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Kc R, López de Boer R, Lin M, Vagnozzi AN, Jeannotte L, Philippidou P. Multimodal Hox5 activity generates motor neuron diversity. Commun Biol 2024; 7:1166. [PMID: 39289460 PMCID: PMC11408534 DOI: 10.1038/s42003-024-06835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Motor neurons (MNs) are the final output of circuits driving fundamental behaviors, such as respiration and locomotion. Hox proteins are essential in generating the MN diversity required for accomplishing these functions, but the transcriptional mechanisms that enable Hox paralogs to assign distinct MN subtype identities despite their promiscuous DNA binding motif are not well understood. Here we show that Hoxa5 modifies chromatin accessibility in all mouse spinal cervical MN subtypes and engages TALE co-factors to directly bind and regulate subtype-specific genes. We identify a paralog-specific interaction of Hoxa5 with the phrenic MN-specific transcription factor Scip and show that heterologous expression of Hoxa5 and Scip is sufficient to suppress limb-innervating MN identity. We also demonstrate that phrenic MN identity is stable after Hoxa5 downregulation and identify Klf proteins as potential regulators of phrenic MN maintenance. Our data identify multiple modes of Hoxa5 action that converge to induce and maintain MN identity.
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Affiliation(s)
- Ritesh Kc
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Raquel López de Boer
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Minshan Lin
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Alicia N Vagnozzi
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry & Pathology, Université Laval, Centre Recherche sur le Cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology), Québec, Canada
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA.
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2
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Villarreal-Puente A, Altamirano-Torres C, Jiménez-Mejía G, Hernández-Bautista C, Montalvo-Méndez R, Vázquez M, Zurita M, Reséndez-Pérez D. Novel Antennapedia and Ultrabithorax trimeric complexes with TBP and Exd regulate transcription. Hereditas 2024; 161:25. [PMID: 39080786 PMCID: PMC11290222 DOI: 10.1186/s41065-024-00327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Hox proteins interact with DNA and many other proteins, co-factors, transcriptional factors, chromatin remodeling components, non-coding RNAs and even the extracellular matrix that assembles the Hox complexes. The number of interacting partners continues to grow with diverse components and more transcriptional factors than initially thought. Hox complexes present many activities, but their molecular mechanisms to modulate their target genes remain unsolved. RESULTS In this paper we showed the protein-protein interaction of Antp with Ubx through the homeodomain using BiFC in Drosophila. Analysis of Antp-deletional mutants showed that AntpHD helixes 1 and 2 are required for the interaction with Ubx. Also, we found a novel interaction of Ubx with TBP, in which the PolyQ domain of TBP is required for the interaction. Moreover, we also detected the formation of two new trimeric complexes of Antp with Ubx, TBP and Exd using BiFC-FRET; these proteins, however, do not form a trimeric interaction with BIP2 or TFIIEβ. The novel trimeric complexes reduced Antp transcriptional activity, indicating that they could confer specificity for repression. CONCLUSIONS Our results increase the number of transcriptional factors in the Antp and Ubx interactomes that form two novel trimeric complexes with TBP and Exd. We also report a new Ubx interaction with TBP. These novel interactions provide important clues of the dynamics of Hox-interacting complexes involved in transcriptional regulation, contributing to better understand Hox function.
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Affiliation(s)
- Alely Villarreal-Puente
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Claudia Altamirano-Torres
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Gustavo Jiménez-Mejía
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Carolina Hernández-Bautista
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Rubén Montalvo-Méndez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Martha Vázquez
- Instituto de Biotecnología, Departamento de Fisiología Molecular y Genética del Desarrollo, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Instituto de Biotecnología, Departamento de Fisiología Molecular y Genética del Desarrollo, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Diana Reséndez-Pérez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México.
- Facultad de Ciencias Biológicas, Departamento de Biología Celular y Genética, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México.
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3
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Ritesh KC, de Boer RL, Lin M, Jeannotte L, Philippidou P. Multimodal Hox5 activity generates motor neuron diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579338. [PMID: 38370781 PMCID: PMC10871347 DOI: 10.1101/2024.02.08.579338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Motor neurons (MNs) are the final output of circuits driving fundamental behaviors, such as respiration and locomotion. Hox proteins are essential in generating the MN diversity required for accomplishing these functions, but the transcriptional mechanisms that enable Hox paralogs to assign distinct MN subtype identities despite their promiscuous DNA binding motif are not well understood. Here we show that Hoxa5 controls chromatin accessibility in all mouse spinal cervical MN subtypes and engages TALE co-factors to directly bind and regulate subtype-specific genes. We identify a paralog-specific interaction of Hoxa5 with the phrenic MN-specific transcription factor Scip and show that heterologous expression of Hoxa5 and Scip is sufficient to suppress limb-innervating MN identity. We also demonstrate that phrenic MN identity is stable after Hoxa5 downregulation and identify Klf proteins as potential regulators of phrenic MN maintenance. Our data identify multiple modes of Hoxa5 action that converge to induce and maintain MN identity.
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Affiliation(s)
- K C Ritesh
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Raquel López de Boer
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Minshan Lin
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry & Pathology, Université Laval, Centre Recherche sur le Cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology), Québec, Canada
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
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4
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Rosales-Vega M, Reséndez-Pérez D, Vázquez M. Antennapedia: The complexity of a master developmental transcription factor. Genesis 2024; 62:e23561. [PMID: 37830148 DOI: 10.1002/dvg.23561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023]
Abstract
Hox genes encode transcription factors that play an important role in establishing the basic body plan of animals. In Drosophila, Antennapedia is one of the five genes that make up the Antennapedia complex (ANT-C). Antennapedia determines the identity of the second thoracic segment, known as the mesothorax. Misexpression of Antennapedia at different developmental stages changes the identity of the mesothorax, including the muscles, nervous system, and cuticle. In Drosophila, Antennapedia has two distinct promoters highly regulated throughout development by several transcription factors. Antennapedia proteins are found with other transcription factors in different ANTENNAPEDIA transcriptional complexes to regulate multiple subsets of target genes. In this review, we describe the different mechanisms that regulate the expression and function of Antennapedia and the role of this Hox gene in the development of Drosophila.
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Affiliation(s)
- Marco Rosales-Vega
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Diana Reséndez-Pérez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Muley VY. Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming. Methods Mol Biol 2024; 2719:199-225. [PMID: 37803120 DOI: 10.1007/978-1-0716-3461-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Transcription factors (TFs) bind to specific regions of DNA known as transcription factor binding sites (TFBSs) and modulate gene expression by interacting with the transcriptional machinery. TFBSs are typically located upstream of target genes, within a few thousand base pairs of the transcription start site. The binding of TFs to TFBSs influences the recruitment of the transcriptional machinery, thereby regulating gene transcription in a precise and specific manner. This chapter provides practical examples and case studies demonstrating the extraction of upstream gene regions from the genome, identification of TFBSs using PWMEnrich R/Bioconductor package, interpretation of results, and preparation of publication-ready figures and tables. The EOMES promoter is used as a case study for single DNA sequence analysis, revealing potential regulation by the LHX9-FOXP1 complex during embryonic development. Additionally, an example is presented on how to investigate TFBSs in the upstream regions of a group of genes, using a case study of differentially expressed genes in response to human parainfluenza virus type 1 (HPIV1) infection and interferon-beta. Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. The presented protocol is designed to be accessible to individuals with basic computer literacy. Understanding the interactions between TFs and TFBSs provides insights into the complex transcriptional regulatory networks that govern gene expression, with broad implications for several fields such as developmental biology, immunology, and disease research.
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Affiliation(s)
- Vijaykumar Yogesh Muley
- Independent Researcher, Hingoli, India
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
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6
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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7
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Khodursky S, Zheng EB, Svetec N, Durkin SM, Benjamin S, Gadau A, Wu X, Zhao L. The evolution and mutational robustness of chromatin accessibility in Drosophila. Genome Biol 2023; 24:232. [PMID: 37845780 PMCID: PMC10578003 DOI: 10.1186/s13059-023-03079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates the understanding of the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different species and tissues of Drosophila. RESULTS We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that our models generalize well across substantially evolutionarily diverged species of insects, implying that the sequence determinants of accessibility are highly conserved. Using our model to examine species-specific gains in accessibility, we find evidence suggesting that these regions may be ancestrally poised for evolution. Using in silico mutagenesis, we show that accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that accessibility is mutationally robust. Subsequently, we show that accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. Conversely, simulations under strong selection demonstrate that accessibility can be extremely malleable despite its robustness. Finally, we identify motifs predictive of accessibility, recovering both novel and previously known motifs. CONCLUSIONS These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks to explore fundamental questions in regulatory genomics and evolution.
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Affiliation(s)
- Samuel Khodursky
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Eric B Zheng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Sylvia M Durkin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
- Present Address: Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Sigi Benjamin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Alice Gadau
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Xia Wu
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA.
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8
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Khodursky S, Zheng EB, Svetec N, Durkin SM, Benjamin S, Gadau A, Wu X, Zhao L. The evolution and mutational robustness of chromatin accessibility in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546587. [PMID: 37425760 PMCID: PMC10327059 DOI: 10.1101/2023.06.26.546587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The evolution of regulatory regions in the genome plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems has made it difficult to understand the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different tissues of Drosophila. We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that a model trained in one species has nearly identical performance when tested in another species, implying that the sequence determinants of accessibility are highly conserved. Indeed, model performance remains excellent even in distantly-related species. By using our model to examine species-specific gains in chromatin accessibility, we find that their orthologous inaccessible regions in other species have surprisingly similar model outputs, suggesting that these regions may be ancestrally poised for evolution. We then use in silico saturation mutagenesis to reveal evidence of selective constraint acting specifically on inaccessible chromatin regions. We further show that chromatin accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that chromatin accessibility is mutationally robust. Subsequently, we demonstrate that chromatin accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. We also perform in silico evolution experiments under the regime of strong selection and weak mutation (SSWM) and show that chromatin accessibility can be extremely malleable despite its mutational robustness. However, selection acting in different directions in a tissue-specific manner can substantially slow adaptation. Finally, we identify motifs predictive of chromatin accessibility and recover motifs corresponding to known chromatin accessibility activators and repressors. These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks as tools to answer fundamental questions in regulatory genomics and evolution.
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Affiliation(s)
- Samuel Khodursky
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
- These authors contributed equally
| | - Eric B Zheng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
- These authors contributed equally
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Sylvia M Durkin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
- Current Address: Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Sigi Benjamin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Alice Gadau
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Xia Wu
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
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Goslin K, Finocchio A, Wellmer F. Floral Homeotic Factors: A Question of Specificity. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051128. [PMID: 36903987 PMCID: PMC10004826 DOI: 10.3390/plants12051128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 05/27/2023]
Abstract
MADS-domain transcription factors are involved in the control of a multitude of processes in eukaryotes, and in plants, they play particularly important roles during reproductive development. Among the members of this large family of regulatory proteins are the floral organ identity factors, which specify the identities of the different types of floral organs in a combinatorial manner. Much has been learned over the past three decades about the function of these master regulators. For example, it has been shown that they have similar DNA-binding activities and that their genome-wide binding patterns exhibit large overlaps. At the same time, it appears that only a minority of binding events lead to changes in gene expression and that the different floral organ identity factors have distinct sets of target genes. Thus, binding of these transcription factors to the promoters of target genes alone may not be sufficient for their regulation. How these master regulators achieve specificity in a developmental context is currently not well understood. Here, we review what is known about their activities and highlight open questions that need to be addressed to gain more detailed insights into the molecular mechanisms underlying their functions. We discuss evidence for the involvement of cofactors as well as the results from studies on transcription factors in animals that may be instructive for a better understanding of how the floral organ identity factors achieve regulatory specificity.
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10
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Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness. Cell Rep 2022; 41:111832. [PMID: 36516782 PMCID: PMC9764455 DOI: 10.1016/j.celrep.2022.111832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
How histone modifications affect animal development remains difficult to ascertain. Despite the prevalence of histone 3 lysine 4 monomethylation (H3K4me1) on enhancers, hypomethylation appears to have minor effects on phenotype and viability. Here, we genetically reduce H3K4me1 deposition in Drosophila melanogaster and find that hypomethylation reduces transcription factor enrichment in nuclear microenvironments, disrupts gene expression, and reduces phenotypic robustness. Using a developmental phenomics approach, we find changes in morphology, metabolism, behavior, and offspring production. However, many phenotypic changes are only detected when hypomethylated flies develop outside of standard laboratory environments or with specific genetic backgrounds. Therefore, quantitative phenomics measurements can unravel how pleiotropic modulators of gene expression affect developmental robustness under conditions resembling the natural environments of a species.
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11
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The pioneering function of the hox transcription factors. Semin Cell Dev Biol 2022:S1084-9521(22)00354-8. [PMID: 36517345 DOI: 10.1016/j.semcdb.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/13/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Ever since the discovery that the Hox family of transcription factors establish morphological diversity in the developing embryo, major efforts have been directed towards understanding Hox-dependent patterning. This has led to important discoveries, notably on the mechanisms underlying the collinear expression of Hox genes and Hox binding specificity. More recently, several studies have provided evidence that Hox factors have the capacity to bind their targets in an inaccessible chromatin context and trigger the switch to an accessible, transcriptional permissive, chromatin state. In this review, we provide an overview of the evidences supporting that Hox factors behave as pioneer factors and discuss the potential mechanisms implicated in Hox pioneer activity as well as the significance of this functional property in Hox-dependent patterning.
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12
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Pinto PB, Domsch K, Lohmann I. Hox function and specificity – A tissue centric view. Semin Cell Dev Biol 2022:S1084-9521(22)00353-6. [PMID: 36517344 DOI: 10.1016/j.semcdb.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Since their discovery, the Hox genes, with their incredible power to reprogram the identity of complete body regions, a phenomenon called homeosis, have captured the fascination of many biologists. Recent research has provided new insights into the function of Hox proteins in different germ layers and the mechanisms they employ to control tissue morphogenesis. We focus in this review on the ectoderm and mesoderm to highlight new findings and discuss them with regards to established concepts of Hox target gene regulation. Furthermore, we highlight the molecular mechanisms involved the transcriptional repression of specific groups of Hox target genes, and summarize the role of Hox mediated gene silencing in tissue development. Finally, we reflect on recent findings identifying a large number of tissue-specific Hox interactor partners, which open up new avenues and directions towards a better understanding of Hox function and specificity in different tissues.
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13
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Jiménez-Mejía G, Montalvo-Méndez R, Hernández-Bautista C, Altamirano-Torres C, Vázquez M, Zurita M, Reséndez-Pérez D. Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity. Hereditas 2022; 159:23. [PMID: 35637493 PMCID: PMC9150345 DOI: 10.1186/s41065-022-00239-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hox proteins finely coordinate antero-posterior axis during embryonic development and through their action specific target genes are expressed at the right time and space to determine the embryo body plan. As master transcriptional regulators, Hox proteins recognize DNA through the homeodomain (HD) and interact with a multitude of proteins, including general transcription factors and other cofactors. HD binding specificity increases by protein–protein interactions with a diversity of cofactors that outline the Hox interactome and determine the transcriptional landscape of the selected target genes. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but its precise mechanism remains to be elucidated. Results Here we report Antennapedia (Antp) Hox protein–protein interaction with the TATA-binding protein (TBP) and the formation of novel trimeric complexes with TFIIEβ and Extradenticle (Exd), as well as its participation in transcriptional regulation. Using Bimolecular Fluorescence Complementation (BiFC), we detected the interaction of Antp-TBP and, in combination with Förster Resonance Energy Transfer (BiFC-FRET), the formation of the trimeric complex with TFIIEβ and Exd in living cells. Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. The trimeric complexes of Antp-TBP with TFIIEβ and Exd were validated using different Antp mutations to disrupt the trimeric complexes. Interestingly, the trimeric complex Antp-TBP-TFIIEβ significantly increased the transcriptional activity of Antp, whereas Exd diminished its transactivation. Conclusions Our findings provide important insights into the Antp interactome with the direct interaction of Antp with TBP and the two new trimeric complexes with TFIIEβ and Exd. These novel interactions open the possibility to analyze promoter function and gene expression to measure transcription factor binding dynamics at target sites throughout the genome. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00239-8.
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Buffry AD, McGregor AP. Micromanagement of Drosophila Post-Embryonic Development by Hox Genes. J Dev Biol 2022; 10:13. [PMID: 35225966 PMCID: PMC8883937 DOI: 10.3390/jdb10010013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/06/2022] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Hox genes function early in development to determine regional identity in animals. Consequently, the loss or gain of Hox gene expression can change this identity and cause homeotic transformations. Over 20 years ago, it was observed that the role of Hox genes in patterning animal body plans involves the fine-scale regulation of cell fate and identity during development, playing the role of 'micromanagers' as proposed by Michael Akam in key perspective papers. Therefore, as well as specifying where structures develop on animal bodies, Hox genes can help to precisely sculpt their morphology. Here, we review work that has provided important insights about the roles of Hox genes in influencing cell fate during post-embryonic development in Drosophila to regulate fine-scale patterning and morphology. We also explore how this is achieved through the regulation of Hox genes, specific co-factors and their complex regulation of hundreds of target genes. We argue that further investigating the regulation and roles of Hox genes in Drosophila post-embryonic development has great potential for understanding gene regulation, cell fate and phenotypic differentiation more generally.
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15
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Cain B, Gebelein B. Mechanisms Underlying Hox-Mediated Transcriptional Outcomes. Front Cell Dev Biol 2021; 9:787339. [PMID: 34869389 PMCID: PMC8635045 DOI: 10.3389/fcell.2021.787339] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Metazoans differentially express multiple Hox transcription factors to specify diverse cell fates along the developing anterior-posterior axis. Two challenges arise when trying to understand how the Hox transcription factors regulate the required target genes for morphogenesis: First, how does each Hox factor differ from one another to accurately activate and repress target genes required for the formation of distinct segment and regional identities? Second, how can a Hox factor that is broadly expressed in many tissues within a segment impact the development of specific organs by regulating target genes in a cell type-specific manner? In this review, we highlight how recent genomic, interactome, and cis-regulatory studies are providing new insights into answering these two questions. Collectively, these studies suggest that Hox factors may differentially modify the chromatin of gene targets as well as utilize numerous interactions with additional co-activators, co-repressors, and sequence-specific transcription factors to achieve accurate segment and cell type-specific transcriptional outcomes.
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Affiliation(s)
- Brittany Cain
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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16
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Blanco MA, Sykes DB, Gu L, Wu M, Petroni R, Karnik R, Wawer M, Rico J, Li H, Jacobus WD, Jambhekar A, Cheloufi S, Meissner A, Hochedlinger K, Scadden DT, Shi Y. Chromatin-state barriers enforce an irreversible mammalian cell fate decision. Cell Rep 2021; 37:109967. [PMID: 34758323 DOI: 10.1016/j.celrep.2021.109967] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/12/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Stem and progenitor cells have the capacity to balance self-renewal and differentiation. Hematopoietic myeloid progenitors replenish more than 25 billion terminally differentiated neutrophils every day under homeostatic conditions and can increase this output in response to stress or infection. At what point along the spectrum of maturation do progenitors lose capacity for self-renewal and become irreversibly committed to differentiation? Using a system of conditional myeloid development that can be toggled between self-renewal and differentiation, we interrogate determinants of this "point of no return" in differentiation commitment. Irreversible commitment is due primarily to loss of open regulatory site access and disruption of a positive feedback transcription factor activation loop. Restoration of the transcription factor feedback loop extends the window of cell plasticity and alters the point of no return. These findings demonstrate how the chromatin state enforces and perpetuates cell fate and identify potential avenues for manipulating cell identity.
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Affiliation(s)
- M Andrés Blanco
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Lei Gu
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Cardiopulmonary Institute (CPI), Bad Nauheim, Germany; Epigenetics Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mengjun Wu
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ricardo Petroni
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul Karnik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Mathias Wawer
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua Rico
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haitao Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William D Jacobus
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ashwini Jambhekar
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Sihem Cheloufi
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Konrad Hochedlinger
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Department of Molecular Biology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, Oxford, UK.
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17
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Singh NP. Gene regulation: Context is everything. Curr Biol 2021; 31:R1115-R1117. [PMID: 34637709 DOI: 10.1016/j.cub.2021.08.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
How transcription factors regulate a distinct set of target genes in different cell types is a fundamental question. A new study demonstrates how Ultrabithorax, a Hox transcription factor, acts as both a repressor and an activator in a cell type-specific manner to alter chromatin accessibility and gene regulation.
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Affiliation(s)
- Narendra P Singh
- Stowers Institute for Medical Research, Kansas City, MI 64110, USA.
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18
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Loker R, Sanner JE, Mann RS. Cell-type-specific Hox regulatory strategies orchestrate tissue identity. Curr Biol 2021; 31:4246-4255.e4. [PMID: 34358443 PMCID: PMC8511240 DOI: 10.1016/j.cub.2021.07.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 07/13/2021] [Indexed: 01/25/2023]
Abstract
Hox proteins are homeodomain transcription factors that diversify serially homologous segments along the animal body axis, as revealed by the classic bithorax phenotype of Drosophila melanogaster, in which mutations in Ultrabithorax (Ubx) transform the third thoracic segment into the likeness of the second thoracic segment. To specify segment identity, we show that Ubx both increases and decreases chromatin accessibility, coinciding with its dual role as both an activator and repressor of transcription. However, the choice of transcriptional activity executed by Ubx is spatially regulated and depends on the availability of cofactors, with Ubx acting as a repressor in some populations and as an activator in others. Ubx-mediated changes to chromatin accessibility positively and negatively affect the binding of Scalloped (Sd), a transcription factor that is required for appendage development in both segments. These findings illustrate how a single Hox protein can modify complex gene regulatory networks to transform the identity of an entire tissue.
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Affiliation(s)
- Ryan Loker
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Jordyn E Sanner
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Department of Neuroscience, Columbia University Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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19
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A TALE/HOX code unlocks WNT signalling response towards paraxial mesoderm. Nat Commun 2021; 12:5136. [PMID: 34446717 PMCID: PMC8390530 DOI: 10.1038/s41467-021-25370-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/04/2021] [Indexed: 12/02/2022] Open
Abstract
One fundamental yet unresolved question in biology remains how cells interpret the same signalling cues in a context-dependent manner resulting in lineage specification. A key step for decoding signalling cues is the establishment of a permissive chromatin environment at lineage-specific genes triggering transcriptional responses to inductive signals. For instance, bipotent neuromesodermal progenitors (NMPs) are equipped with a WNT-decoding module, which relies on TCFs/LEF activity to sustain both NMP expansion and paraxial mesoderm differentiation. However, how WNT signalling activates lineage specific genes in a temporal manner remains unclear. Here, we demonstrate that paraxial mesoderm induction relies on the TALE/HOX combinatorial activity that simultaneously represses NMP genes and activates the differentiation program. We identify the BRACHYURY-TALE/HOX code that destabilizes the nucleosomes at WNT-responsive regions and establishes the permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1, unlocking the WNT-mediated transcriptional program that drives NMPs towards the paraxial mesodermal fate. Cells in the developing embryo interpret WNT signalling with context-dependence, but the mechanism decoding these cues is unclear. Here, the authors show that combinatorial TALE/HOX activity destabilizes nucleosomes at WNT-responsive regions to activate paraxial mesodermal genes.
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20
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The Hox protein conundrum: The "specifics" of DNA binding for Hox proteins and their partners. Dev Biol 2021; 477:284-292. [PMID: 34102167 PMCID: PMC8846413 DOI: 10.1016/j.ydbio.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA interactions. It is crucial to study transcription factor binding by incorporating components of more complex, multi-protein interactions in concert with small changes in binding motifs that can significantly impact DNA binding specificity and subsequent alterations in gene expression. To incorporate the multiple elements that can determine HOX protein binding specificity, we propose a more integrative Cooperative Binding model.
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21
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Kishan KC, Subramanya SK, Li R, Cui F. Machine learning predicts nucleosome binding modes of transcription factors. BMC Bioinformatics 2021; 22:166. [PMID: 33784978 PMCID: PMC8008688 DOI: 10.1186/s12859-021-04093-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/18/2021] [Indexed: 11/24/2022] Open
Abstract
Background Most transcription factors (TFs) compete with nucleosomes to gain access to their cognate binding sites. Recent studies have identified several TF-nucleosome interaction modes including end binding (EB), oriented binding, periodic binding, dyad binding, groove binding, and gyre spanning. However, there are substantial experimental challenges in measuring nucleosome binding modes for thousands of TFs in different species. Results We present a computational prediction of the binding modes based on TF protein sequences. With a nested cross-validation procedure, our model outperforms several fine-tuned off-the-shelf machine learning (ML) methods in the multi-label classification task. Our binary classifier for the EB mode performs better than these ML methods with the area under precision-recall curve achieving 75%. The end preference of most TFs is consistent with low nucleosome occupancy around their binding site in GM12878 cells. The nucleosome occupancy data is used as an alternative dataset to confirm the superiority of our EB classifier. Conclusions We develop the first ML-based approach for efficient and comprehensive analysis of nucleosome binding modes of TFs. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04093-9.
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Affiliation(s)
- K C Kishan
- Golisano College of Computing and Information Sciences, Rochester Institute of Technology, 20 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Sridevi K Subramanya
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 1 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Rui Li
- Golisano College of Computing and Information Sciences, Rochester Institute of Technology, 20 Lomb Memorial Drive, Rochester, NY, 14623, USA
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 1 Lomb Memorial Drive, Rochester, NY, 14623, USA.
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22
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Bridoux L, Zarrineh P, Mallen J, Phuycharoen M, Latorre V, Ladam F, Losa M, Baker SM, Sagerstrom C, Mace KA, Rattray M, Bobola N. HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation. PLoS Genet 2020; 16:e1009162. [PMID: 33315856 PMCID: PMC7769617 DOI: 10.1371/journal.pgen.1009162] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 12/28/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022] Open
Abstract
Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.
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Affiliation(s)
- Laure Bridoux
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Peyman Zarrineh
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Joshua Mallen
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Mike Phuycharoen
- Department of Computer Science, University of Manchester, Manchester, United Kingdom
| | - Victor Latorre
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Frank Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusets, United States of America
| | - Marta Losa
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Syed Murtuza Baker
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Charles Sagerstrom
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusets, United States of America
| | - Kimberly A. Mace
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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23
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Bulajić M, Srivastava D, Dasen JS, Wichterle H, Mahony S, Mazzoni EO. Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns. Development 2020; 147:dev194761. [PMID: 33028607 PMCID: PMC7710020 DOI: 10.1242/dev.194761] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022]
Abstract
Although Hox genes encode for conserved transcription factors (TFs), they are further divided into anterior, central and posterior groups based on their DNA-binding domain similarity. The posterior Hox group expanded in the deuterostome clade and patterns caudal and distal structures. We aimed to address how similar Hox TFs diverge to induce different positional identities. We studied Hox TF DNA-binding and regulatory activity during an in vitro motor neuron differentiation system that recapitulates embryonic development. We found diversity in the genomic binding profiles of different Hox TFs, even among the posterior group paralogs that share similar DNA-binding domains. These differences in genomic binding were explained by differing abilities to bind to previously inaccessible sites. For example, the posterior group HOXC9 had a greater ability to bind occluded sites than the posterior HOXC10, producing different binding patterns and driving differential gene expression programs. From these results, we propose that the differential abilities of posterior Hox TFs to bind to previously inaccessible chromatin drive patterning diversification.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Milica Bulajić
- Department of Biology, New York University, New York, NY 10003, USA
| | - Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jeremy S Dasen
- Neuroscience Institute, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neuroscience, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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24
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Martin PC, Zabet NR. Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. Comput Struct Biotechnol J 2020; 18:3590-3605. [PMID: 33304457 PMCID: PMC7708957 DOI: 10.1016/j.csbj.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 01/22/2023] Open
Abstract
Transcription Factors (TFs) bind to DNA and control activity of target genes. Here, we present ChIPanalyser, a user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of TFs. We focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). While CTCF preferentially binds only to a subset of high affinity sites located mainly in open chromatin, BEAF-32 binds to most of its high affinity binding sites available in open chromatin. In contrast, su(Hw) binds to both open chromatin and also partially closed chromatin. Most importantly, differences in TF binding profiles between cell lines for these TFs are mainly driven by differences in DNA accessibility and not by differences in TF concentrations between cell lines. Finally, we investigated binding of Hox TFs in Drosophila and found that Ubx binds only in open chromatin, while Abd-B and Dfd are capable to bind in both open and partially closed chromatin. Overall, our results show that TFs display different binding mechanisms and that our model is able to recapitulate their specific binding behaviour.
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Affiliation(s)
- Patrick C.N. Martin
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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25
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Gurska D, Vargas Jentzsch IM, Panfilio KA. Unexpected mutual regulation underlies paralogue functional diversification and promotes epithelial tissue maturation in Tribolium. Commun Biol 2020; 3:552. [PMID: 33020571 PMCID: PMC7536231 DOI: 10.1038/s42003-020-01250-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 08/21/2020] [Indexed: 02/03/2023] Open
Abstract
Insect Hox3/zen genes represent an evolutionary hotspot for changes in function and copy number. Single orthologues are required either for early specification or late morphogenesis of the extraembryonic tissues, which protect the embryo. The tandemly duplicated zen paralogues of the beetle Tribolium castaneum present a unique opportunity to investigate both functions in a single species. We dissect the paralogues' expression dynamics (transcript and protein) and transcriptional targets (RNA-seq after RNAi) throughout embryogenesis. We identify an unexpected role of Tc-Zen2 in repression of Tc-zen1, generating a negative feedback loop that promotes developmental progression. Tc-Zen2 regulation is dynamic, including within co-expressed multigene loci. We also show that extraembryonic development is the major event within the transcriptional landscape of late embryogenesis and provide a global molecular characterization of the extraembryonic serosal tissue. Altogether, we propose that paralogue mutual regulation arose through multiple instances of zen subfunctionalization, leading to their complementary extant roles.
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Affiliation(s)
- Daniela Gurska
- Institute of Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Iris M Vargas Jentzsch
- Institute of Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Kristen A Panfilio
- Institute of Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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26
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Tsai A, Galupa R, Crocker J. Robust and efficient gene regulation through localized nuclear microenvironments. Development 2020; 147:147/19/dev161430. [PMID: 33020073 DOI: 10.1242/dev.161430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Developmental enhancers drive gene expression in specific cell types during animal development. They integrate signals from many different sources mediated through the binding of transcription factors, producing specific responses in gene expression. Transcription factors often bind low-affinity sequences for only short durations. How brief, low-affinity interactions drive efficient transcription and robust gene expression is a central question in developmental biology. Localized high concentrations of transcription factors have been suggested as a possible mechanism by which to use these enhancer sites effectively. Here, we discuss the evidence for such transcriptional microenvironments, mechanisms for their formation and the biological consequences of such sub-nuclear compartmentalization for developmental decisions and evolution.
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Affiliation(s)
- Albert Tsai
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Rafael Galupa
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin Crocker
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Gonçalves CS, Le Boiteux E, Arnaud P, Costa BM. HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours. Cell Mol Life Sci 2020; 77:3797-3821. [PMID: 32239260 PMCID: PMC11105007 DOI: 10.1007/s00018-020-03508-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
HOX genes encode a family of evolutionarily conserved homeodomain transcription factors that are crucial both during development and adult life. In humans, 39 HOX genes are arranged in four clusters (HOXA, B, C, and D) in chromosomes 7, 17, 12, and 2, respectively. During embryonic development, particular epigenetic states accompany their expression along the anterior-posterior body axis. This tightly regulated temporal-spatial expression pattern reflects their relative chromosomal localization, and is critical for normal embryonic brain development when HOX genes are mainly expressed in the hindbrain and mostly absent in the forebrain region. Epigenetic marks, mostly polycomb-associated, are dynamically regulated at HOX loci and regulatory regions to ensure the finely tuned HOX activation and repression, highlighting a crucial epigenetic plasticity necessary for homeostatic development. HOX genes are essentially absent in healthy adult brain, whereas they are detected in malignant brain tumours, namely gliomas, where HOX genes display critical roles by regulating several hallmarks of cancer. Here, we review the major mechanisms involved in HOX genes (de)regulation in the brain, from embryonic to adult stages, in physiological and oncologic conditions. We focus particularly on the emerging causes of HOX gene deregulation in glioma, as well as on their functional and clinical implications.
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Affiliation(s)
- Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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28
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Majidi SP, Reddy NC, Moore MJ, Chen H, Yamada T, Andzelm MM, Cherry TJ, Hu LS, Greenberg ME, Bonni A. Chromatin Environment and Cellular Context Specify Compensatory Activity of Paralogous MEF2 Transcription Factors. Cell Rep 2020; 29:2001-2015.e5. [PMID: 31722213 PMCID: PMC6874310 DOI: 10.1016/j.celrep.2019.10.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/04/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Compensation among paralogous transcription factors (TFs) confers genetic robustness of cellular processes, but how TFs dynamically respond to paralog depletion on a genome-wide scale in vivo remains incompletely understood. Using single and double conditional knockout of myocyte enhancer factor 2 (MEF2) family TFs in granule neurons of the mouse cerebellum, we find that MEF2A and MEF2D play functionally redundant roles in cerebellar-dependent motor learning. Although both TFs are highly expressed in granule neurons, transcriptomic analyses show MEF2D is the predominant genomic regulator of gene expression in vivo. Strikingly, genome-wide occupancy analyses reveal upon depletion of MEF2D, MEF2A occupancy robustly increases at a subset of sites normally bound to MEF2D. Importantly, sites experiencing compensatory MEF2A occupancy are concentrated within open chromatin and undergo functional compensation for genomic activation and gene expression. Finally, motor activity induces a switch from non-compensatory to compensatory MEF2-dependent gene regulation. These studies uncover genome-wide functional interdependency between paralogous TFs in the brain. Majidi et al. study how transcription factors respond to paralog depletion by conditionally depleting MEF2A and MEF2D in mouse cerebellum. Depletion of MEF2D induces functionally compensatory genomic occupancy by MEF2A. Compensation occurs within accessible chromatin in a context-dependent manner. This study explores the interdependency between paralogous transcription factors.
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Affiliation(s)
- Shahriyar P Majidi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; MD-PhD Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Naveen C Reddy
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Milena M Andzelm
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9(th) Ave., Seattle, WA 98101, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda S Hu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA.
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29
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MiR-126 Regulates Properties of SOX9 + Liver Progenitor Cells during Liver Repair by Targeting Hoxb6. Stem Cell Reports 2020; 15:706-720. [PMID: 32763157 PMCID: PMC7486193 DOI: 10.1016/j.stemcr.2020.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
Liver progenitor cells (LPCs) have a remarkable contribution to the hepatocytes and ductal cells when normal hepatocyte proliferation is severely impaired. As a biomarker for LPCs, Sry-box 9 (Sox9) plays critical roles in liver homeostasis and repair in response to injury. However, the regulation mechanism of Sox9 in liver physiological and pathological state remains unknown. In this study, we found that miR-126 positively regulated the expression of Sox9, the proliferation and differentiation of SOX9+ LPCs by suppressing the translation of homeobox b6 (Hoxb6). As a transcription factor, HOXB6 directly binds to the promoter of Sox9 to inhibit Sox9 expression, resulting in the destruction of the properties of SOX9+ LPCs in CCl4-induced liver injury. These findings revealed the role of miR-126 in regulating SOX9+ LPCs fate by targeting Hoxb6 in liver injury repair. Our findings suggest the potential role of miR-126 as a nucleic acid therapy drug target for liver failure. miR-126 promotes Sox9 expression and maintains SOX9+ LPCs in adult mouse livers HOXB6 suppresses properties of SOX9+ LPCs in chronic liver injury model HOXB6 negatively regulates Sox9 trans-activity miR-126 regulates properties of SOX9+ LPCs by targeting Hoxb6
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30
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HOX13-dependent chromatin accessibility underlies the transition towards the digit development program. Nat Commun 2020; 11:2491. [PMID: 32427842 PMCID: PMC7237422 DOI: 10.1038/s41467-020-16317-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/20/2020] [Indexed: 12/05/2022] Open
Abstract
Hox genes encode transcription factors (TFs) that establish morphological diversity in the developing embryo. The similar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent genetic programs. The influence of the chromatin context on HOX binding specificity remains elusive. Here, we used the developing limb as a model system to compare the binding specificity of HOXA13 and HOXD13 (HOX13 hereafter), which are required for digit formation, and HOXA11, involved in forearm/leg development. We find that upon ectopic expression in distal limb buds, HOXA11 binds sites normally HOX13-specific. Importantly, these sites are loci whose chromatin accessibility relies on HOX13. Moreover, we show that chromatin accessibility specific to the distal limb requires HOX13 function. Based on these results, we propose that HOX13 TFs pioneer the distal limb-specific chromatin accessibility landscape for the proper implementation of the distal limb developmental program. Pioneer factors direct cell fate through switching inaccessible chromatin to an accessible state at specific target enhancers. Here the authors show that HOX13 transcription factors have a pioneer activity which is required for the proper implementation of the distal limb developmental program.
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31
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Cao Y, Wang X, Tang L, Li Y, Song X, Liu X, Li M, Chen F, Wan H. Engrailed-2 promotes a malignant phenotype of esophageal squamous cell carcinoma through upregulating the expression of pro-oncogenic genes. PeerJ 2020; 8:e8662. [PMID: 32117645 PMCID: PMC7036277 DOI: 10.7717/peerj.8662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/29/2020] [Indexed: 01/09/2023] Open
Abstract
Background A number of homeobox genes have been implicated in the development of various cancers. However, the role of engrailed 2 (EN2), a member of the homeobox gene superfamily, in esophageal squamous cell carcinoma (ESCC) remains unknown. Methods The expression of EN2 was examined using quantitative real-time PCR and immunohistochemistry. A stable cell line was established to express exogenous EN2 using a lentivirus system. The malignant phenotype was analyzed with proliferation, clonogenicity, wound-healing and invasion assays. The CRISPR/Cas9 system was adopted to deplete endogenous EN2. RNA profiling was performed using gene expression microarray. The ShRNA-mediated method was used to knock down the expression of SPARC. The structure-function relationship was determined using site-directed mutagenesis. Results EN2 is highly expressed in ESCC. The malignant phenotype of the ESCC cell line was amplified by an overexpression of EN2 but was attenuated by a disruption of EN2. RNA profiling analysis revealed that distinct sets of genes were modulated by the expression of EN2 in various ESCC cell lines and oncogenes were among these. EN2 greatly increased the expression of SPARC in Eca109. Site-directed mutagenesis revealed that the induction of SPARC was closely correlated with the protumor function of EN2. ShRNA-mediated knockdown of SPARC attenuated the malignant phenotype of EN2-infected cells. These data suggest that SPARC is crucial for mediating the protumor function of EN2. Discussion EN2 has an oncogenic function in ESCC that is mediated by upregulating the expression of pro-oncogenic genes downstream. EN2 may potentially act as a diagnostic marker or therapeutic target for ESCC treatment in the future.
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Affiliation(s)
- Yong Cao
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xiaoyan Wang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Li Tang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yan Li
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xueqin Song
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xu Liu
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mingying Li
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Feng Chen
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Haisu Wan
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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