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1.
Mol Cell ; 82(21): 4080-4098.e12, 2022 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-36272410

RESUMO

Growing evidence suggests prevalence of transcriptional condensates on chromatin, yet their mechanisms of formation and functional significance remain largely unclear. In human cancer, a series of mutations in the histone acetylation reader ENL create gain-of-function mutants with increased transcriptional activation ability. Here, we show that these mutations, clustered in ENL's structured acetyl-reading YEATS domain, trigger aberrant condensates at native genomic targets through multivalent homotypic and heterotypic interactions. Mechanistically, mutation-induced structural changes in the YEATS domain, ENL's two disordered regions of opposing charges, and the incorporation of extrinsic elongation factors are all required for ENL condensate formation. Extensive mutagenesis establishes condensate formation as a driver of oncogenic gene activation. Furthermore, expression of ENL mutants beyond the endogenous level leads to non-functional condensates. Our findings provide new mechanistic and functional insights into cancer-associated condensates and support condensate dysregulation as an oncogenic mechanism.


Assuntos
Neoplasias , Corpos Nucleares , Humanos , Domínios Proteicos , Cromatina/genética , Mutação , Neoplasias/genética
2.
Cell ; 159(3): 558-71, 2014 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-25417107

RESUMO

The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known. Here, we show that the AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and utilizes a serine-lined aromatic "sandwiching" cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. ChIP-seq experiments revealed a strong colocalization of AF9 and H3K9 acetylation genome-wide, which is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identified the evolutionarily conserved YEATS domain as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.


Assuntos
Código das Histonas , Metiltransferases/química , Metiltransferases/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Acetilação , Sequência de Aminoácidos , Regulação da Expressão Gênica , Histona Acetiltransferases/química , Histona Acetiltransferases/metabolismo , Histona-Lisina N-Metiltransferase , Histonas/metabolismo , Humanos , Metilação , Modelos Moleculares , Dados de Sequência Molecular , Processamento de Proteína Pós-Traducional , Estrutura Terciária de Proteína , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Alinhamento de Sequência , Transcrição Gênica
3.
Development ; 151(6)2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38546043

RESUMO

The timely degradation of proteins that regulate the cell cycle is essential for oocyte maturation. Oocytes are equipped to degrade proteins via the ubiquitin-proteasome system. In meiosis, anaphase promoting complex/cyclosome (APC/C), an E3 ubiquitin-ligase, is responsible for the degradation of proteins. Ubiquitin-conjugating enzyme E2 S (UBE2S), an E2 ubiquitin-conjugating enzyme, delivers ubiquitin to APC/C. APC/C has been extensively studied, but the functions of UBE2S in oocyte maturation and mouse fertility are not clear. In this study, we used Ube2s knockout mice to explore the role of UBE2S in mouse oocytes. Ube2s-deleted oocytes were characterized by meiosis I arrest with normal spindle assembly and spindle assembly checkpoint dynamics. However, the absence of UBE2S affected the activity of APC/C. Cyclin B1 and securin are two substrates of APC/C, and their levels were consistently high, resulting in the failure of homologous chromosome separation. Unexpectedly, the oocytes arrested in meiosis I could be fertilized and the embryos could become implanted normally, but died before embryonic day 10.5. In conclusion, our findings reveal an indispensable regulatory role of UBE2S in mouse oocyte meiosis and female fertility.


Assuntos
Pontos de Checagem da Fase M do Ciclo Celular , Meiose , Animais , Feminino , Camundongos , Ciclossomo-Complexo Promotor de Anáfase/genética , Ciclossomo-Complexo Promotor de Anáfase/metabolismo , Oócitos/metabolismo , Ubiquitinas/metabolismo
4.
Nature ; 598(7879): 174-181, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34616072

RESUMO

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.


Assuntos
Encéfalo/citologia , Forma Celular , Neurônios/classificação , Neurônios/metabolismo , Análise de Célula Única , Atlas como Assunto , Biomarcadores/metabolismo , Encéfalo/anatomia & histologia , Encéfalo/embriologia , Encéfalo/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Humanos , Neocórtex/anatomia & histologia , Neocórtex/citologia , Neocórtex/embriologia , Neocórtex/metabolismo , Neurogênese , Neuroglia/citologia , Neurônios/citologia , RNA-Seq , Reprodutibilidade dos Testes
5.
Mol Cell ; 73(3): 547-561.e6, 2019 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-30735655

RESUMO

Chromatin organization undergoes drastic reconfiguration during gametogenesis. However, the molecular reprogramming of three-dimensional chromatin structure in this process remains poorly understood for mammals, including primates. Here, we examined three-dimensional chromatin architecture during spermatogenesis in rhesus monkey using low-input Hi-C. Interestingly, we found that topologically associating domains (TADs) undergo dissolution and reestablishment in spermatogenesis. Strikingly, pachytene spermatocytes, where synapsis occurs, are strongly depleted for TADs despite their active transcription state but uniquely show highly refined local compartments that alternate between transcribing and non-transcribing regions (refined-A/B). Importantly, such chromatin organization is conserved in mouse, where it remains largely intact upon transcription inhibition. Instead, it is attenuated in mutant spermatocytes, where the synaptonemal complex failed to be established. Intriguingly, this is accompanied by the restoration of TADs, suggesting that the synaptonemal complex may restrict TADs and promote local compartments. Thus, these data revealed extensive reprogramming of higher-order meiotic chromatin architecture during mammalian gametogenesis.


Assuntos
Reprogramação Celular , Montagem e Desmontagem da Cromatina , Cromatina/metabolismo , Meiose , Espermatogênese , Espermatozoides/metabolismo , Animais , Cromatina/química , Cromatina/genética , Regulação da Expressão Gênica no Desenvolvimento , Células HCT116 , Humanos , Macaca mulatta , Masculino , Camundongos Endogâmicos C57BL , Camundongos Knockout , Conformação de Ácido Nucleico , Estágio Paquíteno , Conformação Proteica , Relação Estrutura-Atividade , Fatores de Tempo , Transcrição Gênica , Inativação do Cromossomo X
6.
Hum Mol Genet ; 33(8): 667-676, 2024 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-38224683

RESUMO

More than 60 monogenic genes mutated in steroid-resistant nephrotic syndrome (SRNS) have been identified. Our previous study found that mutations in nucleoporin 160 kD (NUP160) are implicated in SRNS. The NUP160 gene encodes a component of the nuclear pore complex. Recently, two siblings with homozygous NUP160 mutations presented with SRNS and a nervous system disorder. However, replication of nephrotic syndrome (NS)-associated phenotypes in a mammalian model following loss of Nup160 is needed to prove that NUP160 mutations cause SRNS. Here, we generated a podocyte-specific Nup160 knockout (Nup160podKO) mouse model using CRISPR/Cas9 and Cre/loxP technologies. We investigated NS-associated phenotypes in these Nup160podKO mice. We verified efficient abrogation of Nup160 in Nup160podKO mice at both the DNA and protein levels. We showed that Nup160podKO mice develop typical signs of NS. Nup160podKO mice exhibited progression of proteinuria to average albumin/creatinine ratio (ACR) levels of 15.06 ± 2.71 mg/mg at 26 weeks, and had lower serum albumin levels of 13.13 ± 1.34 g/l at 30 weeks. Littermate control mice had urinary ACR mean values of 0.03 mg/mg and serum albumin values of 22.89 ± 0.34 g/l at the corresponding ages. Further, Nup160podKO mice exhibited glomerulosclerosis compared with littermate control mice. Podocyte-specific Nup160 knockout in mice led to NS and glomerulosclerosis. Thus, our findings strongly support that mutations in NUP160 cause SRNS. The newly generated Nup160podKO mice are a reliable mammalian model for future study of the pathogenesis of NUP160-associated SRNS.


Assuntos
Síndrome Nefrótica , Podócitos , Animais , Camundongos , Camundongos Knockout , Mutação , Síndrome Nefrótica/genética , Síndrome Nefrótica/diagnóstico , Síndrome Nefrótica/patologia , Proteinúria/genética , Albumina Sérica/genética
7.
Development ; 150(14)2023 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-37485540

RESUMO

Accurate chromosome segregation, monitored by the spindle assembly checkpoint (SAC), is crucial for the production of euploid cells. Previous in vitro studies by us and others showed that Mad2, a core member of the SAC, performs a checkpoint function in oocyte meiosis. Here, through an oocyte-specific knockout approach in mouse, we reconfirmed that Mad2-deficient oocytes exhibit an accelerated metaphase-to-anaphase transition caused by premature degradation of securin and cyclin B1 and subsequent activation of separase in meiosis I. However, it was surprising that the knockout mice were completely fertile and the resulting oocytes were euploid. In the absence of Mad2, other SAC proteins, including BubR1, Bub3 and Mad1, were normally recruited to the kinetochores, which likely explains the balanced chromosome separation. Further studies showed that the chromosome separation in Mad2-null oocytes was particularly sensitive to environmental changes and, when matured in vitro, showed chromosome misalignment, lagging chromosomes, and aneuploidy with premature separation of sister chromatids, which was exacerbated at a lower temperature. We reveal for the first time that Mad2 is dispensable for proper chromosome segregation but acts to mitigate environmental stress in meiotic oocytes.


Assuntos
Proteínas de Ciclo Celular , Fuso Acromático , Animais , Camundongos , Proteínas de Ciclo Celular/metabolismo , Fuso Acromático/metabolismo , Proteínas Mad2/genética , Proteínas Mad2/metabolismo , Segregação de Cromossomos/genética , Oócitos/metabolismo , Cinetocoros/metabolismo , Meiose/genética
8.
Nat Methods ; 20(2): 268-275, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36646896

RESUMO

Cryo-electron tomography (cryo-ET) is a revolutionary technique for resolving the structure of subcellular organelles and macromolecular complexes in their cellular context. However, the application of the cryo-ET is hampered by the sample preparation step. Performing cryo-focused ion beam milling at an arbitrary position on the sample is inefficient, and the target of interest is not guaranteed to be preserved when thinning the cell from several micrometers to less than 300 nm thick. Here, we report a cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) technique that is capable of preparing cryo-lamellae under the guidance of three-dimensional confocal imaging. Moreover, we demonstrate a workflow to preselect and preserve nanoscale target regions inside the finished cryo-lamellae. By successfully preparing cryo-lamellae that contain a single centriole or contact sites between subcellular organelles, we show that this approach is generally applicable, and shall help in innovating more applications of cryo-ET.


Assuntos
Tomografia com Microscopia Eletrônica , Manejo de Espécimes , Tomografia com Microscopia Eletrônica/métodos , Substâncias Macromoleculares/química , Manejo de Espécimes/métodos , Elétrons , Imageamento Tridimensional/métodos , Microscopia Crioeletrônica/métodos
9.
Nature ; 577(7788): 121-126, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31853060

RESUMO

Modifications of histone proteins have essential roles in normal development and human disease. Recognition of modified histones by 'reader' proteins is a key mechanism that mediates the function of histone modifications, but how the dysregulation of these readers might contribute to disease remains poorly understood. We previously identified the ENL protein as a reader of histone acetylation via its YEATS domain, linking it to the expression of cancer-driving genes in acute leukaemia1. Recurrent hotspot mutations have been found in the ENL YEATS domain in Wilms tumour2,3, the most common type of paediatric kidney cancer. Here we show, using human and mouse cells, that these mutations impair cell-fate regulation by conferring gain-of-function in chromatin recruitment and transcriptional control. ENL mutants induce gene-expression changes that favour a premalignant cell fate, and, in an assay for nephrogenesis using murine cells, result in undifferentiated structures resembling those observed in human Wilms tumour. Mechanistically, although bound to largely similar genomic loci as the wild-type protein, ENL mutants exhibit increased occupancy at a subset of targets, leading to a marked increase in the recruitment and activity of transcription elongation machinery that enforces active transcription from target loci. Furthermore, ectopically expressed ENL mutants exhibit greater self-association and form discrete and dynamic nuclear puncta that are characteristic of biomolecular hubs consisting of local high concentrations of regulatory factors. Such mutation-driven ENL self-association is functionally linked to enhanced chromatin occupancy and gene activation. Collectively, our findings show that hotspot mutations in a chromatin-reader domain drive self-reinforced recruitment, derailing normal cell-fate control during development and leading to an oncogenic outcome.


Assuntos
Linhagem da Célula , Cromatina/genética , Proteínas de Ligação a DNA/metabolismo , Mutação com Ganho de Função , Fatores de Transcrição/metabolismo , Animais , Diferenciação Celular , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Células HEK293 , Humanos , Camundongos , Néfrons/metabolismo , Néfrons/patologia , Fatores de Transcrição/química , Fatores de Transcrição/genética
10.
Mol Cell ; 72(4): 673-686.e6, 2018 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-30444999

RESUMO

The epigenome plays critical roles in controlling gene expression and development. However, how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show that parental-to-zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory, starting with methylating gametic enhancers. Surprisingly, this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4-cell stage, and zygotic enhancers are not activated until around zygotic genome activation (ZGA). By contrast, many promoters remain hypomethylated and, unexpectedly, acquire histone acetylation before ZGA at as early as the 4-cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally, such reprogramming is largely driven by maternal factors, with zygotic products mainly contributing to embryonic enhancer activation. These data reveal widespread enhancer dememorization and promoter priming during parental-to-zygotic transition.


Assuntos
Código das Histonas/genética , Código das Histonas/fisiologia , Peixe-Zebra/embriologia , Acetilação , Animais , Metilação de DNA/genética , Epigênese Genética/genética , Epigênese Genética/fisiologia , Epigenômica , Regulação da Expressão Gênica no Desenvolvimento/genética , Genoma/genética , Histonas/genética , Masculino , Oócitos , Regiões Promotoras Genéticas/genética , Processamento de Proteína Pós-Traducional , Sequências Reguladoras de Ácido Nucleico/genética , Espermatozoides , Transcrição Gênica/genética , Peixe-Zebra/genética , Proteínas de Peixe-Zebra , Zigoto/fisiologia
11.
Nucleic Acids Res ; 52(6): 2808-2820, 2024 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-38426933

RESUMO

Chemical modifications in RNAs play crucial roles in diversifying their structures and regulating numerous biochemical processes. Since the 1990s, several hydrophobic prenyl-modifications have been discovered in various RNAs. Prenyl groups serve as precursors for terpenes and many other biological molecules. The processes of prenylation in different macromolecules have been extensively studied. We introduce here a novel chemical biology toolkit that not only labels i6A, a prenyl-modified RNA residue, by leveraging the unique reactivity of the prenyl group, but also provides a general strategy to incorporate fluorescence functionalities into RNAs for molecular tracking purposes. Our findings revealed that iodine-mediated cyclization reactions of the prenyl group occur rapidly, transforming i6A from a hydrogen-bond acceptor to a donor. Based on this reactivity, we developed an Iodine-Mediated Cyclization and Reverse Transcription (IMCRT) tRNA-seq method, which can profile all nine endogenous tRNAs containing i6A residues in Saccharomyces cerevisiae with single-base resolution. Furthermore, under stress conditions, we observed a decline in i6A levels in budding yeast, accompanied by significant decrease of mutation rate at A37 position. Thus, the IMCRT tRNA-seq method not only permits semi-quantification of i6A levels in tRNAs but also holds potential for transcriptome-wide detection and analysis of various RNA species containing i6A modifications.


Assuntos
Isopenteniladenosina , Processamento Pós-Transcricional do RNA , RNA de Transferência , Iodo , Neopreno , RNA de Transferência/metabolismo , Saccharomyces cerevisiae , Análise de Sequência de RNA
12.
Plant J ; 2024 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-38804089

RESUMO

The successful interaction between pollen and stigma is a critical process for plant sexual reproduction, involving a series of intricate molecular and physiological events. After self-compatible pollination, a significant reduction in reactive oxygen species (ROS) production has been observed in stigmas, which is essential for pollen grain rehydration and subsequent pollen tube growth. Several scavenging enzymes tightly regulate ROS homeostasis. However, the potential role of these ROS-scavenging enzymes in the pollen-stigma interaction in Brassica napus remains unclear. Here, we showed that the activity of ascorbate peroxidase (APX), an enzyme that plays a crucial role in the detoxification of hydrogen peroxide (H2O2), was modulated depending on the compatibility of pollination in B. napus. We then identified stigma-expressed APX1s and generated pentuple mutants of APX1s using CRISPR/Cas9 technology. After compatible pollination, the BnaAPX1 pentuple mutants accumulated higher levels of H2O2 in the stigma, while the overexpression of BnaA09.APX1 resulted in lower levels of H2O2. Furthermore, the knockout of BnaAPX1 delayed the compatible response-mediated pollen rehydration and germination, which was consistent with the effects of a specific APX inhibitor, ρ-Aminophenol, on compatible pollination. In contrast, the overexpression of BnaA09.APX1 accelerated pollen rehydration and germination after both compatible and incompatible pollinations. However, delaying and promoting pollen rehydration and germination did not affect the seed set after compatible and incompatible pollination in APX1 pentuple mutants and overexpression lines, respectively. Our results demonstrate the fundamental role of BnaAPX1 in pollen rehydration and germination by regulating ROS homeostasis during the pollen-stigma interaction in B. napus.

13.
EMBO J ; 40(8): e106276, 2021 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-33729590

RESUMO

Dynamic chemical modifications of RNA represent novel and fundamental mechanisms that regulate stemness and tissue homeostasis. Rejuvenation and wound repair of mammalian skin are sustained by epidermal progenitor cells, which are localized within the basal layer of the skin epidermis. N6 -methyladenosine (m6 A) is one of the most abundant modifications found in eukaryotic mRNA and lncRNA (long noncoding RNA). In this report, we survey changes of m6 A RNA methylomes upon epidermal differentiation and identify Pvt1, a lncRNA whose m6 A modification is critically involved in sustaining stemness of epidermal progenitor cells. With genome-editing and a mouse genetics approach, we show that ablation of m6 A methyltransferase or Pvt1 impairs the self-renewal and wound healing capability of skin. Mechanistically, methylation of Pvt1 transcripts enhances its interaction with MYC and stabilizes the MYC protein in epidermal progenitor cells. Our study presents a global view of epitranscriptomic dynamics that occur during epidermal differentiation and identifies the m6 A modification of Pvt1 as a key signaling event involved in skin tissue homeostasis and wound repair.


Assuntos
Adenosina/análogos & derivados , Diferenciação Celular , Células Epidérmicas/citologia , Processamento Pós-Transcricional do RNA , RNA Longo não Codificante/metabolismo , Células-Tronco/citologia , Adenosina/metabolismo , Animais , Células Cultivadas , Células Epidérmicas/metabolismo , Células Epidérmicas/fisiologia , Cobaias , Metiltransferases/genética , Camundongos , Ligação Proteica , Proteínas Proto-Oncogênicas c-myc/metabolismo , RNA Longo não Codificante/genética , Células-Tronco/metabolismo , Células-Tronco/fisiologia , Cicatrização
14.
Nat Methods ; 19(6): 759-769, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35654951

RESUMO

Advances in multiplexed in situ imaging are revealing important insights in spatial biology. However, cell type identification remains a major challenge in imaging analysis, with most existing methods involving substantial manual assessment and subjective decisions for thousands of cells. We developed an unsupervised machine learning algorithm, CELESTA, which identifies the cell type of each cell, individually, using the cell's marker expression profile and, when needed, its spatial information. We demonstrate the performance of CELESTA on multiplexed immunofluorescence images of colorectal cancer and head and neck squamous cell carcinoma (HNSCC). Using the cell types identified by CELESTA, we identify tissue architecture associated with lymph node metastasis in HNSCC, and validate our findings in an independent cohort. By coupling our spatial analysis with single-cell RNA-sequencing data on proximal sections of the same specimens, we identify cell-cell crosstalk associated with lymph node metastasis, demonstrating the power of CELESTA to facilitate identification of clinically relevant interactions.


Assuntos
Neoplasias de Cabeça e Pescoço , Estudos de Coortes , Humanos , Metástase Linfática , Carcinoma de Células Escamosas de Cabeça e Pescoço
15.
Nat Methods ; 19(1): 111-118, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34887551

RESUMO

Recent whole-brain mapping projects are collecting large-scale three-dimensional images using modalities such as serial two-photon tomography, fluorescence micro-optical sectioning tomography, light-sheet fluorescence microscopy, volumetric imaging with synchronous on-the-fly scan and readout or magnetic resonance imaging. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modal image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulting from different sample preparation methods and imaging modalities. We introduce a cross-modal registration method, mBrainAligner, which uses coherent landmark mapping and deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We build a brain atlas for the fluorescence micro-optical sectioning tomography modality to facilitate single-cell mapping, and used our method to generate a whole-brain map of three-dimensional single-neuron morphology and neuron cell types.


Assuntos
Encéfalo/citologia , Encéfalo/diagnóstico por imagem , Imageamento Tridimensional/métodos , Algoritmos , Animais , Aprendizado Profundo , Imageamento por Ressonância Magnética , Masculino , Camundongos Endogâmicos C57BL , Fluxo de Trabalho
16.
Bioinformatics ; 40(5)2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38775410

RESUMO

MOTIVATION: Accurate segmentation and recognition of C.elegans cells are critical for various biological studies, including gene expression, cell lineages, and cell fates analysis at single-cell level. However, the highly dense distribution, similar shapes, and inhomogeneous intensity profiles of whole-body cells in 3D fluorescence microscopy images make automatic cell segmentation and recognition a challenging task. Existing methods either rely on additional fiducial markers or only handle a subset of cells. Given the difficulty or expense associated with generating fiducial features in many experimental settings, a marker-free approach capable of reliably segmenting and recognizing C.elegans whole-body cells is highly desirable. RESULTS: We report a new pipeline, called automated segmentation and recognition (ASR) of cells, and applied it to 3D fluorescent microscopy images of L1-stage C.elegans with 558 whole-body cells. A novel displacement vector field based deep learning model is proposed to address the problem of reliable segmentation of highly crowded cells with blurred boundary. We then realize the cell recognition by encoding and exploiting statistical priors on cell positions and structural similarities of neighboring cells. To the best of our knowledge, this is the first method successfully applied to the segmentation and recognition of C.elegans whole-body cells. The ASR-segmentation module achieves an F1-score of 0.8956 on a dataset of 116 C.elegans image stacks with 64 728 cells (accuracy 0.9880, AJI 0.7813). Based on the segmentation results, the ASR recognition module achieved an average accuracy of 0.8879. We also show ASR's applicability to other cell types, e.g. platynereis and rat kidney cells. AVAILABILITY AND IMPLEMENTATION: The code is available at https://github.com/reaneyli/ASR.


Assuntos
Caenorhabditis elegans , Caenorhabditis elegans/citologia , Animais , Microscopia de Fluorescência/métodos , Imageamento Tridimensional/métodos , Processamento de Imagem Assistida por Computador/métodos , Algoritmos , Aprendizado Profundo
17.
Plant Physiol ; 195(1): 832-849, 2024 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-38306630

RESUMO

Plant innate immunity mediated by the nucleotide-binding leucine-rich repeat (NLR) class of immune receptors plays an important role in defense against various pathogens. Although key biochemical events involving NLR activation and signaling have been recently uncovered, we know very little about the transcriptional regulation of NLRs and their downstream signaling components. Here, we show that the Toll-Interleukin 1 receptor homology domain containing NLR (TNL) gene N (Necrosis), which confers resistance to Tobacco mosaic virus, is transcriptionally induced upon immune activation. We identified two conserved transcription factors, N required C3H zinc finger 1 (NRZ1) and N required MYB-like transcription factor 1 (NRM1), that activate N in an immune responsive manner. Genetic analyses indicated that NRZ1 and NRM1 positively regulate coiled-coil domain-containing NLR- and TNL-mediated immunity and function independently of the signaling component Enhanced Disease Susceptibility 1. Furthermore, NRZ1 functions upstream of NRM1 in cell death signaling, and their gene overexpression induces ectopic cell death and expression of NLR signaling components. Our findings uncovered a conserved transcriptional regulatory network that is central to NLR-mediated cell death and immune signaling in plants.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Regulação da Expressão Gênica de Plantas , Proteínas NLR , Imunidade Vegetal , Fatores de Transcrição , Imunidade Vegetal/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Arabidopsis/genética , Arabidopsis/imunologia , Proteínas NLR/genética , Proteínas NLR/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Transdução de Sinais/genética , Doenças das Plantas/virologia , Doenças das Plantas/imunologia , Doenças das Plantas/genética , Morte Celular
18.
FASEB J ; 38(7): e23600, 2024 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-38572599

RESUMO

Odontoblast differentiation depends on the orderly recruitment of transcriptional factors (TFs) in the transcriptional regulatory network. The depletion of crucial TFs disturbs dynamic alteration of the chromatin landscape and gene expression profile, leading to developmental defects. Our previous studies have revealed that the basic leucine zipper (bZIP) TF family is crucial in odontoblastic differentiation, but the function of bZIP TF family member XBP1 is still unknown. Here, we showed the stage-specific expression patterns of the spliced form Xbp1s during tooth development. Elevated Xbp1 expression and nuclear translocation of XBP1S in mesenchymal stem cells (MSCs) were induced by differentiation medium in vitro. Diminution of Xbp1 expression impaired the odontogenic differentiation potential of MSCs. The further integration of ATAC-seq and RNA-seq identified Hspa9 as a direct downstream target, an essential mitochondrial chaperonin gene that modulated mitochondrial homeostasis. The amelioration of mitochondrial dysfunction rescued the impaired odontogenic differentiation potential of MSCs caused by the diminution of Xbp1. Furthermore, the overexpression of Hspa9 rescued Xbp1-deficient defects in odontoblastic differentiation. Our study illustrates the crucial role of Xbp1 in odontoblastic differentiation via modulating mitochondrial homeostasis and brings evidence to the therapy of mitochondrial diseases caused by genetic defects.


Assuntos
Proteínas da Matriz Extracelular , Células-Tronco Mesenquimais , Proteínas da Matriz Extracelular/metabolismo , Diferenciação Celular , Fatores de Transcrição/genética , Células-Tronco Mesenquimais/metabolismo , Homeostase
19.
Immunity ; 44(2): 422-37, 2016 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-26885862

RESUMO

Dendritic cells (DCs) orchestrate complex membrane trafficking through an interconnected transportation network linked together by Rab GTPases. Through a tandem affinity purification strategy and mass spectrometry, we depicted an interactomic landscape of major members of the mammalian Rab GTPase family. When complemented with imaging tools, this proteomic analysis provided a global view of intracellular membrane organization. Driven by this analysis, we investigated dynamic changes to the Rab32 subnetwork in DCs induced by L. monocytogenes infection and uncovered an essential role of this subnetwork in controlling the intracellular proliferation of L. monocytogenes. Mechanistically, Rab32 formed a persistent complex with two interacting proteins, PHB and PHB2, to encompass bacteria both during early phagosome formation and after L. monocytogenes escaped the original containment vacuole. Collectively, we have provided a functional compartmentalization overview and an organizational framework of intracellular Rab-mediated vesicle trafficking that can serve as a resource for future investigations.


Assuntos
Células Dendríticas/imunologia , Listeria monocytogenes/imunologia , Listeriose/imunologia , Complexos Multiproteicos/metabolismo , Proteínas rab de Ligação ao GTP/metabolismo , Aciltransferases/metabolismo , Animais , Anti-Infecciosos/uso terapêutico , Linhagem Celular , Biologia Computacional , Contenção de Riscos Biológicos , Células Dendríticas/microbiologia , Listeria monocytogenes/crescimento & desenvolvimento , Listeriose/tratamento farmacológico , Camundongos , Proibitinas , Transporte Proteico , Proteínas Repressoras/metabolismo , Vacúolos/metabolismo
20.
Circ Res ; 133(10): 842-857, 2023 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-37800327

RESUMO

BACKGROUND: Advanced age is unequivocally linked to the development of cardiovascular disease; however, the mechanisms resulting in reduced endothelial cell regeneration remain poorly understood. Here, we investigated novel mechanisms involved in endothelial cell senescence that impact endothelial cell transcription and vascular repair after injury. METHODS: Native endothelial cells were isolated from young (20±3.4 years) and aged (80±2.3 years) individuals and subjected to molecular analyses to assess global transcriptional and metabolic changes. In vitro studies were conducted using primary human and murine endothelial cells. A murine aortic re-endothelialization model was used to examine endothelial cell regenerative capacity in vivo. RESULTS: RNA sequencing of native endothelial cells revealed that aging resulted in p53-mediated reprogramming to express senescence-associated genes and suppress glycolysis. Reduced glucose uptake and ATP contributed to attenuated assembly of the telomerase complex, which was required for endothelial cell proliferation. Enhanced p53 activity in aging was linked to its acetylation on K120 due to enhanced activity of the acetyltransferase MOZ (monocytic leukemic zinc finger). Mechanistically, p53 acetylation and translocation were, at least partially, attributed to the loss of the vasoprotective enzyme, CSE (cystathionine γ-lyase). CSE physically anchored p53 in the cytosol to prevent its nuclear translocation and CSE absence inhibited AKT (Protein kinase B)-mediated MOZ phosphorylation, which in turn increased MOZ activity and subsequently p53 acetylation. In mice, the endothelial cell-specific deletion of CSE activated p53, induced premature endothelial senescence, and arrested vascular repair after injury. In contrast, the adeno-associated virus 9-mediated re-expression of an active CSE mutant retained p53 in the cytosol, maintained endothelial glucose metabolism and proliferation, and prevented endothelial cell senescence. Adenoviral overexpression of CSE in native endothelial cells from aged individuals maintained low p53 activity and reactivated telomerase to revert endothelial cell senescence. CONCLUSIONS: Aging-associated impairment of vascular repair is partly determined by the vasoprotective enzyme CSE.


Assuntos
Sulfeto de Hidrogênio , Telomerase , Animais , Humanos , Camundongos , Senescência Celular , Cistationina gama-Liase/genética , Cistationina gama-Liase/metabolismo , Células Endoteliais/metabolismo , Sulfeto de Hidrogênio/metabolismo , Telomerase/genética , Telomerase/metabolismo , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismo
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