1
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Saibo NV, Maiti S, Boral S, Banerjee P, Kushwaha T, Inampudi KK, Goswami R, De S. The intrinsically disordered transactivation region of HOXA9 regulates its function by auto-inhibition of its DNA-binding activity. Int J Biol Macromol 2024; 273:132704. [PMID: 38825283 DOI: 10.1016/j.ijbiomac.2024.132704] [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] [Received: 11/15/2023] [Revised: 02/19/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
HOXA9 transcription factor is expressed in hematopoietic stem cells and is involved in the regulation of their differentiation and maturation to various blood cells. HOXA9 is linked to various leukemia and is a marker for poor prognosis of acute myeloid leukemia (AML). This protein has a conserved DNA-binding homeodomain and a transactivation domain. We show that this N-terminal transactivation domain is intrinsically disordered and inhibits DNA-binding by the homeodomain. Using NMR spectroscopy and molecular dynamics simulation, we show that the hexapeptide 197AANWLH202 in the disordered region transiently occludes the DNA-binding interface. The hexapeptide also forms a rigid segment, as determined by NMR dynamics, in an otherwise flexible disordered region. Interestingly, this hexapeptide is known to mediate the interaction of HOXA9 and its TALE partner proteins, such as PBX1, and help in cooperative DNA binding. Mutation of tryptophan to alanine in the hexapeptide abrogates the DNA-binding auto-inhibition. We propose that the disordered transactivation region plays a dual role in the regulation of HOXA9 function. In the absence of TALE partners, it inhibits DNA binding, and in the presence of TALE partners it interacts with the TALE protein and facilitates the cooperative DNA binding by the HOX-TALE complex.
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Affiliation(s)
- Nikita V Saibo
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Snigdha Maiti
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Soumendu Boral
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Puja Banerjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Ritobrata Goswami
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB 721302, India.
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2
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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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3
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Yang M, Tang Y, Zhu P, Lu H, Wan X, Guo Q, Xiao L, Liu C, Guo L, Liu W, Yang Y. The advances of E2A-PBX1 fusion in B-cell acute lymphoblastic Leukaemia. Ann Hematol 2023:10.1007/s00277-023-05595-7. [PMID: 38148344 DOI: 10.1007/s00277-023-05595-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
The E2A-PBX1 gene fusion is a common translocation in B-cell acute lymphoblastic leukaemia. Patients harbouring the E2A-PBX1 fusion gene typically exhibit an intermediate prognosis. Furthermore, minimal residual disease has unsatisfactory prognostic value in E2A-PBX1 B-cell acute lymphoblastic leukaemia. However, the mechanism of E2A-PBX1 in the occurrence and progression of B-cell acute lymphoblastic leukaemia is not well understood. Here, we mainly review the roles of E2A and PBX1 in the differentiation and development of B lymphocytes, the mechanism of E2A-PBX1 gene fusion in B-cell acute lymphoblastic leukaemia, and the potential therapeutic approaches.
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Affiliation(s)
- Mengting Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Yanhui Tang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Peng Zhu
- School of Pharmacy, Wannan Medical College, Wuhu, 241000, People's Republic of China
| | - Haiquan Lu
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaohong Wan
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Lan Xiao
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Chunyan Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Ling Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Wenjun Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
| | - You Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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Lee SY, Kim MY, Han JH, Park SS, Yun Y, Jee SC, Han JJ, Lee JH, Seok H, Choi BY. Ramifications of POU4F3 variants associated with autosomal dominant hearing loss in various molecular aspects. Sci Rep 2023; 13:12584. [PMID: 37537203 PMCID: PMC10400627 DOI: 10.1038/s41598-023-38272-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
POU4F3, a member of the POU family of transcription factors, commonly causes autosomal dominant deafness. Exome sequencing was used to identify four novel variants in POU4F3 (NM_002700.2), including c.564dupA: p.Ala189SerfsTer26, c.743T > C:p.Leu248Pro, c.879C > A:p.Phe293Leu, and c.952G > A:p.Val318Met, and diverse aspects of the molecular consequences of their protein expression, stability, subcellular localization, and transcriptional activity were investigated. The expression of three mutant proteins, encoded by missense variants, was reduced compared to the wild-type protein, demonstrating that the mutants were unstable and vulnerable to degradation. Additionally, all the mutant proteins had distinct subcellular localization patterns. A mutant protein carrying p.Ala189SerfsTer26, in which both mono- and bi-partite nuclear localization signals were disrupted, showed abnormal subcellular localization. Resultantly, all the mutant proteins significantly reduced the transcriptional activity required to regulate the downstream target gene expression. Furthermore, we identified the altered expression of 14 downstream target genes associated with inner ear development using patient-derived lymphoblastoid cell lines. There was a significant correlation of the expression profile between patient-derived cells and the cochlear hair cells, which provided a breakthrough for cases where the collection of human cochlear samples for transcriptome studies was unfeasible. This study expanded the genotypic spectrum of POU4F3 in DFNA15, and further refined the molecular mechanisms underlying POU4F3-associated DFNA15.
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Affiliation(s)
- Sang-Yeon Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Sang Soo Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yejin Yun
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung-Cheol Jee
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae Joon Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Heeyoung Seok
- Department of Transdisciplinary Research and Collaboration, Genomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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Maskalenka K, Alagöz G, Krueger F, Wright J, Rostovskaya M, Nakhuda A, Bendall A, Krueger C, Walker S, Scally A, Rugg-Gunn PJ. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells. Development 2023; 150:286291. [PMID: 36621005 PMCID: PMC10110494 DOI: 10.1242/dev.201155] [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: 07/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
Gene duplication events can drive evolution by providing genetic material for new gene functions, and they create opportunities for diverse developmental strategies to emerge between species. To study the contribution of duplicated genes to human early development, we examined the evolution and function of NANOGP1, a tandem duplicate of the transcription factor NANOG. We found that NANOGP1 and NANOG have overlapping but distinct expression profiles, with high NANOGP1 expression restricted to early epiblast cells and naïve-state pluripotent stem cells. Sequence analysis and epitope-tagging revealed that NANOGP1 is protein coding with an intact homeobox domain. The duplication that created NANOGP1 occurred earlier in primate evolution than previously thought and has been retained only in great apes, whereas Old World monkeys have disabled the gene in different ways, including homeodomain point mutations. NANOGP1 is a strong inducer of naïve pluripotency; however, unlike NANOG, it is not required to maintain the undifferentiated status of human naïve pluripotent cells. By retaining expression, sequence and partial functional conservation with its ancestral copy, NANOGP1 exemplifies how gene duplication and subfunctionalisation can contribute to transcription factor activity in human pluripotency and development.
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Affiliation(s)
| | - Gökberk Alagöz
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - Joshua Wright
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Asif Nakhuda
- Gene Targeting Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Christel Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Simon Walker
- Imaging Facility, Babraham Institute, Cambridge CB22 3AT, UK
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
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Lee SY, Soon Yoo H, Hee Han J, Hee Lee D, Soo Park S, Hwan Suh M, Ho Lee J, Oh SH, Choi BY. Novel Molecular Genetic Etiology of Asymmetric Hearing Loss: Autosomal-Dominant LMX1A Variants. Ear Hear 2022; 43:1698-1707. [PMID: 35711095 DOI: 10.1097/aud.0000000000001237] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Sensorineural hearing loss is the most common sensory disorder in humans. Genetic analyses have greatly increased our understanding of the pathogenic mechanisms in play. Thus, characterization of audiologic phenotypes by the genetic etiology may aid elucidation of the etiologies of certain types of inherited hearing loss. Further, delineation of specific audiologic phenotypes based on the genetic etiology aids our understanding of some types of inherited hearing loss in terms of the prediction of clinical course, revelation of genotype-phenotype correlations, and application of appropriate audiologic rehabilitation. Here, we describe the interesting audiologic characteristics of LMX1A -associated deafness, which revealed significant asymmetry between two ears. METHODS Among 728 probands of which genomic DNA went through exome sequencing regardless of any specific audiologic phenotypes, probands for which exome sequencing was performed and a causative LMX1A variant was found were all included. Five LMX1A -associated DFNA7 families (approximately 0.7%), the pedigrees of whom indicated autosomal-dominant hearing loss, were identified, and segregation was studied using Sanger sequencing. The affected individuals underwent comprehensive evaluations, including medical history reviews, physical examinations, imaging, and auditory phenotyping. We functionally characterized the novel LMX1A variants via computational structural modeling and luciferase reporter assays. RESULTS Among 728 probands of which genomic DNA went through exome sequencing, we identified four novel LMX1A heterozygous variants related to DFNA7 (c.622C>T:p.Arg208*, c.719A>G:p.Gln240Arg, c.721G>A:p.Val241Met, and c.887dup:p.Gln297Thrfs*41) and one harboring a de novo heterozygous missense LMX1A variant (c.595A>G;p.Arg199Gly) previously reported. It is important to note that asymmetric hearing loss was identified in all probands and most affected individuals, although the extent of asymmetry varied. Structural modeling revealed that the two missense variants, p.Gln240Arg and p.Val241Met, affected conserved residues of the homeodomain, thus attenuating LMX1A-DNA interaction. In addition, Arg208*-induced premature termination of translation destroyed the structure of the LMX1A protein, including the DNA-binding homeodomain, and p.Gln297Thrfs*41 led to the loss of the C-terminal helix involved in LIM2 domain interaction. Compared with the wild-type protein, all mutant LMX1A proteins had significantly reduced transactivation efficiency, indicating that the ability to elicit transcription of the downstream target genes of LMX1A was severely compromised. Thus, in line with the American College of Medical Genetics and Genomics guideline specified to genetic hearing loss, the four novel LMX1A variants were identified as "pathogenic" (p.Arg208* and p.Gln297Thrfs*41), "likely pathogenic" (p.Val241Met), and as a "variant of uncertain significance'' (p.Gln240Arg). CONCLUSION For the first time, we suggest that LMX1A is one of the candidate genes which, if altered, could be associated with dominantly inherited asymmetric hearing loss. We also expand the genotypic spectrum of disease-causing variants of LMX1A causing DFNA7 by doubling the number of LMX1A variants reported thus far in the literature.
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Affiliation(s)
- Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea
| | - Hyo Soon Yoo
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Dae Hee Lee
- CTCELLS, Inc., Yuseong-gu, Daejeon, South Korea
| | - Sang Soo Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Myung Hwan Suh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
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Belpaire M, Taminiau A, Geerts D, Rezsohazy R. HOXA1, a breast cancer oncogene. Biochim Biophys Acta Rev Cancer 2022; 1877:188747. [PMID: 35675857 DOI: 10.1016/j.bbcan.2022.188747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/27/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
More than 25 years ago, the first literature records mentioned HOXA1 expression in human breast cancer. A few years later, HOXA1 was confirmed as a proper oncogene in mammary tissue. In the following two decades, molecular data about the mode of action of the HOXA1 protein, the factors contributing to activate and maintain HOXA1 gene expression and the identity of its target genes have accumulated and provide a wider view on the association of this transcription factor to breast oncogenesis. Large-scale transcriptomic data gathered from wide cohorts of patients further allowed refining the relationship between breast cancer type and HOXA1 expression. Several recent reports have reviewed the connection between cancer hallmarks and the biology of HOX genes in general. Here we take HOXA1 as a paradigm and propose an extensive overview of the molecular data centered on this oncoprotein, from what its expression modulators, to the interactors contributing to its oncogenic activities, and to the pathways and genes it controls. The data converge to an intricate picture that answers questions on the multi-modality of its oncogene activities, point towards better understanding of breast cancer aetiology and thereby provides an appraisal for treatment opportunities.
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Affiliation(s)
- Magali Belpaire
- Animal Molecular and Cellular Biology Group (AMCB), Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium
| | - Arnaud Taminiau
- Animal Molecular and Cellular Biology Group (AMCB), Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium
| | - Dirk Geerts
- Heart Failure Research Center, Amsterdam University Medical Center (AMC), Universiteit van Amsterdam, Amsterdam, the Netherlands.
| | - René Rezsohazy
- Animal Molecular and Cellular Biology Group (AMCB), Louvain Institute of Biomolecular Science and Technology (LIBST), UCLouvain, Louvain-la-Neuve, Belgium.
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8
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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9
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Alerasool N, Leng H, Lin ZY, Gingras AC, Taipale M. Identification and functional characterization of transcriptional activators in human cells. Mol Cell 2022; 82:677-695.e7. [PMID: 35016035 DOI: 10.1016/j.molcel.2021.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. By combining interaction proteomics and chemical inhibitors, we delineate the preference of these transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct cofactors. We also identify potent transactivation domains among the hits and use AlphaFold2 to predict and experimentally validate interaction interfaces of two activation domains with BRD4. Finally, we show that many novel activators are partners in fusion events in tumors and functionally characterize a myofibroma-associated fusion between SRF and C3orf62, a potent p300-dependent activator. Our work provides a functional catalog of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
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Affiliation(s)
- Nader Alerasool
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - He Leng
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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Veiga RN, de Oliveira JC, Gradia DF. PBX1: a key character of the hallmarks of cancer. J Mol Med (Berl) 2021; 99:1667-1680. [PMID: 34529123 DOI: 10.1007/s00109-021-02139-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022]
Abstract
Pre-B-cell leukemia homeobox transcription factor 1 (PBX1) was first identified as part of a fusion protein resulting from the chromosomal translocation t(1;19) in pre-B cell acute lymphoblastic leukemias. Since then, PBX1 has been associated with important developmental programs, and its expression dysregulation has been related to multifactorial disorders, including cancer. As PBX1 overexpression in many cancers is correlated to poor prognosis, we sought to understand how this transcription factor contributes to carcinogenesis, and to organize PBX1's roles in the hallmarks of cancer. There is enough evidence to associate PBX1 with at least five hallmarks: sustaining proliferative signaling, activating invasion and metastasis, inducing angiogenesis, resisting cell death, and deregulating cellular energetics. The lack of studies investigating a possible role for PBX1 on the remaining hallmarks made it impossible to defend or refute its contribution on them. However, the functions of some of the PBX1's transcription targets indicate a potential engagement of PBX1 in the avoidance of immune destruction and in the tumor-promoting inflammation hallmarks. Interestingly, PBX1 might be a player in tumor suppression by activating the transcription of some DNA damage response genes. This is the first review organizing PBX1 roles into the hallmarks of cancer. Thus, we encourage future studies to uncover the PBX1's underlying mechanisms to promote carcinogenesis, for it is a promising diagnostic and prognostic biomarker, as well as a potential target in cancer treatment.
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Affiliation(s)
- Rafaela Nasser Veiga
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Postgraduate Program in Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Jaqueline Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Postgraduate Program in Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil
| | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Postgraduate Program in Genetics, Universidade Federal Do Paraná, Rua Coronel Francisco Heráclito Dos Santos, 100, Jardim das AméricasCuritiba, CEP, 81531-980, Brazil.
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11
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Shen YA, Jung J, Shimberg GD, Hsu FC, Rahmanto YS, Gaillard SL, Hong J, Bosch J, Shih IM, Chuang CM, Wang TL. Development of small molecule inhibitors targeting PBX1 transcription signaling as a novel cancer therapeutic strategy. iScience 2021; 24:103297. [PMID: 34816098 PMCID: PMC8591422 DOI: 10.1016/j.isci.2021.103297] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/10/2021] [Accepted: 10/14/2021] [Indexed: 12/01/2022] Open
Abstract
PBX1 is a transcription factor involved in diverse cellular functions including organ development, stem cell renewal, and tumorigenesis. PBX1 is localized at chr1q23.3, a frequently amplified chromosomal region, and it is overexpressed in many human malignancies. Cancer cells with elevated PBX1 signaling are particularly vulnerable to PBX1 withdrawal. We designed a series of small molecule compounds capable of docking to the interface between PBX1 and its cognate DNA target sequence. Among them, T417 is found to be a lead compound. In cell-based assays, T417 significantly suppressed self-renewal and proliferation of cancer cells expressing high levels of PBX1. T417 also re-sensitized platinum-resistant ovarian tumors to carboplatin. T417 did not affect healthy tissues likely due to their lower PBX1 expression levels. Therefore, targeting PBX-DNA interface can be a promising strategy for treating human tumors reliant on PBX1 for survival.
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Affiliation(s)
- Yao-An Shen
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jin Jung
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Geoffrey D. Shimberg
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fang-Chi Hsu
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
| | - Yohan Suryo Rahmanto
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie L. Gaillard
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaxin Hong
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jürgen Bosch
- Division of Pulmonology and Allergy/Immunology, Case Western Reserve University, Cleveland, OH, USA
- InterRayBio, LLC, Baltimore MD, USA
| | - Ie-Ming Shih
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chi-Mu Chuang
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Midwifery and Women Health Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Tian-Li Wang
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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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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13
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Gulotta MR, De Simone G, John J, Perricone U, Brancale A. A Computer-Based Methodology to Design Non-Standard Peptides Potentially Able to Prevent HOX-PBX1-Associated Cancer Diseases. Int J Mol Sci 2021; 22:5670. [PMID: 34073517 PMCID: PMC8198631 DOI: 10.3390/ijms22115670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. HOX proteins execute their activity by exploiting a cooperative binding to PBX proteins and DNA. Therefore, an increase or decrease in HOX activity has been associated with both solid and haematological cancer diseases. Thus, inhibiting HOX-PBX interaction represents a potential strategy to prevent these malignancies, as demonstrated by the patented peptide HTL001 that is being studied in clinical trials. In this work, a computational study is described to identify novel potential peptides designed by employing a database of non-natural amino acids. For this purpose, residue scanning of the HOX minimal active sequence was performed to select the mutations to be further processed. According to these results, the peptides were point-mutated and used for Molecular Dynamics (MD) simulations in complex with PBX1 protein and DNA to evaluate complex binding stability. MM-GBSA calculations of the resulting MD trajectories were exploited to guide the selection of the most promising mutations that were exploited to generate twelve combinatorial peptides. Finally, the latter peptides in complex with PBX1 protein and DNA were exploited to run MD simulations and the ΔGbinding average values of the complexes were calculated. Thus, the analysis of the results highlighted eleven combinatorial peptides that will be considered for further assays.
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Affiliation(s)
- Maria Rita Gulotta
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Giada De Simone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Justin John
- NRN Tech LTD, Henstaff Court, Llantrisant Road, Groesfaen CF72 8NG, UK;
| | - Ugo Perricone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK;
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14
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Wolberger C. How structural biology transformed studies of transcription regulation. J Biol Chem 2021; 296:100741. [PMID: 33957125 PMCID: PMC8163980 DOI: 10.1016/j.jbc.2021.100741] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022] Open
Abstract
The past 4 decades have seen remarkable advances in our understanding of the structural basis of gene regulation. Technological advances in protein expression, nucleic acid synthesis, and structural biology made it possible to study the proteins that regulate transcription in the context of ever larger complexes containing proteins bound to DNA. This review, written on the occasion of the 50th anniversary of the founding of the Protein Data Bank focuses on the insights gained from structural studies of protein-DNA complexes and the role the PDB has played in driving this research. I cover highlights in the field, beginning with X-ray crystal structures of the first DNA-binding domains to be studied, through recent cryo-EM structures of transcription factor binding to nucleosomal DNA.
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Affiliation(s)
- Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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15
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Reichlmeir M, Elias L, Schulte D. Posttranslational Modifications in Conserved Transcription Factors: A Survey of the TALE-Homeodomain Superclass in Human and Mouse. Front Cell Dev Biol 2021; 9:648765. [PMID: 33768097 PMCID: PMC7985065 DOI: 10.3389/fcell.2021.648765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022] Open
Abstract
Transcription factors (TFs) guide effector proteins like chromatin-modifying or -remodeling enzymes to distinct sites in the genome and thereby fulfill important early steps in translating the genome’s sequence information into the production of proteins or functional RNAs. TFs of the same family are often highly conserved in evolution, raising the question of how proteins with seemingly similar structure and DNA-binding properties can exert physiologically distinct functions or respond to context-specific extracellular cues. A good example is the TALE superclass of homeodomain-containing proteins. All TALE-homeodomain proteins share a characteristic, 63-amino acid long homeodomain and bind to similar sequence motifs. Yet, they frequently fulfill non-redundant functions even in domains of co-expression and are subject to regulation by different signaling pathways. Here we provide an overview of posttranslational modifications that are associated with murine and human TALE-homeodomain proteins and discuss their possible importance for the biology of these TFs.
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Affiliation(s)
- Marina Reichlmeir
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Lena Elias
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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16
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Zhang Y, Liu Z, Zong Y, Zheng Y, Li Y, Han Z, Wang L, Song L. The Increased Expression of an Engrailed to Sustain Shell Formation in Response to Ocean Acidification. Front Physiol 2021; 11:530435. [PMID: 33424616 PMCID: PMC7793958 DOI: 10.3389/fphys.2020.530435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/10/2020] [Indexed: 11/13/2022] Open
Abstract
Engrailed is a transcription factor required in numerous species for important developmental steps such as neurogenesis, segment formation, preblastoderm organization, and compartment formation. Recent study has proved that engrailed is also a key gene related to shell formation in marine bivalves. In the present study, the expression pattern of an engrailed gene (Cgengrailed-1) in Pacific oyster Crassostrea gigas under CO2-driven acidification was investigated to understand its possible role in the regulation of shell formation and adaptation to ocean acidification (OA). The open reading frame (ORF) of Cgengrailed-1 was obtained, which was of 690 bp encoding a polypeptide of 229 amino acids with a HOX domain. Phylogenetic analysis indicated that the deduced amino acid sequence of Cgengrailed-1 shared high homology with other engraileds from Drosophila melanogaster, Mizuhopecten yessoensi, and Crassostrea virginica. The mRNA transcripts of Cgengrailed-1 were constitutively expressed in various tissues with the highest expression levels detected in labial palp and mantle, which were 86.83-fold (p < 0.05) and 75.87-fold (p < 0.05) higher than that in hepatopancreas. The mRNA expression of Cgengrailed-1 in mantle decreased dramatically after moderate (pH 7.8) and severe (pH 7.4) acidification treatment (0.75- and 0.15-fold of that in control group, p < 0.05). The results of immunofluorescence assay demonstrated that the expression level of Cgengrailed-1 in the middle fold of mantle increased significantly upon moderate and severe acidification treatment. Moreover, after the oyster larvae received acidification treatment at trochophore stage, the mRNA expression levels of Cgengrailed-1 increased significantly in D-shape larvae stages, which was 3.11- (pH 7.8) and 4.39-fold (pH 7.4) of that in control group (p < 0.05). The whole-mount immunofluorescence assay showed that Cgengrailed-1 was mainly expressed on the margin of shell gland, and the periostracum in trochophore, early D-shape larvae and D-shape larvae in both control and acidification treatment groups, and the intensity of positive signals in early D-shape larvae and D-shape larvae increased dramatically under acidification treatment. These results collectively suggested that the expression of Cgengrailed-1 could be triggered by CO2-driven acidification treatment, which might contribute to induce the initial shell formation in oyster larvae and the formation of periostracum in adult oyster to adapt to the acidifying marine environment.
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Affiliation(s)
- Yukun Zhang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yanan Zong
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Yan Zheng
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Yinan Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Zirong Han
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, China.,Liaoning Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, China.,Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control Dalian Ocean University, Dalian, China.,Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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17
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Singh NP, De Kumar B, Paulson A, Parrish ME, Zhang Y, Florens L, Conaway JW, Si K, Krumlauf R. A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. Genes Dev 2020; 34:1680-1696. [PMID: 33184220 PMCID: PMC7706710 DOI: 10.1101/gad.342329.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/09/2020] [Indexed: 01/19/2023]
Abstract
Gene duplication and divergence is a major driver in the emergence of evolutionary novelties. How variations in amino acid sequences lead to loss of ancestral activity and functional diversification of proteins is poorly understood. We used cross-species functional analysis of Drosophila Labial and its mouse HOX1 orthologs (HOXA1, HOXB1, and HOXD1) as a paradigm to address this issue. Mouse HOX1 proteins display low (30%) sequence similarity with Drosophila Labial. However, substituting endogenous Labial with the mouse proteins revealed that HOXA1 has retained essential ancestral functions of Labial, while HOXB1 and HOXD1 have diverged. Genome-wide analysis demonstrated similar DNA-binding patterns of HOXA1 and Labial in mouse cells, while HOXB1 binds to distinct targets. Compared with HOXB1, HOXA1 shows an enrichment in co-occupancy with PBX proteins on target sites and exists in the same complex with PBX on chromatin. Functional analysis of HOXA1-HOXB1 chimeric proteins uncovered a novel six-amino-acid C-terminal motif (CTM) flanking the homeodomain that serves as a major determinant of ancestral activity. In vitro DNA-binding experiments and structural prediction show that CTM provides an important domain for interaction of HOXA1 proteins with PBX. Our findings show that small changes outside of highly conserved DNA-binding regions can lead to profound changes in protein function.
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Affiliation(s)
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Molecular and Integrative Physiology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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18
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Bruckmann C, Tamburri S, De Lorenzi V, Doti N, Monti A, Mathiasen L, Cattaneo A, Ruvo M, Bachi A, Blasi F. Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis. Sci Rep 2020; 10:16809. [PMID: 33033354 PMCID: PMC7545097 DOI: 10.1038/s41598-020-74032-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/25/2020] [Indexed: 02/08/2023] Open
Abstract
Both onco-suppressor PREP1 and the oncogene MEIS1 bind to PBX1. This interaction stabilizes the two proteins and allows their translocation into the nucleus and thus their transcriptional activity. Here, we have combined cross-linking mass-spectrometry and systematic mutagenesis to detail the binding geometry of the PBX1-PREP1 (and PBX1-MEIS1) complexes, under native in vivo conditions. The data confirm the existence of two distinct interaction sites within the PBC domain of PBX1 and unravel differences among the highly similar binding sites of MEIS1 and PREP1. The HR2 domain has a fundamental role in binding the PBC-B domain of PBX1 in both PREP1 and MEIS1. The HR1 domain of MEIS1, however, seem to play a less stringent role in PBX1 interaction with respect to that of PREP1. This difference is also reflected by the different binding affinity of the two proteins to PBX1. Although partial, this analysis provides for the first time some ideas on the tertiary structure of the complexes not available before. Moreover, the extensive mutagenic analysis of PREP1 identifies the role of individual hydrophobic HR1 and HR2 residues, both in vitro and in vivo.
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Affiliation(s)
- Chiara Bruckmann
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
| | - Simone Tamburri
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina De Lorenzi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56124, Pisa, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Lisa Mathiasen
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Angela Cattaneo
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Cogentech S.R.L. Benefit Corporation IT, Via Adamello 16, 20139, Milan, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Angela Bachi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
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19
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Doti N, Monti A, Bruckmann C, Calvanese L, Smaldone G, Caporale A, Falcigno L, D'Auria G, Blasi F, Ruvo M, Vitagliano L. Identification and characterization of cytotoxic amyloid-like regions in human Pbx-regulating protein-1. Int J Biol Macromol 2020; 163:618-629. [PMID: 32634512 DOI: 10.1016/j.ijbiomac.2020.06.271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/19/2020] [Accepted: 06/30/2020] [Indexed: 01/05/2023]
Abstract
The ability of many proteins to fold into well-defined structures has been traditionally considered a prerequisite for fulfilling their functions. Protein folding is also regarded as a valuable loophole to escape uncontrolled and harmful aggregations. Here we show that the PBX-regulating protein-1 (PREP1), an important homeodomain transcription factor involved in cell growth and differentiation during embryogenesis, is endowed with an uncommon thermostability. Indeed, circular dichroism analyses indicate that it retains most of its secondary structure at very high temperatures. These findings have important implications for PREP1 functions since it is a stabilizing factor of its partner PBX1. Predictive analyses suggest that the observed PREP1 thermostability could be related to the presence of aggregation-prone regions. Interestingly, synthetic peptides corresponding to these regions exhibit a remarkable propensity to form toxic β-rich amyloid-like aggregates in physiological conditions. On this basis, we suggest that PREP1 stability is an effective way to prevent or limit the formation of harmful aggregates. Notably, one of these PREP1 fragments (residues 117-132) is able to reversibly switch from α-helical to β-rich states depending on the environmental conditions. The chameleon conformational behavior of this peptide makes it an ideal system to study this intriguing and widespread structural transition.
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Affiliation(s)
- Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy; Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Chiara Bruckmann
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research), Institute of Molecular Oncology, Milan, Italy
| | - Luisa Calvanese
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | | | - Andrea Caporale
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Lucia Falcigno
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy; Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Naples, Italy
| | - Gabriella D'Auria
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy; Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Naples, Italy
| | - Francesco Blasi
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research), Institute of Molecular Oncology, Milan, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134 Naples, Italy.
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20
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Zhang C, Featherstone M. A zebrafish hox gene acts before gastrulation to specify the hemangioblast. Genesis 2020; 58:e23363. [PMID: 32302038 DOI: 10.1002/dvg.23363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/09/2020] [Accepted: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Hox genes encode transcription factors that have been implicated in embryonic, adult and disease processes. The earliest developmental program known to be directed by Hox genes is the timing of ingression of presumptive axial mesoderm during gastrulation. We previously used morpholino (MO)-based knockdown to implicate the zebrafish hoxd4a gene in the specification of the hemangioblast, an event occurring at pre-gastrulation stages, well before the earliest known Hox gene function. The precise time at which hoxd4a function is required for this specification is not defined. We therefore fused the hoxd4a coding region to the human estrogen receptor (hERT2 ). Following co-injection of anti-hoxd4a MO with mRNA encoding the Hoxd4a-ERT2 fusion protein, hemangioblast specification was fully rescued when embryos were exposed to the estrogen analog 4-hydroxy-tamoxifen (4-OHT) at 4 hr post-fertilization (hpf), but only poorly at 6 hpf and not at all at 8 hpf, thereby defining a pre-gastrulation role for Hoxd4a, the earliest developmental function of a vertebrate Hox gene so far described. Both DNA binding and interaction with cofactor Pbx were further shown to be required for rescue of the morphant phenotype. Confirmation of the morphant phenotype was sought via the generation of hoxd4a null mutants using CRISPR/Cas9 technology. Null mutants of hoxd4a up to the third generation (F3 ) failed to recapitulate the morphant phenotype, and were largely refractory to the effects of injected anti-hoxd4a MO suggesting the action of genetic compensation.
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Affiliation(s)
- Changqing Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Mark Featherstone
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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21
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Cao X, Wang J, Xiong Y, Yang H, Yang M, Ye P, Bencivenga S, Sablowski R, Jiao Y. A Self-Activation Loop Maintains Meristematic Cell Fate for Branching. Curr Biol 2020; 30:1893-1904.e4. [PMID: 32243852 DOI: 10.1016/j.cub.2020.03.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 02/17/2020] [Accepted: 03/12/2020] [Indexed: 11/16/2022]
Abstract
In plants and animals, self-renewing stem cell populations play fundamental roles in many developmental contexts. Plants differ from most animals in their retained ability to initiate new cycles of growth and development, which relies on the establishment and activity of branch meristems. In seed plants, branching is achieved by stem-cell-containing axillary meristems, which are initiated from a leaf axil meristematic cell population originally detached from the shoot apical meristem. It remains unclear how the meristematic cell fate is maintained. Here, we show that ARABIDOPSISTHALIANAHOMEOBOXGENE1 (ATH1) maintains the meristem marker gene SHOOT MERISTEMLESS (STM) expression in the leaf axil to enable meristematic cell fate maintenance. Furthermore, ATH1 protein interacts with STM protein to form a STM self-activation loop. Genetic and biochemical data suggest that ATH1 anchors STM to activate STM as well as other axillary meristem regulatory genes. This auto-regulation allows the STM locus to remain epigenetically active. Taken together, our findings provide a striking example of a self-activation loop that maintains the flexibility required for stem cell niche re-establishment during organogenesis.
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Affiliation(s)
- Xiuwei Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Xiong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haibian Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Minglei Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Peiyi Ye
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Stefano Bencivenga
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Sablowski
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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22
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Xu X, Zhou Y, Fu B, Zhang J, Dong Z, Zhang X, Shen N, Sun R, Tian Z, Wei H. PBX1 promotes development of natural killer cells by binding directly to the Nfil3 promoter. FASEB J 2020; 34:6479-6492. [PMID: 32190943 DOI: 10.1096/fj.202000121r] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 01/23/2023]
Abstract
The transcription factor nuclear factor interleukin-3-regulated protein (NFIL3, also called E4BP4) is crucial for commitment of natural killer (NK) cells from common lymphoid progenitors (CLPs). However, the identity of the factor that can regulate NFIL3 directly during the NK-cell development is not known. Here, we reveal that pre-B-cell leukemia transcription factor 1 (PBX1) can upregulate the NFIL3 expression directly. We used conditional knockout mice in which PBX1 in hematopoietic cells was specifically absent. The number of NK-committed progenitor pre-NKP cells and rNKP cells was reduced significantly in the absence of PBX1, which was consistent with NFIL3 deficiency. Also, the NFIL3 expression in NK cells was decreased if PBX1 was absent. We demonstrated that PBX1 was bound directly to the promoter of Nfil3 and facilitated transcription. Upon knockout of the binding site of PBX1 in the Nfil3 promoter, mice showed fewer NK-precursor cells and NK cells, just like that observed in Nfil3 knockout mice. Furthermore, asparagine N286 in the homeodomain of PBX1 controlled the binding of PBX1 to the Nfil3 promoter. Collectively, these findings demonstrate that the transcription factor PBX1 promotes the early development of NK cells by upregulating the Nfil3 expression directly.
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Affiliation(s)
- Xiuxiu Xu
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China
| | - Yonggang Zhou
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China.,First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Binqing Fu
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China
| | - Jinghe Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China
| | - Zhongjun Dong
- School of Medicine, Tsinghua University, Beijing, China
| | - Xiaoren Zhang
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Sun
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China
| | - Zhigang Tian
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China
| | - Haiming Wei
- Hefei National Laboratory for Physical Sciences at Microscale, Division of Molecular Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institue of Immunology, University of Science and Technology of China, Hefei, China
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23
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Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS. Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites. Cell Rep 2020; 24:2221-2230. [PMID: 30157419 DOI: 10.1016/j.celrep.2018.07.100] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/14/2018] [Accepted: 07/28/2018] [Indexed: 11/26/2022] Open
Abstract
Transcription factors bind to their binding sites over a wide range of affinities, yet how differences in affinity are encoded in DNA sequences is not well understood. Here, we report X-ray crystal structures of four heterodimers of the Hox protein AbdominalB bound with its cofactor Extradenticle to four target DNA molecules that differ in affinity by up to ∼20-fold. Remarkably, despite large differences in affinity, the overall structures are very similar in all four complexes. In contrast, the predicted shapes of the DNA binding sites (i.e., the intrinsic DNA shape) in the absence of bound protein are strikingly different from each other and correlate with affinity: binding sites that must change conformations upon protein binding have lower affinities than binding sites that have more optimal conformations prior to binding. Together, these observations suggest that intrinsic differences in DNA shape provide a robust mechanism for modulating affinity without affecting other protein-DNA interactions.
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Affiliation(s)
- Tim Zeiske
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Nithya Baburajendran
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna Kaczynska
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Julia Brasch
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University, 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, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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24
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Lee JK, Bosnakovski D, Toso EA, Dinh T, Banerjee S, Bohl TE, Shi K, Orellana K, Kyba M, Aihara H. Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA. Cell Rep 2019; 25:2955-2962.e3. [PMID: 30540931 DOI: 10.1016/j.celrep.2018.11.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 11/18/2022] Open
Abstract
Double homeobox (DUX) transcription factors are unique to eutherian mammals. DUX4 regulates expression of repetitive elements during early embryogenesis, but misexpression of DUX4 causes facioscapulohumeral muscular dystrophy (FSHD) and translocations overexpressing the DUX4 double homeodomain cause B cell leukemia. Here, we report the crystal structure of the tandem homeodomains of DUX4 bound to DNA. The homeodomains bind DNA in a head-to-head fashion, with the linker making anchoring DNA minor-groove interactions and unique protein contacts. Remarkably, despite being tandem duplicates, the DUX4 homeodomains recognize different core sequences. This results from an arginine-to-glutamate mutation, unique to primates, causing alternative positioning of a key arginine side chain in the recognition helix. Mutational studies demonstrate that this primate-specific change is responsible for the divergence in sequence recognition that likely drove coevolution of embryonically regulated repeats in primates. Our work provides a framework for understanding the endogenous function of DUX4 and its role in FSHD and cancer.
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Affiliation(s)
- John K Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Darko Bosnakovski
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Faculty of Medical Sciences, Goce Delcev University-Stip, Krste Misirkov b.b., 2000 Stip, Republic of Macedonia
| | - Erik A Toso
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tracy Dinh
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, IL 60439, USA
| | - Thomas E Bohl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kayo Orellana
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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25
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Ma Q, Wang N, Hao P, Sun H, Wang C, Ma L, Wang H, Zhang X, Wei H, Yu S. Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis. BMC PLANT BIOLOGY 2019; 19:432. [PMID: 31623554 PMCID: PMC6798366 DOI: 10.1186/s12870-019-2026-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 09/11/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.). RESULTS In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers. CONCLUSION We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.
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Affiliation(s)
- Qiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Nuohan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Congcong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Xianlong Zhang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 Henan China
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26
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Paço A, Freitas R. HOX genes as transcriptional and epigenetic regulators during tumorigenesis and their value as therapeutic targets. Epigenomics 2019; 11:1539-1552. [PMID: 31556724 DOI: 10.2217/epi-2019-0090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Several HOX genes are aberrantly expressed in a wide range of cancers interfering with their development and resistance to treatment. This seems to be often caused by alterations in the methylation profiles of their promoters. The role of HOX gene products in cancer is highly 'tissue specific', relying ultimately on their ability to regulate oncogenes or tumor-suppressor genes, directly as transcriptional regulators or indirectly interfering with the levels of epigenetic regulators. Nowadays, different strategies have been tested the use of HOX genes as therapeutic targets for cancer diagnosis and treatment. Here, we trace the history of the research concerning the involvement of HOX genes in cancer, their connection with epigenetic regulation and their potential use as therapeutic targets.
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Affiliation(s)
- Ana Paço
- Laboratório de Microbiologia do Solo, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Instituto de Investigação e Formação Avançada (IIFA), Universidade de Évora, 7006-554 Évora, Portugal
| | - Renata Freitas
- I3S - Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal.,IBMC - Institute for Molecular & Cell Biology, University of Porto, 4200-135 Porto, Portugal.,ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
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27
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Schulte D, Geerts D. MEIS transcription factors in development and disease. Development 2019; 146:146/16/dev174706. [PMID: 31416930 DOI: 10.1242/dev.174706] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
MEIS transcription factors are key regulators of embryonic development and cancer. Research on MEIS genes in the embryo and in stem cell systems has revealed novel and surprising mechanisms by which these proteins control gene expression. This Primer summarizes recent findings about MEIS protein activity and regulation in development, and discusses new insights into the role of MEIS genes in disease, focusing on the pathogenesis of solid cancers.
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Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, 60528 Frankfurt, Germany
| | - Dirk Geerts
- Department of Medical Biology L2-109, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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28
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Nolte C, De Kumar B, Krumlauf R. Hox genes: Downstream "effectors" of retinoic acid signaling in vertebrate embryogenesis. Genesis 2019; 57:e23306. [PMID: 31111645 DOI: 10.1002/dvg.23306] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022]
Abstract
One of the major regulatory challenges of animal development is to precisely coordinate in space and time the formation, specification, and patterning of cells that underlie elaboration of the basic body plan. How does the vertebrate plan for the nervous and hematopoietic systems, heart, limbs, digestive, and reproductive organs derive from seemingly similar population of cells? These systems are initially established and patterned along the anteroposterior axis (AP) by opposing signaling gradients that lead to the activation of gene regulatory networks involved in axial specification, including the Hox genes. The retinoid signaling pathway is one of the key signaling gradients coupled to the establishment of axial patterning. The nested domains of Hox gene expression, which provide a combinatorial code for axial patterning, arise in part through a differential response to retinoic acid (RA) diffusing from anabolic centers established within the embryo during development. Hence, Hox genes are important direct effectors of retinoid signaling in embryogenesis. This review focuses on describing current knowledge on the complex mechanisms and regulatory processes, which govern the response of Hox genes to RA in several tissue contexts including the nervous system during vertebrate development.
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Affiliation(s)
- Christof Nolte
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas
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29
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Shen LY, Zhou T, Du YB, Shi Q, Chen KN. Targeting HOX/PBX dimer formation as a potential therapeutic option in esophageal squamous cell carcinoma. Cancer Sci 2019; 110:1735-1745. [PMID: 30844117 PMCID: PMC6501045 DOI: 10.1111/cas.13993] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022] Open
Abstract
Homeobox genes are known to be classic examples of the intimate relationship between embryogenesis and tumorigenesis, which are a family of transcriptional factors involved in determining cell identity during early development, and also dysregulated in many malignancies. Previously, HOXB7, HOXC6 and HOXC8 were found abnormally upregulated in esophageal squamous cell carcinoma (ESCC) tissues compared with normal mucosa and seen as poor prognostic predictors for ESCC patients, and were shown to promote cell proliferation and anti‐apoptosis in ESCC cells. These three HOX members have a high level of functional redundancy, making it difficult to target a single HOX gene. The aim of the present study was to explore whether ESCC cells are sensitive to HXR9 disrupting the interaction between multiple HOX proteins and their cofactor PBX, which is required for HOX functions. ESCC cell lines (KYSE70, KYSE150, KYSE450) were treated with HXR9 or CXR9, and coimmunoprecipitation and immunofluorescent colocalization were carried out to observe HOX/PBX dimer formation. To further investigate whether HXR9 disrupts the HOX pro‐oncogenic function, CCK‐8 assay and colony formation assay were carried out. Apoptosis was assessed by flow cytometry, and tumor growth in vivo was investigated in a xenograft model. RNA‐seq was used to study the transcriptome of HXR9‐treated cells. Results showed that HXR9 blocked HOX/PBX interaction, leading to subsequent transcription alteration of their potential target genes, which are involved in JAK‐signal transducer and activator of transcription (STAT) activation and apoptosis inducement. Meanwhile, HXR9 showed an antitumor phenotype, such as inhibiting cell proliferation, inducing cell apoptosis and significantly retarding tumor growth. Therefore, it is suggested that targeting HOX/PBX may be a novel effective treatment for ESCC.
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Affiliation(s)
- Lu-Yan Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ting Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ya-Bing Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing, China
| | - Qi Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ke-Neng Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing, China
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The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors. Sci Rep 2019; 9:5664. [PMID: 30952900 PMCID: PMC6450960 DOI: 10.1038/s41598-019-42096-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/22/2019] [Indexed: 12/15/2022] Open
Abstract
HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, leading to a global dispensability of the HX motif for trimeric complex formation in the large majority of HOX proteins. In addition, it was shown that the anterior HOXB3 and central HOXA7 and HOXC8 proteins could use different alternative TALE interaction motifs, with or without the HX motif, depending on the DNA-binding site and cell context. Here we dissected the molecular interaction properties of the human posterior HOXA9 protein with its TALE cofactors, PBX1 and MEIS1. Analysis was performed on different DNA-binding sites in vitro and by doing Bimolecular Fluorescence Complementation (BiFC) in different cell lines. Notably, we observed that the HOXA9-TALE interaction relies consistently on the redundant activity of the HX motif and two paralog-specific residues of the HOXA9 HD. Together with previous work, our results show that HOX proteins interact with their generic TALE cofactors through various modalities, ranging from unique and context-independent to versatile and context-dependent TALE binding interfaces.
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31
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Luo Z, Rhie SK, Farnham PJ. The Enigmatic HOX Genes: Can We Crack Their Code? Cancers (Basel) 2019; 11:cancers11030323. [PMID: 30866492 PMCID: PMC6468460 DOI: 10.3390/cancers11030323] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
Homeobox genes (HOX) are a large family of transcription factors that direct the formation of many body structures during early embryonic development. There are 39 genes in the subgroup of homeobox genes that constitute the human HOX gene family. Correct embryonic development of flies and vertebrates is, in part, mediated by the unique and highly regulated expression pattern of the HOX genes. Disruptions in these fine-tuned regulatory mechanisms can lead to developmental problems and to human diseases such as cancer. Unfortunately, the molecular mechanisms of action of the HOX family of transcription factors are severely under-studied, likely due to idiosyncratic details of their structure, expression, and function. We suggest that a concerted and collaborative effort to identify interacting protein partners, produce genome-wide binding profiles, and develop HOX network inhibitors in a variety of human cell types will lead to a deeper understanding of human development and disease. Within, we review the technological challenges and possible approaches needed to achieve this goal.
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Affiliation(s)
- Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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Saurin AJ, Delfini MC, Maurel-Zaffran C, Graba Y. The Generic Facet of Hox Protein Function. Trends Genet 2018; 34:941-953. [PMID: 30241969 DOI: 10.1016/j.tig.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/07/2018] [Accepted: 08/21/2018] [Indexed: 11/16/2022]
Abstract
Hox transcription factors are essential to promote morphological diversification of the animal body. A substantial number of studies have focused on how Hox proteins reach functional specificity, an issue that arises from the fact that these transcription factors control distinct developmental functions despite sharing similar molecular properties. In this review, we highlight that, besides specific functions, for which these transcription factors are renowned, Hox proteins also often have nonspecific functions. We next discuss some emerging principles of these generic functions and how they relate to specific functions and explore our current grasp of the underlying molecular mechanisms.
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Affiliation(s)
- Andrew J Saurin
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/.
| | - Marie Claire Delfini
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/
| | - Corinne Maurel-Zaffran
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/
| | - Yacine Graba
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; http://www.ibdm.univ-mrs.fr/equipe/mechanisms-of-gene-regulation-by-transcription-factors/.
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Li S, Hu R, Yao H, Long D, Luo F, Zhou X, Zhang X, Liu M, Zhu J, Yang Y. Characterization of the interaction interface and conformational dynamics of human TGIF1 homeodomain upon the binding of consensus DNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1021-1028. [PMID: 30048701 DOI: 10.1016/j.bbapap.2018.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/28/2018] [Accepted: 07/17/2018] [Indexed: 01/17/2023]
Abstract
The TG interacting factor-1 homeodomain (TGIF1-HD) binds with the consensus DNA motif 5'-TGTCA-3' in gene promoters through its three-amino acid loop extension (TALE) type homeodomain, and then recruits co-regulators to regulate gene expression. Although the solution NMR structure of human TGIF1-HD has been reported previously, little is known about its DNA binding mechanism. NMR titrations have been extensively used to study mechanisms of ligand binding to target proteins; however, an intermediate exchange occurred predominantly between TGIF1-HD in the free and bound states when titrated with the consensus DNA, which resulted in poor-quality NMR spectra and precluded further exploration of its interaction interface and conformational dynamics. Here, the helix α3 of TGIF1-HD was speculated as the specific DNA binding interface by hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments, and subsequently confirmed by chemical exchange saturation transfer (CEST) spectroscopy. In addition, simultaneous conformational changes in other regions, including α1 and α2, were induced by DNA binding, explaining the observation of chemical shift perturbations from extensive residues besides those located in α3. Further, low-populated DNA-bound TGIF1-HD undergoing a slow exchange at a rate of 130.2 ± 3.6 s-1 was derived from the analysis of the CEST data, and two residues, R220 and R221, located in the middle of α3 were identified to be crucial for DNA binding. Our study provides structural and dynamic insights into the mechanisms of TGIF1-HD recognition of extensive promoter DNA.
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Affiliation(s)
- Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China
| | - Haijie Yao
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Long
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Fan Luo
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of sciences, Wuhan 430071, China.
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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35
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Wotton D, Taniguchi K. Functions of TGIF homeodomain proteins and their roles in normal brain development and holoprosencephaly. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2018; 178:128-139. [PMID: 29749689 DOI: 10.1002/ajmg.c.31612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 01/08/2023]
Abstract
Holoprosencephaly (HPE) is a frequent human forebrain developmental disorder with both genetic and environmental causes. Multiple loci have been associated with HPE in humans, and potential causative genes at 14 of these loci have been identified. Although TGIF1 (originally TGIF, for Thymine Guanine-Interacting Factor) is among the most frequently screened genes in HPE patients, an understanding of how mutations in this gene contribute to the pathogenesis of HPE has remained elusive. However, mouse models based on loss of function of Tgif1, and the related Tgif2 gene, have shed some light on how human TGIF1 variants might cause HPE. Functional analyses of TGIF proteins and of TGIF1 single nucleotide variants from HPE patients, combined with analysis of forebrain development in mouse embryos lacking both Tgif1 and Tgif2, suggest that TGIFs regulate the transforming growth factor ß/Nodal signaling pathway and sonic hedgehog (SHH) signaling independently. Although, some developmental processes that are regulated by TGIFs may be Nodal-dependent, it appears that the forebrain patterning defects and HPE in Tgif mutant mouse embryos is primarily due to altered signaling via the Shh pathway.
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Affiliation(s)
- David Wotton
- Department of Biochemistry and Molecular Genetics, Center for Cell Signaling, University of Virginia, Charlottesville, Virginia
| | - Kenichiro Taniguchi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
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Gandhi NS, Blancafort P, Mancera RL. Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps). Oncotarget 2018; 9:22383-22397. [PMID: 29854286 PMCID: PMC5976472 DOI: 10.18632/oncotarget.25025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/15/2018] [Indexed: 12/21/2022] Open
Abstract
The neural-specific transcription factor Engrailed 1 - is overexpressed in basal-like breast tumours. Synthetic interference peptides - comprising a cell-penetrating peptide/nuclear localisation sequence and the Engrailed 1-specific sequence from the N-terminus have been engineered to produce a strong apoptotic response in tumour cells overexpressing EN1, with no toxicity to normal or non Engrailed 1-expressing cells. Here scaled molecular dynamics simulations were used to study the conformational dynamics of these interference peptides in aqueous solution to characterise their structure and dynamics. Transitions from disordered to α-helical conformation, stabilised by hydrogen bonds and proline-aromatic interactions, were observed throughout the simulations. The backbone of the wild-type peptide folds to a similar conformation as that found in ternary complexes of anterior Hox proteins with conserved hexapeptide motifs important for recognition of pre-B-cell leukemia Homeobox 1, indicating that the motif may possess an intrinsic preference for helical structure. The predicted NMR chemical shifts of these peptides are consistent with the Hox hexapeptides in solution and Engrailed 2 NMR data. These findings highlight the importance of aromatic residues in determining the structure of Engrailed 1 interference peptides, shedding light on the rational design strategy of molecules that could be adopted to inhibit other transcription factors overexpressed in other cancer types, potentially including other transcription factor families that require highly conserved and cooperative protein-protein partnerships for biological activity.
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Affiliation(s)
- Neha S Gandhi
- School of Mathematical Sciences and Institute for Health and Biomedical Innovation, Queensland University of Technology, Gardens Point Campus, Brisbane QLD 4000, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth WA 6845, Australia
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37
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He C, Wang Z, Zhang L, Yang L, Li J, Chen X, Zhang J, Chang Q, Yu Y, Liu B, Zhu Z. A hydrophobic residue in the TALE homeodomain of PBX1 promotes epithelial-to-mesenchymal transition of gastric carcinoma. Oncotarget 2018; 8:46818-46833. [PMID: 28514754 PMCID: PMC5564525 DOI: 10.18632/oncotarget.17473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/12/2017] [Indexed: 01/24/2023] Open
Abstract
Pre-B-cell leukemia homeobox 1 (PBX1) was originally identified as a proto-oncogene in human leukemia. Although this protein has been shown to contribute to cellular development and tumorigenesis, the role of PBX1 in gastric carcinoma (GC) remains unclear. In this study, we observed increased expression of PBX1 in GC tissues compared with adjacent normal tissues. This increase in PBX1 expression levels negatively correlated with HOXB9 mRNA expression and was also associated with malignancy and metastasis. PBX1 promoted proliferation and metastasis of GC cells both in vitro and in vivo. These phenomena were also accompanied by epithelial-to-mesenchymal transition (EMT). Additionally, we observed that PBX1 promotes the expression of tumor growth and angiogenic factors. A structural model of the PBX1-HOX complex revealed that hydrophobic binding between PBX1 and the hexapeptide motif might be required for EMT induction. This analysis also demonstrated that the Phe252 residue in the first helix of the TALE homeodomain is involved in the latter hydrophobic binding reaction. In vitro data from PBX1 mutants suggest that PBX1 cannot promote tumorigenesis of GC cells via EMT induction when Phe252 residues lose hydrophobicity. It is likely that the presence of this residue is essential in facilitating hydrophobic binding with the hexapeptide motif. These findings suggest that PBX1 may be a potential target for GC treatment and this study provides a platform to elucidate the molecular mechanisms that underpin the role of PBX1 in GC tumorigenesis.
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Affiliation(s)
- Changyu He
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenqiang Wang
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhang
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liyun Yang
- Department of Otolaryngology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfang Li
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuehua Chen
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Clinical Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Chang
- Clinical Research Center, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yingyan Yu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenggang Zhu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J. Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima. eLife 2018; 7:32963. [PMID: 29638214 PMCID: PMC5896879 DOI: 10.7554/elife.32963] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/12/2018] [Indexed: 11/17/2022] Open
Abstract
Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar ΔG. However, the interaction with the CAA sequence was driven by change in enthalpy (ΔH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (ΔS). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as ΔG depends on two partially independent variables ΔH and ΔS according to the central equation of thermodynamics, ΔG = ΔH - TΔS. Genes are sections of DNA that carry the instructions needed to build other molecules including all the proteins that the cell needs to fulfill its role. The information in the DNA is stored as a code consisting of four chemical bases, often referred to simply as “A”, “C”, “G” and “T”. The order or sequence of these bases determines the role of a protein. Many organisms – including humans – are built of many different types of cells that perform unique roles. Almost all cells carry the same genetic information, but proteins called transcription factors can regulate the activity of genes so that only a relevant subset of genes is switched on at a particular time. Transcription factors glide along DNA and bind to short DNA sequences by attaching to the DNA bases directly or through bridges made up of water molecules. Two physical concepts known as enthalpy and entropy determine the strength of the connection. Enthalpy relates to how strong the chemical bonds that form between the transcription factors and the DNA bases are, compared to a situation where the transcription factor and DNA do not form a complex and bind to water molecules around them. Entropy measures the disorder of the system – the more disordered the solvent and protein-DNA complex are compared to solvent-containing free DNA and protein, the stronger the binding. A water molecule that bridges a DNA base with an amino-acid of a protein contributes to enthalpy, but results in loss of entropy, because the system becomes more ordered since the water molecule can no longer move freely. Most transcription factors can only bind to DNA sequences that are very similar to each other, but some transcription factors can recognize several different kinds of sequences, and until now it was not clear how they could do this. Morgunova et al. studied four different human transcription factors that can each bind to two distinct DNA sequences. The results showed that the transcription factors bound to both DNA sequences with similar strength, but via different mechanisms. For one DNA sequence, an enthalpy-based mechanism essentially ‘froze’ the transcription factor to the DNA through rigid water bridges. The other DNA sequence was bound equally strongly but through moving water molecules, because this increased the entropy of the system. It is possible that these mechanisms could also apply to many other molecules that interact with each other through water-molecule bridges. A better knowledge of the chemical bonds between transcription factors and DNA bases may in future help efforts to develop new treatments that depend on molecules being able to bind to other molecules. In addition, these findings may one day help scientists to predict how strongly two molecules will interact simply by knowing the structures of the molecules involved.
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Affiliation(s)
- Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yimeng Yin
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pratyush K Das
- Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Arttu Jolma
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fangjie Zhu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - You Xu
- Department of Bioscience and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Lennart Nilsson
- Department of Bioscience and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Draime A, Bridoux L, Belpaire M, Pringels T, Degand H, Morsomme P, Rezsohazy R. The O-GlcNAc transferase OGT interacts with and post-translationally modifies the transcription factor HOXA1. FEBS Lett 2018; 592:1185-1201. [PMID: 29465778 DOI: 10.1002/1873-3468.13015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/26/2018] [Accepted: 02/13/2018] [Indexed: 11/06/2022]
Abstract
HOXA1 belongs to the HOX family of transcription factors which are key regulators of animal development. Little is known about the molecular pathways controlling HOXA1. Recent data from our group revealed distinct partner proteins interacting with HOXA1. Among them, OGT is an O-linked N-acetylglucosamine (O-GlcNAc) transferase modifying a variety of proteins involved in different cellular processes including transcription. Here, we confirm OGT as a HOXA1 interactor, we characterise which domains of HOXA1 and OGT are required for the interaction, and we provide evidence that OGT post-translationally modifies HOXA1. Mass spectrometry experiments indeed reveal that HOXA1 can be phosphorylated on the AGGTVGSPQYIHHSY peptide and that upon OGT expression, the phosphate adduct is replaced by an O-GlcNAc group.
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Affiliation(s)
- Amandine Draime
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Magali Belpaire
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Molecular Physiology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Molecular Physiology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, Louvain-la-Neuve, Belgium
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40
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Morgan R, El-Tanani M, Hunter KD, Harrington KJ, Pandha HS. Targeting HOX/PBX dimers in cancer. Oncotarget 2018; 8:32322-32331. [PMID: 28423659 PMCID: PMC5458287 DOI: 10.18632/oncotarget.15971] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/23/2017] [Indexed: 12/30/2022] Open
Abstract
The HOX and PBX gene families encode transcription factors that have key roles in establishing the identity of cells and tissues in early development. Over the last 20 years it has become apparent that they are also dysregulated in a wide range of solid and haematological malignancies and have a predominantly pro-oncogenic function. A key mode of transcriptional regulation by HOX and PBX proteins is through their interaction as a heterodimer or larger complex that enhances their binding affinity and specificity for DNA, and there is growing evidence that this interaction is a potential therapeutic target in malignancies that include prostate, breast, renal, ovarian and lung cancer, melanoma, myeloma, and acute myeloid leukaemia. This review summarizes the roles of HOX and PBX genes in cancer and assesses the therapeutic potential of HOX/PBX dimer inhibition, including the availability of biomarkers for its application in precision medicine.
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Affiliation(s)
- Richard Morgan
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, UK
| | - Mohamed El-Tanani
- Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, UK
| | - Keith D Hunter
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Kevin J Harrington
- Targeted Therapy Team, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Hardev S Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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41
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Dard A, Reboulet J, Jia Y, Bleicher F, Duffraisse M, Vanaker JM, Forcet C, Merabet S. Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors. Cell Rep 2018. [DOI: 10.1016/j.celrep.2018.02.070] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Draime A, Bridoux L, Belpaire M, Pringels T, Tys J, Rezsohazy R. PRDM14, a putative histone methyl-transferase, interacts with and decreases the stability and activity of the HOXA1 transcription factor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:534-542. [PMID: 29471045 DOI: 10.1016/j.bbagrm.2018.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022]
Abstract
Understanding how the activity of transcription factors like HOX proteins is regulated remains a widely open question. In a recent screen for proteins interacting with HOXA1, we identified a PRDM protein family member, PRDM14, which is known to be transiently co-expressed with HOXA1 in epiblast cells before their specification towards somatic versus germ cell fate. Here, we confirm PRDM14 is an interactor of HOXA1 and we identify the homeodomain of HOXA1 as well as the PR domain and Zinc fingers of PRDM14 to be required for the interaction. An 11-His repeat of HOXA1 previously highlighted to contribute to HOXA1-mediated protein-protein interactions is also involved. At a functional level, we provide evidence that HOXA1 displays an unexpectedly long half-life and demonstrate that PRDM14 can reduce the stability and affect the transcriptional activity of HOXA1.
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Affiliation(s)
- Amandine Draime
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Magali Belpaire
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Janne Tys
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium.
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43
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Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 2018; 356:356/6337/eaaj2239. [PMID: 28473536 DOI: 10.1126/science.aaj2239] [Citation(s) in RCA: 679] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
Abstract
The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.
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Affiliation(s)
- Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Ekaterina Morgunova
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Arttu Jolma
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Eevi Kaasinen
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Biswajyoti Sahu
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Syed Khund-Sayeed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA
| | - Pratyush K Das
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Teemu Kivioja
- Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
| | - Kashyap Dave
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Fan Zhong
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Kazuhiro R Nitta
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Minna Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Paul A Ginno
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Silvia Domcke
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Jian Yan
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden
| | - Dirk Schübeler
- Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden. .,Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland
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44
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Kawai Y, Oda A, Kanai Y, Goitsuka R. Germ cell-intrinsic requirement for the homeodomain transcription factor PKnox1/Prep1 in adult spermatogenesis. PLoS One 2018; 13:e0190702. [PMID: 29293683 PMCID: PMC5749842 DOI: 10.1371/journal.pone.0190702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/19/2017] [Indexed: 01/15/2023] Open
Abstract
PKnox1 (also known as Prep1) belongs to the TALE family of homeodomain transcription factors that are critical for regulating growth and differentiation during embryonic and postnatal development in vertebrates. We demonstrate here that PKnox1 is required for adult spermatogenesis in a germ cell-intrinsic manner. Tamoxifen-mediated PKnox1 loss in the adult testes, as well as its germ cell-specific ablation, causes testis hypotrophy with germ cell apoptosis and, as a consequence, compromised spermatogenesis. In PKnox1-deficient testes, spermatogenesis was arrested at the c-Kit+ spermatogonia stage, with a complete loss of the meiotic spermatocytes, and was accompanied by compromised differentiation of the c-Kit+ spermatogonia. Taken together, these results indicate that PKnox1 is a critical regulator of maintenance and subsequent differentiation of the c-Kit+ stage of spermatogonia in the adult testes.
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Affiliation(s)
- Yasuhiro Kawai
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Akihisa Oda
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Goitsuka
- Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
- Center for Animal Disease Models, Research Institute for Science & Technology, Tokyo University of Science, Noda, Chiba, Japan
- * E-mail:
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45
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De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R. HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets. Genome Res 2017; 27:1501-1512. [PMID: 28784834 PMCID: PMC5580710 DOI: 10.1101/gr.219386.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/24/2017] [Indexed: 01/02/2023]
Abstract
Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for clusters of consensus binding motifs for HOX, PBX, and MEIS, and many display co-occupancy of PBX and MEIS. PBX and MEIS are members of the TALE family and genome-wide analysis of multiple TALE members (PBX, MEIS, TGIF, PREP1, and PREP2) shows that nearly all HOXA1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins define distinct classes of HOXA1 targets, which may create functional diversity. Transgenic reporter assays in zebrafish confirm enhancer activities for many HOXA1-bound regions and the importance of HOX-PBX and TGIF motifs for their regulation. Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions. Therefore, TALE proteins appear to represent a wide repertoire of HOX cofactors, which may coregulate enhancers through distinct mechanisms. We also discover extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes, indicating that the specificity of HOXA1 during development may be regulated though a complex cross-regulatory network of HOXA1 and TALE proteins. This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Pathology
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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46
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Morgunova E, Taipale J. Structural perspective of cooperative transcription factor binding. Curr Opin Struct Biol 2017; 47:1-8. [PMID: 28349863 DOI: 10.1016/j.sbi.2017.03.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/07/2017] [Indexed: 12/27/2022]
Abstract
In prokaryotes, individual transcription factors (TFs) can recognize long DNA motifs that are alone sufficient to define the genes that they induce or repress. In contrast, in higher organisms that have larger genomes, TFs recognize sequences that are too short to define unique genomic positions. In addition, development of multicellular organisms requires molecular systems that are capable of executing combinatorial logical operations. Co-operative recognition of DNA by multiple TFs allows both definition of unique genomic positions in large genomes, and complex information processing at the level of individual regulatory elements. The TFs can co-operate in multiple different ways, and the precise mechanism used for co-operation determines important features of the regulatory interactions. Here, we present an overview of the structural basis of the different mechanisms by which TFs can cooperate, focusing on insight from recent functional studies and structural analyses of specific TF-TF-DNA complexes.
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Affiliation(s)
- Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden; Genome-Scale Biology Research Program, P.O. Box 63, FI-00014 University of Helsinki, Finland.
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47
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Blasi F, Bruckmann C, Penkov D, Dardaei L. A tale of TALE, PREP1, PBX1, and MEIS1: Interconnections and competition in cancer. Bioessays 2017; 39. [DOI: 10.1002/bies.201600245] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Francesco Blasi
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology; Milan Italy
| | - Chiara Bruckmann
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology; Milan Italy
| | - Dmitry Penkov
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology; Milan Italy
| | - Leila Dardaei
- Massachusetts General Hospital Cancer Center; Charlestown MA USA
- Department of Medicine; Harvard Medical School; Boston MA USA
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48
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New Insights into Cooperative Binding of Homeodomain Transcription Factors PREP1 and PBX1 to DNA. Sci Rep 2017; 7:40665. [PMID: 28094776 PMCID: PMC5240567 DOI: 10.1038/srep40665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/09/2016] [Indexed: 01/13/2023] Open
Abstract
PREP1 and PBX1 are homeodomain (HD) transcription factors that play crucial roles in embryonic development. Here, we present the first biophysical characterization of a PREP1 HD, and the NMR spectroscopic study of its DNA binding pocket. The data show that residues flanking the HD participate in DNA binding. The kinetic parameters for DNA binding of individual PREP1 and PBX1 HDs, and of their combination, show that isolated PREP1 and PBX1 HDs bind to DNA in a cooperative manner. A novel PREP1 motif, flanking the HD at the C-terminus, is required for cooperativity.
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49
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Ortiz-Lombardia M, Foos N, Maurel-Zaffran C, Saurin AJ, Graba Y. Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction. Bioessays 2017; 39. [PMID: 28092121 DOI: 10.1002/bies.201600246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox-PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity.
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Affiliation(s)
- Miguel Ortiz-Lombardia
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France.,Aix-Marseille-Université, CNRS UMR 7256, AFMB, Marseille, France
| | - Nicolas Foos
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France
| | | | - Andrew J Saurin
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
| | - Yacine Graba
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
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50
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