positive bone marrow progenitors. These studies provide a model for the pathology and treatment of CSF1R mutations in humans and the innate immune deficiency associated with prematurity.

{"title":"Wild-type bone marrow cells repopulate tissue resident macrophages and reverse the impacts of homozygous CSF1R mutation.","authors":"Dylan Carter-Cusack, Stephen Huang, Sahar Keshvari, Omkar Patkar, Anuj Sehgal, Rachel Allavena, Robert A J Byrne, B Paul Morgan, Stephen J Bush, Kim M Summers, Katharine M Irvine, David A Hume","doi":"10.1371/journal.pgen.1011525","DOIUrl":"10.1371/journal.pgen.1011525","url":null,"abstract":"<p><p>Adaptation to existence outside the womb is a key event in the life of a mammal. The absence of macrophages in rats with a homozygous mutation in the colony-stimulating factor 1 receptor (Csf1r) gene (Csf1rko) severely compromises pre-weaning somatic growth and maturation of organ function. Transfer of wild-type bone marrow cells (BMT) at weaning rescues tissue macrophage populations permitting normal development and long-term survival. To dissect the phenotype and function of macrophages in postnatal development, we generated transcriptomic profiles of all major organs of wild-type and Csf1rko rats at weaning and in selected organs following rescue by BMT. The transcriptomic profiles revealed subtle effects of macrophage deficiency on development of all major organs. Network analysis revealed a common signature of CSF1R-dependent resident tissue macrophages that includes the components of complement C1Q (C1qa/b/c genes). Circulating C1Q was almost undetectable in Csf1rko rats and rapidly restored to normal levels following BMT. Tissue-specific macrophage signatures were also identified, notably including sinus macrophage populations in the lymph nodes. Their loss in Csf1rko rats was confirmed by immunohistochemical localisation of CD209B (SIGNR1). By 6-12 weeks, Csf1rko rats succumb to emphysema-like pathology associated with the selective loss of interstitial macrophages and granulocytosis. This pathology was reversed by BMT. Along with physiological rescue, BMT precisely regenerated the abundance and expression profiles of resident macrophages. The exception was the brain, where BM-derived microglia-like cells had a distinct expression profile compared to resident microglia. In addition, the transferred BM failed to restore blood monocyte or CSF1R-positive bone marrow progenitors. These studies provide a model for the pathology and treatment of CSF1R mutations in humans and the innate immune deficiency associated with prematurity.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"21 1","pages":"e1011525"},"PeriodicalIF":4.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11785368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A versatile site-directed gene trap strategy to manipulate gene activity and control gene expression in Caenorhabditis elegans.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-22 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011541
Haania Khan, Xinyu Huang, Vishnu Raj, Han Wang

The ability to manipulate gene activity and control transgene expression is essential to study gene function. While several genetic tools for modifying genes or controlling expression separately are available for Caenorhabditis elegans, there are no genetic approaches to generate mutations that simultaneously disrupt gene function and provide genetic access to the cells expressing the disrupted gene. To achieve this, we developed a versatile gene trap strategy based on cGAL, a GAL4-UAS bipartite expression system for C. elegans. We designed a cGAL gene trap cassette and used CRISPR/Cas9 to insert it into the target gene, creating a bicistronic operon that simultaneously expresses a truncated endogenous protein and the cGAL driver in the cells expressing the target gene. We demonstrate that our cGAL gene trap strategy robustly generated loss-of-function alleles. Combining the cGAL gene trap lines with different UAS effector strains allowed us to rescue the loss-of-function phenotype, observe the gene expression pattern, and manipulate cell activity spatiotemporally. We show that, by recombinase-mediated cassette exchange (RMCE) via microinjection or genetic crossing, the cGAL gene trap lines can be further engineered in vivo to easily swap cGAL with other bipartite expression systems' drivers, including QF/QF2, Tet-On/Tet-Off, and LexA, to generate new gene trap lines with different drivers at the same genomic locus. These drivers can be combined with their corresponding effectors for orthogonal transgenic control. Thus, our cGAL-based gene trap is versatile and represents a powerful genetic tool for gene function analysis in C. elegans, which will ultimately provide new insights into how genes in the genome control the biology of an organism.

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引用次数: 0
The Cul3 ubiquitin ligase engages Insomniac as an adaptor to impact sleep and synaptic homeostasis.
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-22 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011574
Qiuling Li, Kayla Y Lim, Raad Altawell, Faith Verderose, Xiling Li, Wanying Dong, Joshua Martinez, Dion Dickman, Nicholas Stavropoulos

Mutations of the Cullin-3 (Cul3) E3 ubiquitin ligase are associated with autism and schizophrenia, neurological disorders characterized by sleep disturbances and altered synaptic function. Cul3 engages dozens of adaptor proteins to recruit hundreds of substrates for ubiquitination, but the adaptors that impact sleep and synapses remain ill-defined. Here we implicate Insomniac (Inc), a conserved protein required for normal sleep and synaptic homeostasis in Drosophila, as a Cul3 adaptor. Inc binds Cul3 in vivo, and mutations within the N-terminal BTB domain of Inc that weaken Inc-Cul3 associations impair Inc activity, suggesting that Inc function requires binding to the Cul3 complex. Deletion of the conserved C-terminus of Inc does not alter Cul3 binding but abolishes Inc activity in the context of sleep and synaptic homeostasis, indicating that the Inc C-terminus has the properties of a substrate recruitment domain. Mutation of a conserved, disease-associated arginine in the Inc C-terminus also abolishes Inc function, suggesting that this residue is vital for recruiting Inc targets. Inc levels are negatively regulated by Cul3 in neurons, consistent with Inc degradation by autocatalytic ubiquitination, a hallmark of Cullin adaptors. These findings link Inc and Cul3 in vivo and support the notion that Inc-Cul3 complexes are essential for normal sleep and synaptic function. Furthermore, these results indicate that dysregulation of conserved substrates of Inc-Cul3 complexes may contribute to altered sleep and synaptic function in autism and schizophrenia associated with Cul3 mutations.

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引用次数: 0
F-box protein Fbx23 acts as a transcriptional coactivator to recognize and activate transcription factor Ace1. F-box蛋白Fbx23作为转录辅激活因子识别和激活转录因子Ace1。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-01-21 eCollection Date: 2025-01-01 DOI: 10.1371/journal.pgen.1011539
Zhongjiao Liu, Kexuan Ma, Panpan Zhang, Siqi Zhang, Xin Song, Yuqi Qin

Protein ubiquitination is usually coupled with proteasomal degradation and is crucial in regulating protein quality. The E3 ubiquitin-protein ligase SCF (Skp1-Cullin-F-box) complex directly recognizes the target substrate via interaction between the F-box protein and the substrate. F-box protein is the determinant of substrate specificity. The limited number of identified ubiquitin ligase-substrate pairs is a major bottleneck in the ubiquitination field. Penicillium oxalicum contains many transcription factors, such as BrlA, CreA, XlnR, and Ace1, conserved in filamentous fungi that regulate the fungal development and transcription of (hemi)cellulase genes. Transcription factor Ace1 (also known as SltA) positively correlated with fungal growth and conidiation and negatively correlated with the expression of (hemi)cellulase genes. A ubiquitin ligase-substrate pair, SCFFbx23-Ace1, is identified in P. oxalicum. Most of PoFbx23 is present in free form within the nucleus. A small portion of PoFbx23 associates with Skp1 to form PoFbx23-Skp1 heterodimer or assembles with the three invariable core components (Skp1, Cul1, and Rbx1) of SCF to form the SCFFbx23 complex. Under glucose signal, PoFbx23 absence (Δfbx23) results in decreased transcription levels of the brlA gene which encodes the master regulator for asexual development and six spore pigmentation genes (abrB→abrA→aygB→arpA→arpB→albA) which encode the proteins in the dihydroxynaphthalene-melanin pathway, along with impaired conidiation. Under cellulose signal, transcription levels of (hemi)cellulase genes in the Δfbx23 mutant are significantly upregulated. When PoFbx23 is present, PoAce1 exists as a full-length version and several low-molecular-weight degraded versions. PoAce1 has polyubiquitin modification. Deleting the Pofbx23 gene does not affect Poace1 gene transcription but results in the remarkable accumulation of all versions of the PoAce1 protein. Accumulated PoAce1 protein is a dysfunctional form that no longer binds promoters of the target gene, including the cellulase genes cbh1 and eg1, the hemicellulase gene xyn11A, and the pigmentation-related gene abrB. PoFbx23 acts as a transcriptional coactivator, recognizing and activating PoAce1, allowing the latter to regulate the transcription of target genes with different effects (activating or repressing) under different signals.

蛋白质泛素化通常伴随着蛋白酶体降解,在调节蛋白质质量中起着至关重要的作用。E3泛素蛋白连接酶SCF (Skp1-Cullin-F-box)复合体通过F-box蛋白与底物之间的相互作用直接识别目标底物。F-box蛋白是底物特异性的决定因素。已鉴定的泛素连接酶-底物对数量有限是泛素化领域的主要瓶颈。草酸青霉含有多种转录因子,如BrlA、CreA、XlnR和Ace1,这些转录因子在丝状真菌中保守,调控真菌发育和(半)纤维素酶基因的转录。转录因子Ace1(也称为SltA)与真菌生长和分生呈正相关,与(半)纤维素酶基因的表达负相关。在草藻中发现了一个泛素连接酶底物对SCFFbx23-Ace1。大多数PoFbx23以自由形式存在于细胞核内。一小部分PoFbx23与Skp1结合形成PoFbx23-Skp1异源二聚体,或与SCF的三个不变核心组分(Skp1, Cul1和Rbx1)组装形成SCFFbx23复合物。在葡萄糖信号下,PoFbx23缺失(Δfbx23)导致编码无性发育主调控因子brlA基因和编码二羟苯-黑色素通路蛋白的6个孢子色素沉着基因(abrB→abrA→aygB→arpA→arpB→albA)的转录水平降低,同时孢子萌发受损。在纤维素信号下,Δfbx23突变体(半)纤维素酶基因的转录水平显著上调。当PoFbx23存在时,PoAce1以全长版本和几个低分子量的降级版本存在。PoAce1有多泛素修饰。删除Pofbx23基因不会影响Poace1基因的转录,但会导致Poace1蛋白所有版本的显著积累。积累的PoAce1蛋白是一种功能失调的形式,它不再结合靶基因的启动子,包括纤维素酶基因cbh1和eg1、半纤维素酶基因xyn11A和色素相关基因abrB。PoFbx23作为转录辅激活因子,识别并激活PoAce1,使后者在不同信号下以不同作用(激活或抑制)调节靶基因的转录。
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引用次数: 0
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