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Fang Y, Wang L, Liu K, Wu H, Zheng Y, Duan Y, Feng S, Wang Y. Genome-wide investigation of HD-ZIP gene family and functional characterization of BnaHDZ149 and BnaHDZ22 in salt and drought response in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112130. [PMID: 38795751 DOI: 10.1016/j.plantsci.2024.112130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/08/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
HD-ZIP proteins comprise a plant-specific transcription factor family, which play pivotal roles in plant development and adaptation to ever-changing environment. Although HD-ZIP family members have been identified in some plant species, so far our knowledge about HD-ZIP genes in rapeseed is still limited. In this study, 178 Brassica napus HD-ZIP (BnaHDZ) family members were identified in the rapeseed genome. The phylogenetic relationship, chromosomal locations, intron-exon structures, motif composition, and expression patterns of the BnaHDZ members were analyzed. The BnaHDZ family can be phylogenetically divided into four categories (Ⅰ, Ⅱ, Ⅲ and Ⅳ). Genome-wide transcriptome analysis revealed that most of the HD-ZIP I members respond to at least one abiotic stress. Two closely homologous stress-responsive HD-ZIP Ⅰ genes, BnaHDZ22 and BnaHDZ149, were identified to be involved in drought and salt responses, and selected for further functional characterization. Overexpressing BnaHDZ149 in rapeseed increased salt sensitivity of the transgenic plants, whereas overexpressing BnaHDZ22 increased sensitivity of the transgenic plants to polyethylene glycol (PEG)-simulated drought stress. This research provides not only a comprehensive landscape of BnaHDZ genes, but also a theoretical basis for elucidating the molecular mechanism of the abiotic stress responses of the HD-ZIP family in rapeseed.
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Affiliation(s)
- Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Kuan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Han Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yuqian Zheng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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St. Peter C, Hossain WA, Lovell S, Rafi SK, Butler MG. Mowat-Wilson Syndrome: Case Report and Review of ZEB2 Gene Variant Types, Protein Defects and Molecular Interactions. Int J Mol Sci 2024; 25:2838. [PMID: 38474085 PMCID: PMC10932183 DOI: 10.3390/ijms25052838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/12/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Mowat-Wilson syndrome (MWS) is a rare genetic neurodevelopmental congenital disorder associated with various defects of the zinc finger E-box binding homeobox 2 (ZEB2) gene. The ZEB2 gene is autosomal dominant and encodes six protein domains including the SMAD-binding protein, which functions as a transcriptional corepressor involved in the conversion of neuroepithelial cells in early brain development and as a mediator of trophoblast differentiation. This review summarizes reported ZEB2 gene variants, their types, and frequencies among the 10 exons of ZEB2. Additionally, we summarized their corresponding encoded protein defects including the most common variant, c.2083 C>T in exon 8, which directly impacts the homeodomain (HD) protein domain. This single defect was found in 11% of the 298 reported patients with MWS. This review demonstrates that exon 8 encodes at least three of the six protein domains and accounts for 66% (198/298) of the variants identified. More than 90% of the defects were due to nonsense or frameshift changes. We show examples of protein modeling changes that occurred as a result of ZEB2 gene defects. We also report a novel pathogenic variant in exon 8 in a 5-year-old female proband with MWS. This review further explores other genes predicted to be interacting with the ZEB2 gene and their predicted gene-gene molecular interactions with protein binding effects on embryonic multi-system development such as craniofacial, spine, brain, kidney, cardiovascular, and hematopoiesis.
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Affiliation(s)
- Caroline St. Peter
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
| | - Waheeda A. Hossain
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047, USA;
| | - Syed K. Rafi
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
| | - Merlin G. Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, 3901 Rainbow Blvd. MS 4015, Kansas City, KS 66160, USA; (C.S.P.); (W.A.H.); (S.K.R.)
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3
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Aase-Remedios ME, Janssen R, Leite DJ, Sumner-Rooney L, McGregor AP. Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication. Mol Biol Evol 2023; 40:msad239. [PMID: 37935059 PMCID: PMC10726417 DOI: 10.1093/molbev/msad239] [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: 05/26/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.
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Affiliation(s)
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Daniel J Leite
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
| | - Lauren Sumner-Rooney
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, 10115, Germany
| | - Alistair P McGregor
- Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom
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Zhang S, Zhang X, Zhang C, Xu S, Wang D, Guo C. Developmental Genetic Basis of Hoxd9 Homeobox Domain Deletion in Pampus argenteus Pelvic Fin Deficiency. Int J Mol Sci 2023; 24:11769. [PMID: 37511526 PMCID: PMC10380636 DOI: 10.3390/ijms241411769] [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: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Pampus argenteus is important for commercial fishery catch species and is an emerging target for aquaculture production. Notably, P. argenteus has a bizarre morphology and lacks pelvic fins. However, the reason for the lack of pelvic fins remains unclear, ultimately leading to frequent upside-down floating of P. argenteus during breeding and marked consumption of physical energy. Some lineages, including whales, fugu, snakes, and seahorse, independently lost the pelvic appendages over evolutionary time. Do different taxa employ the same molecular genetic pathways when they independently evolve similar developmental morphologies? Through analysis of the gene responsible for appendage localization, Hoxd9, it was discovered that the Hox domain was absent in the Hoxd9 gene of P. argenteus, and the Hoxd9b gene lacked the Hox9 activation region, a feature not observed in the Hoxd9 gene of other fish species. Interestingly, those distinctive characteristics are not observed in the Hoxd9 gene of other fish species. To determine the association between the Hoxd9 gene characteristics and the pelvic fin deletion in P. argenteus, the full-length cDNA of the Hoxd9a gene was cloned, and morphological observations of the species' juveniles were performed using stereomicroscopy and scanning electron microscopy. Thereafter, the tissue localization of Hoxd9a in the species was analyzed at the gene and protein levels. Based on the results, deletion of the Hoxd9a structural domain possibly leads to disruptions in the protein translation and the pelvic fin localization in P. argenteus during its early ontogenetic developmental stage, resulting in the absence of pelvic fins.
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Affiliation(s)
- Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Xiaodong Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Green Mariculture (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo 315211, China
| | - Chunyang Guo
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Green Mariculture (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo University, Ningbo 315211, China
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5
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Balbhim SS, Sarkar S, Vasudevan M, Ghosh SK. Three-amino acid loop extension homeodomain proteins regulate stress responses and encystation in Entamoeba. Mol Microbiol 2023. [PMID: 37424153 DOI: 10.1111/mmi.15121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
It is interesting to identify factors involved in the regulation of the encystation of Entamoeba histolytica that differentiate trophozoites into cysts. Evolutionarily conserved three amino acid loop extension (TALE) homeodomain proteins act as transcription factors and execute a variety of functions that are essential for life. A TALE homeodomain (EhHbox) protein-encoding gene has been identified in E. histolytica (Eh) that is highly upregulated during heat shock, glucose, and serum starvation. Its ortholog, EiHbox1, a putative homeobox protein in E. invadens (Ei), is also highly upregulated during the early hours of encystation, glucose starvation, and heat shock. They belong to the PBX family of TALE homeobox proteins and have conserved residues in the homeodomain that are essential for DNA binding. Both are localized in the nucleus during encystation and under different stress conditions. The electrophoretic mobility shift assay confirmed that the recombinant GST-EhHbox binds to the reported TGACAG and TGATTGAT motifs. Down-regulation of EiHbox1 by gene silencing reduced Chitin synthase, Jacob, and increased Jessie gene expression, resulting in defective cysts and decreased encystation efficiency and viability. Overall, our results suggest that the TALE homeobox family has been conserved during evolution and acts as a transcription factor to control the differentiation of Entamoeba by regulating the key encystation-induced genes.
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Affiliation(s)
- Sonar Shubham Balbhim
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shilpa Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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Park JW, Lee EJ, Moon E, Kim HL, Kim IB, Hodzic D, Kim N, Kweon HS, Kim JW. Orthodenticle homeobox 2 is transported to lysosomes by nuclear budding vesicles. Nat Commun 2023; 14:1111. [PMID: 36849521 PMCID: PMC9971051 DOI: 10.1038/s41467-023-36697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Transcription factors (TFs) are transported from the cytoplasm to the nucleus and disappear from the nucleus after they regulate gene expression. Here, we discover an unconventional nuclear export of the TF, orthodenticle homeobox 2 (OTX2), in nuclear budding vesicles, which transport OTX2 to the lysosome. We further find that torsin1a (Tor1a) is responsible for scission of the inner nuclear vesicle, which captures OTX2 using the LINC complex. Consistent with this, in cells expressing an ATPase-inactive Tor1aΔE mutant and the LINC (linker of nucleoskeleton and cytoskeleton) breaker KASH2, OTX2 accumulated and formed aggregates in the nucleus. Consequently, in the mice expressing Tor1aΔE and KASH2, OTX2 could not be secreted from the choroid plexus for transfer to the visual cortex, leading to failed development of parvalbumin neurons and reduced visual acuity. Together, our results suggest that unconventional nuclear egress and secretion of OTX2 are necessary not only to induce functional changes in recipient cells but also to prevent aggregation in donor cells.
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Affiliation(s)
- Jun Woo Park
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Eun Jung Lee
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Eunyoung Moon
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Hong-Lim Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - In-Beom Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Didier Hodzic
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Namsuk Kim
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.,Neurovascular Unit, Korea Brain Research Institute, Daegu, 41062, South Korea
| | - Hee-Seok Kweon
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju, 28119, South Korea
| | - Jin Woo Kim
- Department of Biological Sciences and Stem Cell Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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Liao L, Yao Z, Kong J, Zhang X, Li H, Chen W, Xie Q. Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo. BMC Genomics 2022; 23:825. [PMID: 36513979 PMCID: PMC9746114 DOI: 10.1186/s12864-022-09054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo. RESULTS In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified. CONCLUSION Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.
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Affiliation(s)
- Liqin Liao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Ziqi Yao
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China
| | - Jie Kong
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Xinheng Zhang
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Hongxin Li
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
| | - Weiguo Chen
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China
| | - Qingmei Xie
- grid.20561.300000 0000 9546 5767Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China ,grid.484195.5Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, Guangzhou, 510642 China ,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642 P. R. China ,Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, Guangdong 510642 P. R. China
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Ventx Family and Its Functional Similarities with Nanog: Involvement in Embryonic Development and Cancer Progression. Int J Mol Sci 2022; 23:ijms23052741. [PMID: 35269883 PMCID: PMC8911082 DOI: 10.3390/ijms23052741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 12/27/2022] Open
Abstract
The Ventx family is one of the subfamilies of the ANTP (antennapedia) superfamily and belongs to the NK-like (NKL) subclass. Ventx is a homeobox transcription factor and has a DNA-interacting domain that is evolutionarily conserved throughout vertebrates. It has been extensively studied in Xenopus, zebrafish, and humans. The Ventx family contains transcriptional repressors widely involved in embryonic development and tumorigenesis in vertebrates. Several studies have documented that the Ventx family inhibited dorsal mesodermal formation, neural induction, and head formation in Xenopus and zebrafish. Moreover, Ventx2.2 showed functional similarities to Nanog and Barx1, leading to pluripotency and neural-crest migration in vertebrates. Among them, Ventx protein is an orthologue of the Ventx family in humans. Studies have demonstrated that human Ventx was strongly associated with myeloid-cell differentiation and acute myeloid leukemia. The therapeutic potential of Ventx family inhibition in combating cancer progression in humans is discussed. Additionally, we briefly discuss genome evolution, gene duplication, pseudo-allotetraploidy, and the homeobox family in Xenopus.
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Wang H, Tong X, Tang L, Wang Y, Zhao J, Li Z, Liu X, Shu Y, Yin M, Adegoke TV, Liu W, Wang S, Xu H, Ying J, Yuan W, Yao J, Zhang J. RLB (RICE LATERAL BRANCH) recruits PRC2-mediated H3K27 tri-methylation on OsCKX4 to regulate lateral branching. PLANT PHYSIOLOGY 2022; 188:460-476. [PMID: 34730827 PMCID: PMC8774727 DOI: 10.1093/plphys/kiab494] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 09/24/2021] [Indexed: 05/26/2023]
Abstract
Lateral branches such as shoot and panicle are determining factors and target traits for rice (Oryza sativa L.) yield improvement. Cytokinin promotes rice lateral branching; however, the mechanism underlying the fine-tuning of cytokinin homeostasis in rice branching remains largely unknown. Here, we report the map-based cloning of RICE LATERAL BRANCH (RLB) encoding a nuclear-localized, KNOX-type homeobox protein from a rice cytokinin-deficient mutant showing more tillers, sparser panicles, defected floret morphology as well as attenuated shoot regeneration from callus. RLB directly binds to the promoter and represses the transcription of OsCKX4, a cytokinin oxidase gene with high abundance in panicle branch meristem. OsCKX4 over-expression lines phenocopied rlb, which showed upregulated OsCKX4 levels. Meanwhile, RLB physically binds to Polycomb repressive complex 2 (PRC2) components OsEMF2b and co-localized with H3K27me3, a suppressing histone modification mediated by PRC2, in the OsCKX4 promoter. We proposed that RLB recruits PRC2 to the OsCKX4 promoter to epigenetically repress its transcription, which suppresses the catabolism of cytokinin, thereby promoting rice lateral branching. Moreover, antisense inhibition of OsCKX4 under the LOG promoter successfully increased panicle size and spikelet number per plant without affecting other major agronomic traits. This study provides insight into cytokinin homeostasis, lateral branching in plants, and also promising target genes for rice genetic improvement.
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Affiliation(s)
- Huimei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Xiaohong Tong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yifeng Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Juan Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhiyong Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Xixi Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Yazhou Shu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Man Yin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Tosin Victor Adegoke
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Wanning Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Shuang Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Huayu Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Jiezheng Ying
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China
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Guo H, Xu G, Wu R, Li Z, Yan M, Jia Z, Li Z, Chen M, Bao X, Qu Y. A Homeodomain-Containing Transcriptional Factor PoHtf1 Regulated the Development and Cellulase Expression in Penicillium oxalicum. Front Microbiol 2021; 12:671089. [PMID: 34177850 PMCID: PMC8222722 DOI: 10.3389/fmicb.2021.671089] [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: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
Homeodomain-containing transcription factors (Htfs) play important roles in animals, fungi, and plants during some developmental processes. Here, a homeodomain-containing transcription factor PoHtf1 was functionally characterized in the cellulase-producing fungi Penicillium oxalicum 114-2. PoHtf1 was shown to participate in colony growth and conidiation through regulating the expression of its downstream transcription factor BrlA, the key regulator of conidiation in P. oxalicum 114-2. Additionally, PoHtf1 inhibited the expression of the major cellulase genes by coordinated regulation of cellulolytic regulators CreA, AmyR, ClrB, and XlnR. Furthermore, transcriptome analysis showed that PoHtf1 participated in the secondary metabolism including the pathway synthesizing conidial yellow pigment. These data show that PoHtf1 mediates the complex transcriptional-regulatory network cascade between developmental processes and cellulolytic gene expression in P. oxalicum 114-2. Our results should assist the development of strategies for the metabolic engineering of mutants for applications in the enzymatic hydrolysis for biochemical production.
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Affiliation(s)
- Hao Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Gen Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Ruimei Wu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhigang Li
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Mengdi Yan
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Zhilei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Mei Chen
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,School of Bioengineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Shandong Academy of Sciences, Qilu University of Technology, Jinan, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, School of Life Sciences, National Glycoengineering Research Center, Shandong University, Qingdao, China
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11
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Perotti MF, Arce AL, Chan RL. The underground life of homeodomain-leucine zipper transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4005-4021. [PMID: 33713412 DOI: 10.1093/jxb/erab112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) transcription factors in root development. This family is divided into four subfamilies (I-IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip transcription factors in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several individuals from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.
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Affiliation(s)
- María Florencia Perotti
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
| | - Agustín Lucas Arce
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
| | - Raquel Lía Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, FBCB, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe,Argentina
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12
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Kim JL, Mestre B, Shin SH, Futerman AH. Ceramide synthases: Reflections on the impact of Dr. Lina M. Obeid. Cell Signal 2021; 82:109958. [PMID: 33607256 DOI: 10.1016/j.cellsig.2021.109958] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/16/2022]
Abstract
Sphingolipids are a family of lipids that are critical to cell function and survival. Much of the recent work done on sphingolipids has been performed by a closely-knit family of sphingolipid researchers, which including our colleague, Dr. Lina Obeid, who recently passed away. We now briefly review where the sphingolipid field stands today, focusing in particular on areas of sphingolipid research to which Dr. Obeid made valued contributions. These include the 'many-worlds' view of ceramides and the role of a key enzyme in the sphingolipid biosynthetic pathway, namely the ceramide synthases (CerS). The CerS contain a number of functional domains and also interact with a number of other proteins in lipid metabolic pathways, fulfilling Dr. Obeid's prophecy that ceramides, and the enzymes that generate ceramides, form the critical hub of the sphingolipid metabolic pathway.
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Affiliation(s)
- Jiyoon L Kim
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Beatriz Mestre
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sun-Hye Shin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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13
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Hu L, Zhang S, Zhou Y, Liao K, Xu S, Wang D. Cloning and expression of Hoxc6 gene from Pampus argenteus and its relationship with pelvic fin absence. Gene Expr Patterns 2020; 39:119161. [PMID: 33309862 DOI: 10.1016/j.gep.2020.119161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 10/22/2022]
Abstract
Hoxc6 gene can be described as having roles in axial patterning in early embryogenesis, and in at least some species, having a contribution to limb positioning. In this study, we cloned and characterised Pampus argenteus Hoxc6. The highly conserved HOXC6 protein sequence contains a homeodomain and a low-complexity region. Expression of Hoxc6 mRNA was measured at different developmental stages and in different tissues by real-time PCR (p < 0.05), and was high during eye capsule and brain differentiation stages, but low in 7 and 13-day-old larvae. Hoxc6 mRNA was more abundant in fin tissue than brain and eye tissues. Western blotting showed that HOXC6 protein levels were high at embryonic stages, but decreased significantly in 7, 13, 16 and 19-day-old larvae, and levels were essentially consistent with those of mRNA measured by real-time PCR in different tissues. In situ hybridisation showed that the Hoxc6 transcript was strongly expressed in the whole brain and anterior part of the body axis in 1-day-old larvae, but in the hindbrain, pectoral fin, mandible and hypothetical pelvic fin region in 7, 13, 16 and 19-day-old organisms. These results clarify the expression and localisation characteristics of Hoxc6 gene in P. argenteus, and provide a theoretical basis for the molecular mechanism of pelvic fin loss in silver pomfret.
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Affiliation(s)
- Lingzhu Hu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Shun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yu Zhou
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Kai Liao
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China
| | - Shanliang Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology, Ningbo University, Chinese Ministry of Education, Ningbo, China.
| | - Danli Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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14
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Wang Z, Yin J, Zhou W, Bai J, Xie Y, Xu K, Zheng X, Xiao J, Zhou L, Qi X, Li Y, Li X, Xu J. Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types. Nucleic Acids Res 2020; 48:2287-2302. [PMID: 32002550 PMCID: PMC7049702 DOI: 10.1093/nar/gkaa041] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/14/2020] [Indexed: 12/18/2022] Open
Abstract
Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcriptional dysregulation (DMTD) across cancers has not been portrayed. Here, we systematically identified DMTD by integrative analysis of transcriptome, methylome and regulatome across 22 human cancer types. Our results revealed that transcriptional regulation was affected by DNA methylation, involving hundreds of methylation-sensitive TFs (MethTFs). In addition, pan-cancer MethTFs, the regulatory activity of which is generally affected by DNA methylation across cancers, exhibit dominant functional characteristics and regulate several cancer hallmarks. Moreover, pan-cancer MethTFs were found to be affected by DNA methylation in a complex pattern. Finally, we investigated the cooperation among MethTFs and identified a network module that consisted of 43 MethTFs with prognostic potential. In summary, we systematically dissected the transcriptional dysregulation mediated by DNA methylation across cancer types, and our results provide a valuable resource for both epigenetic and transcriptional regulation communities.
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Affiliation(s)
- Zishan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunjin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiangyi Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Li Zhou
- Department of Nephrology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei Province, China
| | - Xiaolin Qi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan 571199, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan 571199, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan 570100, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan 571199, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan 570100, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan 571199, China.,College of Biomedical Information and Engineering, Hainan Medical University, Haikou, Hainan 570100, China
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15
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Velmourougane K, Prasanna R, Supriya P, Ramakrishnan B, Thapa S, Saxena AK. Transcriptome profiling provides insights into regulatory factors involved in Trichoderma viride-Azotobacter chroococcum biofilm formation. Microbiol Res 2019; 227:126292. [PMID: 31421719 DOI: 10.1016/j.micres.2019.06.002] [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] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 06/15/2019] [Indexed: 12/14/2022]
Abstract
Azotobacter chroococcum (Az) and Trichoderma viride (Tv) represent agriculturally important and beneficial plant growth promoting options which contribute towards nutrient management and biocontrol, respectively. When Az and Tv are co-cultured, they form a biofilm, which has proved promising as an inoculant in several crops; however, the basic aspects related to regulation of biofilm formation were not investigated. Therefore, whole transcriptome sequencing (Illumina NextSeq500) and gene expression analyses were undertaken, related to biofilm formation vis a vis Tv and Az growing individually. Significant changes in the transcriptome profiles of biofilm were recorded and validated through qPCR analyses. In-depth evaluation also identified several genes (phoA, phoB, glgP, alg8, sipW, purB, pssA, fadD) specifically involved in biofilm formation in Az, Tv and Tv-Az. Genes coding for RNA-dependent RNA polymerase, ABC transporters, translation elongation factor EF-1, molecular chaperones and double homeobox 4 were either up-regulated or down-regulated during biofilm formation. To our knowledge, this is the first report on the modulation of gene expression in an agriculturally beneficial association, as a biofilm. Our results provide insights into the regulatory factors involved during biofilm formation, which can help to improve the beneficial effects and develop more effective and promising plant- microbe associations.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Puram Supriya
- Centre for Agricultural Bioinformatics, ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Shobit Thapa
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kusmaur, PO Kaitholi, Mau Nath Bhanjan, Uttar Pradesh 275101, India
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16
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Global Analysis of Intercellular Homeodomain Protein Transfer. Cell Rep 2019; 28:712-722.e3. [PMID: 31315049 PMCID: PMC9472292 DOI: 10.1016/j.celrep.2019.06.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 05/06/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
The homeodomain is found in hundreds of transcription factors that play roles in fate determination via cell-autonomous regulation of gene expression. However, some homeodomain-containing proteins (HPs) are thought to be secreted and penetrate neighboring cells to affect the recipient cell fate. To determine whether this is a general characteristic of HPs, we carried out a large-scale validation for intercellular transfer of HPs. Our screening reveals that intercellular transfer is a general feature of HPs, but it occurs in a cell-context-sensitive manner. We also found the secretion is not solely a function of the homeodomain, but it is supported by external motifs containing hydrophobic residues. Thus, mutations of hydrophobic residues of HPs abrogate secretion and consequently interfere with HP function in recipient cells. Collectively, our study proposes that HP transfer is an intercellular communication method that couples the functions of interacting cells. Lee et al. evaluate capabilities of homeodomain proteins (HPs) for transfer between cells. They find that intercellular transfer is a general but cell-context-sensitive property of HP. Intercellular HP transfer can be an unconventional way for the cells to communicate with neighboring cells that associate structurally and functionally.
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17
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A SIX6 Nonsense Variant in Golden Retrievers with Congenital Eye Malformations. Genes (Basel) 2019; 10:genes10060454. [PMID: 31207931 PMCID: PMC6628151 DOI: 10.3390/genes10060454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 12/22/2022] Open
Abstract
Causative genetic variants for more than 30 heritable eye disorders in dogs have been reported. For other clinically described eye disorders, the genetic cause is still unclear. We investigated four Golden Retriever litters segregating for highly variable congenital eye malformations. Several affected puppies had unilateral or bilateral retina dysplasia and/or optic nerve hypoplasia. The four litters shared the same father or grandfather suggesting a heritable condition with an autosomal dominant mode of inheritance. The genome of one affected dog was sequenced and compared to 601 control genomes. A heterozygous private nonsense variant, c.487C>T, was found in the SIX6 gene. This variant is predicted to truncate about a third of the open reading frame, p.(Gln163*). We genotyped all available family members and 464 unrelated Golden Retrievers. All three available cases were heterozygous. Five additional close relatives including the common sire were also heterozygous, but did not show any obvious eye phenotypes. The variant was absent from the 464 unrelated Golden Retrievers and 17 non-affected siblings of the cases. The SIX6 protein is a homeobox transcription factor with a known role in eye development. In humans and other species, SIX6 loss of function variants were reported to cause congenital eye malformations. This strongly suggests that the c.487C>T variant detected contributed to the observed eye malformations. We hypothesize that the residual amount of functional SIX6 protein likely to be expressed in heterozygous dogs is sufficient to explain the observed incomplete penetrance and the varying severity of the eye defects in the affected dogs.
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18
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Cell-Free, Embryo-Specific sncRNA as a Molecular Biological Bridge between Patient Fertility and IVF Efficiency. Int J Mol Sci 2019; 20:ijms20122912. [PMID: 31207900 PMCID: PMC6627040 DOI: 10.3390/ijms20122912] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 01/11/2023] Open
Abstract
Small noncoding RNAs (sncRNAs) are key regulators of the majority of human reproduction events. Understanding their function in the context of gametogenesis and embryogenesis will allow insight into the possible causes of in vitro fertilization (IVF) implantation failure. The aim of this study was to analyze the sncRNA expression profile of the spent culture media on day 4 after fertilization and to reveal a relationship with the morphofunctional characteristics of gametes and resultant embryos, in particular, with the embryo development and implantation potential. Thereto, cell-free, embryo-specific sncRNAs were identified by next generation sequencing (NGS) and quantified by reverse transcription coupled with polymerase chain reaction (RT-PCR) in real-time. Significant differences in the expression level of let-7b-5p, let-7i-5p, piR020401, piR16735, piR19675, piR20326, and piR17716 were revealed between embryo groups of various morphological gradings. Statistically significant correlations were found between the expression profiles of piR16735 and piR020401 with the oocyte-cumulus complex number, let-7b-5p and piR020401 with metaphase II oocyte and two pronuclei embryo numbers, let-7i-5p and piR20497 with the spermatozoid count per milliliter of ejaculate, piR19675 with the percentage of linearly motile spermatozoids, let-7b-5p with the embryo development grade, and let-7i-5p with embryo implantation. According to partial least squares discriminant analysis (PLS-DA), the expression levels of let-7i-5p (Variable Importance in Projection score (VIP) = 1.6262), piR020401 (VIP = 1.45281), and piR20497 (VIP = 1.42765) have the strongest influences on the implantation outcome.
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19
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Chen QY, Des Marais T, Costa M. Deregulation of SATB2 in carcinogenesis with emphasis on miRNA-mediated control. Carcinogenesis 2019; 40:393-402. [PMID: 30916759 PMCID: PMC6514447 DOI: 10.1093/carcin/bgz020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/26/2018] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
The special AT-rich DNA binding protein (SATB2) is a nuclear matrix-associated protein and an important transcription factor for biological development, gene regulation and chromatin remodeling. Aberrant regulation of SATB2 has been found to highly correlate with various types of cancers including lung, colon, prostate, breast, gastric and liver. Recent studies have revealed that a subset of small non-coding RNAs, termed microRNAs (miRNAs), are important regulators of SATB2 function. As post-transcriptional regulators, miRNAs have been found to have fundament importance maintaining normal cellular development. Evidence suggests that multiple miRNAs, including miR-31, miR-34, miR-182, miR-211, miR-599, are capable of regulating SATB2 in cancers of the lung, liver, colon and breast. This review examines the molecular functions of SATB2 and miRNAs in the text of cancer development and potential strategies for cancer therapy with a focus on systemic miRNA delivery.
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Affiliation(s)
- Qiao Yi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Thomas Des Marais
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
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20
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Fu Z, Song J, Zhao J, Jameson PE. Identification and expression of genes associated with the abscission layer controlling seed shattering in Lolium perenne. AOB PLANTS 2019; 11:ply076. [PMID: 30697405 PMCID: PMC6343819 DOI: 10.1093/aobpla/ply076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 05/09/2023]
Abstract
Perennial ryegrass (Lolium perenne) is one of the most important pasture grasses in the world. However, seed production is negatively impacted by the seed shattering (shedding) nature of this species. Recently, genes involved in the seed shattering process have been isolated and functionally characterized in several crop species. The aim of this study was to identify the genes playing critical roles in the seed shattering process in perennial ryegrass. DNA sequences of genes involved in seed shattering in the Poaceae were used to identify and isolate target genes in perennial ryegrass using a comparative genomics strategy. The candidate seed shattering genes were identified using an 'in-house' perennial ryegrass transcriptome database. The relative expression levels of the candidate ryegrass shattering genes were determined using RT-qPCR during different floret and seed developmental stages. Histological analysis of the abscission layer was also conducted. Homologues of seed shattering genes were identified and isolated from perennial ryegrass, and the relative gene expression results suggested that several genes, including LpqSH1 and LpSH1, might have a role in abscission layer formation during seed development. In addition, lignification of the abscission layer may play an important role in the abscission process. A genetic model for seed shattering in perennial ryegrass is suggested and may be useful for directing gene editing towards the production of a reduced-shattering ryegrass.
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Affiliation(s)
- Zeyu Fu
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jiancheng Song
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- School of Life Sciences, Yantai University, Yantai 264005, China
- Corresponding authors’ e-mail addresses: ;
| | - Jiqiang Zhao
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Paula E Jameson
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
- Corresponding authors’ e-mail addresses: ;
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21
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Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell 2019; 172:650-665. [PMID: 29425488 DOI: 10.1016/j.cell.2018.01.029] [Citation(s) in RCA: 1547] [Impact Index Per Article: 309.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) recognize specific DNA sequences to control chromatin and transcription, forming a complex system that guides expression of the genome. Despite keen interest in understanding how TFs control gene expression, it remains challenging to determine how the precise genomic binding sites of TFs are specified and how TF binding ultimately relates to regulation of transcription. This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them. Major classes of human TFs differ markedly in their evolutionary trajectories and expression patterns, underscoring distinct functions. TFs likewise underlie many different aspects of human physiology, disease, and variation, highlighting the importance of continued effort to understand TF-mediated gene regulation.
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Affiliation(s)
- Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Laura F Campitelli
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Pratyush K Das
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jussi Taipale
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland; Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom.
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada.
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
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22
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Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis. Sci Rep 2018; 8:17421. [PMID: 30479355 PMCID: PMC6258689 DOI: 10.1038/s41598-018-35547-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/06/2018] [Indexed: 02/06/2023] Open
Abstract
Recently, human PAIRED-LIKE homeobox transcription factor (TF) genes were discovered whose expression is limited to the period of embryo genome activation up to the 8-cell stage. One of these TFs is LEUTX, but its importance for human embryogenesis is still subject to debate. We confirmed that human LEUTX acts as a TAATCC-targeting transcriptional activator, like other K50-type PAIRED-LIKE TFs. Phylogenetic comparisons revealed that Leutx proteins are conserved across Placentalia and comprise two conserved domains, the homeodomain, and a Leutx-specific domain containing putative transcriptional activation motifs (9aaTAD). Examination of human genotype resources revealed 116 allelic variants in LEUTX. Twenty-four variants potentially affect function, but they occur only heterozygously at low frequency. One variant affects a DNA-specificity determining residue, mutationally reachable by a one-base transition. In vitro and in silico experiments showed that this LEUTX mutation (alanine to valine at position 54 in the homeodomain) results in a transactivational loss-of-function to a minimal TAATCC-containing promoter and a 36 bp motif enriched in genes involved in embryo genome activation. A compensatory change in residue 47 restores function. The results support the notion that human LEUTX functions as a transcriptional activator important for human embryogenesis.
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23
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Feltes BC. Architects meets Repairers: The interplay between homeobox genes and DNA repair. DNA Repair (Amst) 2018; 73:34-48. [PMID: 30448208 DOI: 10.1016/j.dnarep.2018.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
Abstract
Homeobox genes are widely considered the major protagonists of embryonic development and tissue formation. For the past decades, it was established that the deregulation of these genes is intimately related to developmental abnormalities and a broad range of diseases in adults. Since the proper regulation and expression of homeobox genes are necessary for a successful developmental program and tissue function, their relation to DNA repair mechanisms become a necessary discussion. However, important as it is, studies focused on the interplay between homeobox genes and DNA repair are scarce, and there is no critical discussion on the subject. Hence, in this work, I aim to provide the first review of the current knowledge of the interplay between homeobox genes and DNA repair mechanisms, and offer future perspectives on this, yet, young ground for new researches. Critical discussion is conducted, together with a careful assessment of each reviewed topic.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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24
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Losa M, Risolino M, Li B, Hart J, Quintana L, Grishina I, Yang H, Choi IF, Lewicki P, Khan S, Aho R, Feenstra J, Vincent CT, Brown AMC, Ferretti E, Williams T, Selleri L. Face morphogenesis is promoted by Pbx-dependent EMT via regulation of Snail1 during frontonasal prominence fusion. Development 2018; 145:dev157628. [PMID: 29437830 PMCID: PMC5868993 DOI: 10.1242/dev.157628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 01/24/2018] [Indexed: 12/17/2022]
Abstract
Human cleft lip with or without cleft palate (CL/P) is a common craniofacial abnormality caused by impaired fusion of the facial prominences. We have previously reported that, in the mouse embryo, epithelial apoptosis mediates fusion at the seam where the prominences coalesce. Here, we show that apoptosis alone is not sufficient to remove the epithelial layers. We observed morphological changes in the seam epithelia, intermingling of cells of epithelial descent into the mesenchyme and molecular signatures of epithelial-mesenchymal transition (EMT). Utilizing mouse lines with cephalic epithelium-specific Pbx loss exhibiting CL/P, we demonstrate that these cellular behaviors are Pbx dependent, as is the transcriptional regulation of the EMT driver Snail1. Furthermore, in the embryo, the majority of epithelial cells expressing high levels of Snail1 do not undergo apoptosis. Pbx1 loss- and gain-of-function in a tractable epithelial culture system revealed that Pbx1 is both necessary and sufficient for EMT induction. This study establishes that Pbx-dependent EMT programs mediate murine upper lip/primary palate morphogenesis and fusion via regulation of Snail1. Of note, the EMT signatures observed in the embryo are mirrored in the epithelial culture system.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Maurizio Risolino
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Bingsi Li
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - James Hart
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Laura Quintana
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Irina Grishina
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Hui Yang
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Irene F Choi
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patrick Lewicki
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Sameer Khan
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Robert Aho
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Jennifer Feenstra
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
- Karolinska Institute, Department of Physiology and Pharmacology, Nanna svartz väg 2, 17177 Stockholm, Sweden
| | - C Theresa Vincent
- Karolinska Institute, Department of Physiology and Pharmacology, Nanna svartz väg 2, 17177 Stockholm, Sweden
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Anthony M C Brown
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Elisabetta Ferretti
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Trevor Williams
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
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25
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Abstract
Many homeodomain transcription factors can bind methylated DNA
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Affiliation(s)
- Timothy R. Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Samuel A. Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
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26
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Jouhilahti EM, Madissoon E, Vesterlund L, Töhönen V, Krjutškov K, Plaza Reyes A, Petropoulos S, Månsson R, Linnarsson S, Bürglin T, Lanner F, Hovatta O, Katayama S, Kere J. The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation. Development 2016; 143:3459-3469. [PMID: 27578796 PMCID: PMC5087614 DOI: 10.1242/dev.134510] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 08/12/2016] [Indexed: 12/13/2022]
Abstract
Leucine twenty homeobox (LEUTX) is a paired (PRD)-like homeobox gene that is expressed almost exclusively in human embryos during preimplantation development. We previously identified a novel transcription start site for the predicted human LEUTX gene based on the transcriptional analysis of human preimplantation embryos. The novel variant encodes a protein with a complete homeodomain. Here, we provide a detailed description of the molecular cloning of the complete homeodomain-containing LEUTX Using a human embryonic stem cell overexpression model we show that the complete homeodomain isoform is functional and sufficient to activate the transcription of a large proportion of the genes that are upregulated in human embryo genome activation (EGA), whereas the previously predicted partial homeodomain isoform is largely inactive. Another PRD-like transcription factor, DPRX, is then upregulated as a powerful repressor of transcription. We propose a two-stage model of human EGA in which LEUTX acts as a transcriptional activator at the 4-cell stage, and DPRX as a balancing repressor at the 8-cell stage. We conclude that LEUTX is a candidate regulator of human EGA.
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Affiliation(s)
- Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Elo Madissoon
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Liselotte Vesterlund
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Virpi Töhönen
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden Competence Centre on Health Technologies, Tartu 50410, Estonia
| | - Alvaro Plaza Reyes
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Sophie Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, Stockholm 14183, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Thomas Bürglin
- Department of Biomedicine, University of Basel, Basel 4058, Switzerland
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden Science for Life Laboratory, Tomtebodavägen 23 A, Solna 171 21, Sweden Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Biomedicum 1, Haartmaninkatu 8, Helsinki 00290, Finland
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27
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Expression patterns of homeobox genes in the mouse vomeronasal organ at postnatal stages. Gene Expr Patterns 2016; 21:69-80. [PMID: 27521061 DOI: 10.1016/j.gep.2016.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/05/2016] [Accepted: 08/05/2016] [Indexed: 01/27/2023]
Abstract
Homeodomain proteins are encoded by homeobox genes and regulate development and differentiation in many neuronal systems. The mouse vomeronasal organ (VNO) generates in situ mature chemosensory neurons from stem cells. The roles of homeodomain proteins in neuronal differentiation in the VNO are poorly understood. Here we have characterized the expression patterns of 28 homeobox genes in the VNO of C57BL/6 mice at postnatal stages using multicolor fluorescent in situ hybridization. We identified 11 homeobox genes (Dlx3, Dlx4, Emx2, Lhx2, Meis1, Pbx3, Pknox2, Pou6f1, Tshz2, Zhx1, Zhx3) that were expressed exclusively in neurons; 4 homeobox genes (Pax6, Six1, Tgif1, Zfhx3) that were expressed in all non-neuronal cell populations, with Pax6, Six1 and Tgif1 also expressed in some neuronal progenitors and precursors; 12 homeobox genes (Adnp, Cux1, Dlx5, Dlx6, Meis2, Pbx2, Pknox1, Pou2f1, Satb1, Tshz1, Tshz3, Zhx2) with expression in both neuronal and non-neuronal cell populations; and one homeobox gene (Hopx) that was exclusively expressed in the non-sensory epithelium. We studied further in detail the expression of Emx2, Lhx2, Meis1, and Meis2. We found that expression of Emx2 and Lhx2 initiated between neuronal progenitor and neuronal precursor stages. As far as the sensory neurons of the VNO are concerned, Meis1 and Meis2 were only expressed in the apical layer, together with Gnai2, but not in the basal layer.
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28
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Schmitz JF, Zimmer F, Bornberg-Bauer E. Mechanisms of transcription factor evolution in Metazoa. Nucleic Acids Res 2016; 44:6287-97. [PMID: 27288445 PMCID: PMC5291267 DOI: 10.1093/nar/gkw492] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/18/2016] [Accepted: 05/22/2016] [Indexed: 11/12/2022] Open
Abstract
Transcriptions factors (TFs) are pivotal for the regulation of virtually all cellular processes, including growth and development. Expansions of TF families are causally linked to increases in organismal complexity. Here we study the evolutionary dynamics, genetic causes and functional implications of the five largest metazoan TF families. We find that family expansions dominate across the whole metazoan tree; however, some branches experience exceptional family-specific accelerated expansions. Additionally, we find that such expansions are often predated by modular domain rearrangements, which spur the expansion of a new sub-family by separating it from the rest of the TF family in terms of protein-protein interactions. This separation allows for radical shifts in the functional spectrum of a duplicated TF. We also find functional differentiation inside TF sub-families as changes in expression specificity. Furthermore, accelerated family expansions are facilitated by repeats of sequence motifs such as C2H2 zinc fingers. We quantify whole genome duplications and single gene duplications as sources of TF family expansions, implying that some, but not all, TF duplicates are preferentially retained. We conclude that trans-regulatory changes (domain rearrangements) are instrumental for fundamental functional innovations, that cis-regulatory changes (affecting expression) accomplish wide-spread fine tuning and both jointly contribute to the functional diversification of TFs.
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Affiliation(s)
- Jonathan F Schmitz
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Fabian Zimmer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany
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29
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Madissoon E, Jouhilahti EM, Vesterlund L, Töhönen V, Krjutškov K, Petropoulous S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J. Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. Sci Rep 2016; 6:28995. [PMID: 27412763 PMCID: PMC4944136 DOI: 10.1038/srep28995] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 01/07/2023] Open
Abstract
PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes, ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB, NOBOX, TPRX1 and TPRX2, were expressed in human preimplantation embryos. In the current study we characterized these PRD-like homeobox genes in depth and studied their functions as transcription factors. We cloned multiple transcript variants from human embryos and showed that the expression of these genes is specific to embryos and pluripotent stem cells. Overexpression of the genes in human embryonic stem cells confirmed their roles as transcription factors as either activators (CPHX1, CPHX2, ARGFX) or repressors (DPRX, DUXA, TPRX2) with distinct targets that could be explained by the amino acid sequence in homeodomain. Some PRD-like homeodomain transcription factors had high concordance of target genes and showed enrichment for both developmentally important gene sets and a 36 bp DNA recognition motif implicated in Embryo Genome Activation (EGA). Our data implicate a role for these previously uncharacterized PRD-like homeodomain proteins in the regulation of human embryo genome activation and preimplantation embryo development.
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Affiliation(s)
- Elo Madissoon
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | | | - Virpi Töhönen
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kaarel Krjutškov
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Sophie Petropoulous
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Robert Månsson
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | - Shintaro Katayama
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Juha Kere
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
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30
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Parrilla M, Chang I, Degl'Innocenti A, Omura M. Expression of homeobox genes in the mouse olfactory epithelium. J Comp Neurol 2016; 524:2713-39. [PMID: 27243442 DOI: 10.1002/cne.24051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/16/2015] [Accepted: 05/25/2016] [Indexed: 01/22/2023]
Abstract
Homeobox genes constitute a large family of genes widely studied because of their role in the establishment of the body pattern. However, they are also involved in many other events during development and adulthood. The main olfactory epithelium (MOE) is an excellent model to study neurogenesis in the adult nervous system. Analyses of homeobox genes during development show that some of these genes are involved in the formation and establishment of cell diversity in the MOE. Moreover, the mechanisms of expression of odorant receptors (ORs) constitute one of the biggest enigmas in the field. Analyses of OR promoters revealed the presence of homeodomain binding sites in their sequences. Here we characterize the expression patterns of a set of 49 homeobox genes in the MOE with in situ hybridization. We found that seven of them (Dlx3, Dlx5, Dlx6, Msx1, Meis1, Isl1, and Pitx1) are zonally expressed. The homeobox gene Emx1 is expressed in three guanylate cyclase(+) populations, two located in the MOE and the third one in an olfactory subsystem known as Grüneberg ganglion located at the entrance of the nasal cavity. The homeobox gene Tshz1 is expressed in a unique patchy pattern across the MOE. Our findings provide new insights to guide functional studies that aim to understand the complexity of transcription factor expression and gene regulation in the MOE. J. Comp. Neurol. 524:2713-2739, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marta Parrilla
- Max Planck Institut für Biophysik, Frankfurt am Main, Germany
| | - Isabelle Chang
- Max Planck Institut für Biophysik, Frankfurt am Main, Germany
| | - Andrea Degl'Innocenti
- Max Planck Institut für Biophysik, Frankfurt am Main, Germany.,Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Masayo Omura
- Max Planck Institut für Biophysik, Frankfurt am Main, Germany
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31
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eghbx2, a homeobox gene involved in the maturation of calcified structures in Echinococcus granulosus. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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32
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Mariotto A, Pavlova O, Park HS, Huber M, Hohl D. HOPX: The Unusual Homeodomain-Containing Protein. J Invest Dermatol 2016; 136:905-911. [PMID: 27017330 DOI: 10.1016/j.jid.2016.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/23/2015] [Accepted: 01/04/2016] [Indexed: 01/15/2023]
Abstract
The homeodomain-only protein homeobox (HOPX) is the smallest known member of the homeodomain-containing protein family, atypically unable to bind DNA. HOPX is widely expressed in diverse tissues, where it is critically involved in the regulation of proliferation and differentiation. In human skin, HOPX controls epidermal formation through the regulation of late differentiation markers, and HOPX expression correlates with the level of differentiation in cutaneous pathologies. In mouse skin, Hopx was additionally identified as a lineage tracing marker of quiescent hair follicle stem cells. This review discusses current knowledge of HOPX structure and function in normal and pathological conditions.
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Affiliation(s)
- Anita Mariotto
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Olesya Pavlova
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Hyun-Sook Park
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Marcel Huber
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Daniel Hohl
- Laboratory of Cutaneous Biology, Service of Dermatology and Venereology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.
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33
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Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL. Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity (Edinb) 2016; 116:190-9. [PMID: 26419336 PMCID: PMC4806888 DOI: 10.1038/hdy.2015.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
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Affiliation(s)
- N J Kenny
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - K W Chan
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - W Nong
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - Z Qu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - I Maeso
- Centro Andaluz de Biología del
Desarrollo (CABD), Consejo Superior de Investigaciones
Científicas/Universidad Pablo de Olavide, Sevilla,
Spain
| | - H Y Yip
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - T F Chan
- School of Life Sciences, Center of
Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - H S Kwan
- School of Life Sciences, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - P W H Holland
- Department of Zoology, University of
Oxford, Oxford, UK
| | - K H Chu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, The Chinese University of Hong Kong,
Shatin, Hong Kong
| | - J H L Hui
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
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Ghosh AK, Wangsanut T, Fonzi WA, Rolfes RJ. The GRF10 homeobox gene regulates filamentous growth in the human fungal pathogen Candida albicans. FEMS Yeast Res 2015; 15:fov093. [PMID: 26472755 PMCID: PMC4705307 DOI: 10.1093/femsyr/fov093] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/14/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022] Open
Abstract
Candida albicans is the most common human fungal pathogen and can cause life-threatening infections. Filamentous growth is critical in the pathogenicity of C. albicans, as the transition from yeast to hyphal forms is linked to virulence and is also a pivotal process in fungal biofilm development. Homeodomain-containing transcription factors have been linked to developmental processes in fungi and other eukaryotes. We report here on GRF10, a homeobox transcription factor-encoding gene that plays a role in C. albicans filamentation. Deletion of the GRF10 gene, in both C. albicans SN152 and BWP17 strain backgrounds, results in mutants with strongly decreased hyphal growth. The mutants are defective in chlamydospore and biofilm formation, as well as showing dramatically attenuated virulence in a mouse infection model. Expression of the GRF10 gene is highly induced during stationary phase and filamentation. In summary, our study emphasizes a new role for the homeodomain-containing transcription factor in morphogenesis and pathogenicity of C. albicans.
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Affiliation(s)
- Anup K Ghosh
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | | | - William A Fonzi
- Department of Microbiology and Immunology, Georgetown University, Washington, DC 20057, USA
| | - Ronda J Rolfes
- Department of Biology, Georgetown University, Washington, DC 20057, USA
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Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015; 125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
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Affiliation(s)
- Thomas R. Bürglin
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
- />Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Markus Affolter
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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Wilming LG, Boychenko V, Harrow JL. Comprehensive comparative homeobox gene annotation in human and mouse. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav091. [PMID: 26412852 PMCID: PMC4584094 DOI: 10.1093/database/bav091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/31/2015] [Indexed: 11/14/2022]
Abstract
Homeobox genes are a group of genes coding for transcription factors with a DNA-binding helix-turn-helix structure called a homeodomain and which play a crucial role in pattern formation during embryogenesis. Many homeobox genes are located in clusters and some of these, most notably the HOX genes, are known to have antisense or opposite strand long non-coding RNA (lncRNA) genes that play a regulatory role. Because automated annotation of both gene clusters and non-coding genes is fraught with difficulty (over-prediction, under-prediction, inaccurate transcript structures), we set out to manually annotate all homeobox genes in the mouse and human genomes. This includes all supported splice variants, pseudogenes and both antisense and flanking lncRNAs. One of the areas where manual annotation has a significant advantage is the annotation of duplicated gene clusters. After comprehensive annotation of all homeobox genes and their antisense genes in human and in mouse, we found some discrepancies with the current gene set in RefSeq regarding exact gene structures and coding versus pseudogene locus biotype. We also identified previously un-annotated pseudogenes in the DUX, Rhox and Obox gene clusters, which helped us re-evaluate and update the gene nomenclature in these regions. We found that human homeobox genes are enriched in antisense lncRNA loci, some of which are known to play a role in gene or gene cluster regulation, compared to their mouse orthologues. Of the annotated set of 241 human protein-coding homeobox genes, 98 have an antisense locus (41%) while of the 277 orthologous mouse genes, only 62 protein coding gene have an antisense locus (22%), based on publicly available transcriptional evidence.
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Affiliation(s)
- Laurens G Wilming
- HAVANA Group, Informatics Department, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Veronika Boychenko
- HAVANA Group, Informatics Department, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jennifer L Harrow
- HAVANA Group, Informatics Department, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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37
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Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development. Nat Commun 2015; 6:8207. [PMID: 26360614 PMCID: PMC4569847 DOI: 10.1038/ncomms9207] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/29/2015] [Indexed: 12/15/2022] Open
Abstract
Transcriptional program that drives human preimplantation development is largely unknown. Here, by using single-cell RNA sequencing of 348 oocytes, zygotes and single blastomeres from 2- to 3-day-old embryos, we provide a detailed analysis of the human preimplantation transcriptome. By quantifying transcript far 5′-ends (TFEs), we include in our analysis transcripts that derive from alternative promoters. We show that 32 and 129 genes are transcribed during the transition from oocyte to four-cell stage and from four- to eight-cell stage, respectively. A number of identified transcripts originates from previously unannotated genes that include the PRD-like homeobox genes ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB and LEUTX. Employing de novo promoter motif extraction on sequences surrounding TFEs, we identify significantly enriched gene regulatory motifs that often overlap with Alu elements. Our high-resolution analysis of the human transcriptome during preimplantation development may have important implications on future studies of human pluripotent stem cells and cell reprograming. Understanding human preimplantation development is invaluable for human reproduction and stem cell research. By employing single-cell RNA sequencing in oocytes, zygotes and single blastomeres, Töhönen et al. identify new regulatory factors and sequences that drive early human preimplantation development.
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Meng M, Cheng DJ, Peng J, Qian WL, Li JR, Dai DD, Zhang TL, Xia QY. The homeodomain transcription factors antennapedia and POU-M2 regulate the transcription of the steroidogenic enzyme gene Phantom in the silkworm. J Biol Chem 2015; 290:24438-52. [PMID: 26253172 DOI: 10.1074/jbc.m115.651810] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 12/22/2022] Open
Abstract
The steroid hormone ecdysone, which controls insect molting and metamorphosis, is synthesized in the prothoracic gland (PG), and several steroidogenic enzymes that are expressed specifically in the PG are involved in ecdysteroidogenesis. In this study, we identified new regulators that are involved in the transcriptional control of the silkworm steroidogenic enzyme genes. In silico analysis predicted several potential cis-regulatory elements (CREs) for the homeodomain transcription factors Antennapedia (Antp) and POU-M2 in the proximal promoters of steroidogenic enzyme genes. Antp and POU-M2 are expressed dynamically in the PG during larval development, and their overexpression in silkworm embryo-derived (BmE) cells induced the expression of steroidogenic enzyme genes. Importantly, luciferase reporter analyses, electrophoretic mobility shift assays, and chromatin immunoprecipitation assays revealed that Antp and POU-M2 promote the transcription of the silkworm steroidogenic enzyme gene Phantom (Phm) by binding directly to specific motifs within overlapping CREs in the Phm promoter. Mutations of these CREs in the Phm promoter suppressed the transcriptional activities of both Antp and POU-M2 in BmE cells and decreased the activities of mutated Phm promoters in the silkworm PG. In addition, pulldown and co-immunoprecipitation assays demonstrated that Antp can interact with POU-M2. Moreover, RNA interference-mediated down-regulation of either Antp or POU-M2 during silkworm wandering not only decreased the ecdysone titer but also led to the failure of metamorphosis. In summary, our results suggest that Antp and POU-M2 coordinate the transcription of the silkworm Phm gene directly, indicating new roles for homeodomain proteins in regulating insect ecdysteroidogenesis.
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Affiliation(s)
- Meng Meng
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Dao-Jun Cheng
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Jian Peng
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Wen-Liang Qian
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Jia-Rui Li
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Dan-Dan Dai
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Tian-Lei Zhang
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing-You Xia
- From the State Key Laboratory of Silkworm Genome Biology and the Key Sericultural Laboratory of the Ministry of Agriculture, College of Biotechnology, Southwest University, Chongqing 400715, China
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Kim J, Yeon J, Choi SK, Huh YH, Fang Z, Park SJ, Kim MO, Ryoo ZY, Kang K, Kweon HS, Jeon WB, Li C, Kim K. The Evolutionarily Conserved LIM Homeodomain Protein LIM-4/LHX6 Specifies the Terminal Identity of a Cholinergic and Peptidergic C. elegans Sensory/Inter/Motor Neuron-Type. PLoS Genet 2015; 11:e1005480. [PMID: 26305787 PMCID: PMC4549117 DOI: 10.1371/journal.pgen.1005480] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 07/31/2015] [Indexed: 02/01/2023] Open
Abstract
The expression of specific transcription factors determines the differentiated features of postmitotic neurons. However, the mechanism by which specific molecules determine neuronal cell fate and the extent to which the functions of transcription factors are conserved in evolution are not fully understood. In C. elegans, the cholinergic and peptidergic SMB sensory/inter/motor neurons innervate muscle quadrants in the head and control the amplitude of sinusoidal movement. Here we show that the LIM homeobox protein LIM-4 determines neuronal characteristics of the SMB neurons. In lim-4 mutant animals, expression of terminal differentiation genes, such as the cholinergic gene battery and the flp-12 neuropeptide gene, is completely abolished and thus the function of the SMB neurons is compromised. LIM-4 activity promotes SMB identity by directly regulating the expression of the SMB marker genes via a distinct cis-regulatory motif. Two human LIM-4 orthologs, LHX6 and LHX8, functionally substitute for LIM-4 in C. elegans. Furthermore, C. elegans LIM-4 or human LHX6 can induce cholinergic and peptidergic characteristics in the human neuronal cell lines. Our results indicate that the evolutionarily conserved LIM-4/LHX6 homeodomain proteins function in generation of precise neuronal subtypes.
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Affiliation(s)
- Jinmahn Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Jihye Yeon
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Seong-Kyoon Choi
- Laboratory of Biochemistry and Cellular Engineering, Division of NanoBio Technology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Yang Hoon Huh
- Nano-Bio Electron Microscopy Research Group, Korea Basic Science Institute, Daejeon, Korea
| | - Zi Fang
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Seo Jin Park
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), School of Animal BT Science, College of Natural Sciences, Kyungpook National University, Daegu, Korea
| | - Myoung Ok Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), School of Animal BT Science, College of Natural Sciences, Kyungpook National University, Daegu, Korea
| | - Zae Young Ryoo
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), School of Animal BT Science, College of Natural Sciences, Kyungpook National University, Daegu, Korea
| | - Kyeongjin Kang
- Department of Anatomy and Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan School of Medicine, Gyeonggi-Do, Korea
| | - Hee-Seok Kweon
- Nano-Bio Electron Microscopy Research Group, Korea Basic Science Institute, Daejeon, Korea
| | - Won Bae Jeon
- Laboratory of Biochemistry and Cellular Engineering, Division of NanoBio Technology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Chris Li
- Department of Biology, City College of the City University of New York, New York, New York, United States of America
| | - Kyuhyung Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
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40
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Hench J, Henriksson J, Abou-Zied AM, Lüppert M, Dethlefsen J, Mukherjee K, Tong YG, Tang L, Gangishetti U, Baillie DL, Bürglin TR. The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis. PLoS One 2015; 10:e0126947. [PMID: 26024448 PMCID: PMC4448998 DOI: 10.1371/journal.pone.0126947] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022] Open
Abstract
Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.
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Affiliation(s)
- Jürgen Hench
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Johan Henriksson
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Akram M. Abou-Zied
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Martin Lüppert
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Johan Dethlefsen
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Krishanu Mukherjee
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Yong Guang Tong
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Lois Tang
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
| | - Umesh Gangishetti
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
| | - David L. Baillie
- Dept. of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Thomas R. Bürglin
- Dept. of Biosciences and Nutrition & Center for Biosciences, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
- School of Life Sciences, Södertörns Högskola, Huddinge, Sweden
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41
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Gago-Rodrigues I, Fernández-Miñán A, Letelier J, Naranjo S, Tena JJ, Gómez-Skarmeta JL, Martinez-Morales JR. Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis. Nat Commun 2015; 6:7054. [DOI: 10.1038/ncomms8054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 03/26/2015] [Indexed: 11/09/2022] Open
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Paps J, Xu F, Zhang G, Holland PWH. Reinforcing the egg-timer: recruitment of novel lophotrochozoa homeobox genes to early and late development in the pacific oyster. Genome Biol Evol 2015; 7:677-88. [PMID: 25631164 PMCID: PMC5322547 DOI: 10.1093/gbe/evv018] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2015] [Indexed: 11/23/2022] Open
Abstract
The metazoan superclade Lophotrochozoa includes mollusks, annelids, and several other animal phyla. It is reasonable to assume that this organismal diversity may be traced, in part, to changes in developmentally important genes, such as the homeobox genes. Although most comparative studies have focussed on ancient homeobox gene families conserved across bilaterians, there are also "novel" homeobox genes that have arisen more recently in evolution, presumably by duplication followed by radical divergence and functional change. We classify 136 homeobox genes in the genome sequence of the Pacific oyster, Crassostrea gigas. The genome shows an unusually low degree of homeobox gene clustering, with disruption of the NK, Hox, and ParaHox gene clusters. Among the oyster genes, 31 do not fall into ancient metazoan or bilaterian homeobox gene families; we deduce that they originated in the lophotrochozoan clade. We compared eight lophotrochozoan genomes to trace the pattern of homeobox gene evolution across this clade, allowing us to define 19 new lophotrochozoan-specific clades within the ANTP, PRD, TALE, ZF, SIX, and CUT classes. Using transcriptome data, we compared temporal expression of each homeobox gene in oyster development, and discovered that the lophotrochozoan-specific homeobox genes have peak expression either in early development (egg to gastrula) or in late development (after the trochophore larval stage), but rarely in between. This finding is consistent with the egg-timer, hourglass or phylotypic stage model of developmental evolution, in which there is a conserved central phase of development, but more evolutionarily labile early and late phases.
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Affiliation(s)
- Jordi Paps
- Department of Zoology, University of Oxford, United Kingdom
| | - Fei Xu
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guofan Zhang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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43
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Kim N, Min KW, Kang KH, Lee EJ, Kim HT, Moon K, Choi J, Le D, Lee SH, Kim JW. Regulation of retinal axon growth by secreted Vax1 homeodomain protein. eLife 2014; 3:e02671. [PMID: 25201875 PMCID: PMC4178304 DOI: 10.7554/elife.02671] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 09/03/2014] [Indexed: 11/25/2022] Open
Abstract
Retinal ganglion cell (RGC) axons of binocular animals cross the midline at the optic chiasm (OC) to grow toward their synaptic targets in the contralateral brain. Ventral anterior homeobox 1 (Vax1) plays an essential role in the development of the OC by regulating RGC axon growth in a non-cell autonomous manner. In this study, we identify an unexpected function of Vax1 that is secreted from ventral hypothalamic cells and diffuses to RGC axons, where it promotes axonal growth independent of its transcription factor activity. We demonstrate that Vax1 binds to extracellular sugar groups of the heparan sulfate proteoglycans (HSPGs) located in RGC axons. Both Vax1 binding to HSPGs and subsequent penetration into the axoplasm, where Vax1 activates local protein synthesis, are required for RGC axonal growth. Together, our findings demonstrate that Vax1 possesses a novel RGC axon growth factor activity that is critical for the development of the mammalian binocular visual system. DOI:http://dx.doi.org/10.7554/eLife.02671.001 We see the world around us when light bounces off of objects and hits the retina at the back of our eyes. This triggers electrical signals in neurons called retinal ganglion cells (RGCs), which have long structures called axons that extend out from the retina and into the parts of the brain where the signals are interpreted. As the axons grow, various ‘guidance’ molecules direct the axons to the correct part of the brain. One molecule that is important for the growth of retinal ganglion cells' axons is a protein called Vax1. This protein is a transcription factor and binds to DNA to control how and when the molecular templates used to make proteins are made—a process called transcription. Vax1 is not produced in retinal ganglion cells, but it does control the extension of these cells' axons into part of the brain called the ventral hypothalamus. In this study, the axons cross to the other side of the brain by forming a structure called optic chiasm. Humans and mice lacking Vax1 are unable to develop the optic chiasm, and the axons of their retinal ganglion cells do not reach their targets in the brain. These defects were thought to occur because the guidance molecules whose transcription is normally controlled by Vax1 were not produced in the correct amounts when Vax1 is absent. Kim et al. now challenge this view by creating a mutant version of Vax1 that cannot bind to DNA or regulate the transcription of other proteins. Retinal ganglion cell axons could still grow correctly when they were put close to cells expressing this version of the Vax1 protein. This contradicts a hypothesis that Vax1 supports axonal growth by transcribing guidance molecules. Kim et al. followed up these results by examining developing mice and reached the unexpected conclusion that Vax1 is secreted from cells in the ventral hypothalamus and binds to a type of sugar molecule found on the surface of the axons. Once bound, Vax1 can enter the axons where it appears to stimulate the production of proteins inside axons, which helps the axons to grow. These findings reveal unconventional functions for Vax1 that occur in addition to its role as a transcription factor. Vax1 is known to regulate the development of several structures in the brain, so the work of Kim et al. also raises new questions about how Vax1 controls these processes. DOI:http://dx.doi.org/10.7554/eLife.02671.002
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Affiliation(s)
- Namsuk Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kwang Wook Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kyung Hwa Kang
- KAIST Institute of BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Eun Jung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hyoung-Tai Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kyunghwan Moon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jiheon Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dai Le
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sang-Hee Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jin Woo Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc Natl Acad Sci U S A 2013; 110:E4858-66. [PMID: 24277850 DOI: 10.1073/pnas.1311818110] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) are the main players in transcriptional regulation in eukaryotes. However, it remains unclear what role TFs played in the origin of all of the different eukaryotic multicellular lineages. In this paper, we explore how the origin of TF repertoires shaped eukaryotic evolution and, in particular, their role into the emergence of multicellular lineages. We traced the origin and expansion of all known TFs through the eukaryotic tree of life, using the broadest possible taxon sampling and an updated phylogenetic background. Our results show that the most complex multicellular lineages (i.e., those with embryonic development, Metazoa and Embryophyta) have the most complex TF repertoires, and that these repertoires were assembled in a stepwise manner. We also show that a significant part of the metazoan and embryophyte TF toolkits evolved earlier, in their respective unicellular ancestors. To gain insights into the role of TFs in the development of both embryophytes and metazoans, we analyzed TF expression patterns throughout their ontogeny. The expression patterns observed in both groups recapitulate those of the whole transcriptome, but reveal some important differences. Our comparative genomics and expression data reshape our view on how TFs contributed to eukaryotic evolution and reveal the importance of TFs to the origins of multicellularity and embryonic development.
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Cavalieri V, Melfi R, Spinelli G. The Compass-like locus, exclusive to the Ambulacrarians, encodes a chromatin insulator binding protein in the sea urchin embryo. PLoS Genet 2013; 9:e1003847. [PMID: 24086165 PMCID: PMC3784565 DOI: 10.1371/journal.pgen.1003847] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/16/2013] [Indexed: 11/18/2022] Open
Abstract
Chromatin insulators are eukaryotic genome elements that upon binding of specific proteins display barrier and/or enhancer-blocking activity. Although several insulators have been described throughout various metazoans, much less is known about proteins that mediate their functions. This article deals with the identification and functional characterization in Paracentrotus lividus of COMPASS-like (CMPl), a novel echinoderm insulator binding protein. Phylogenetic analysis shows that the CMPl factor, encoded by the alternative spliced Cmp/Cmpl transcript, is the founder of a novel ambulacrarian-specific family of Homeodomain proteins containing the Compass domain. Specific association of CMPl with the boxB cis-element of the sns5 chromatin insulator is demonstrated by using a yeast one-hybrid system, and further corroborated by ChIP-qPCR and trans-activation assays in developing sea urchin embryos. The sns5 insulator lies within the early histone gene cluster, basically between the H2A enhancer and H1 promoter. To assess the functional role of CMPl within this locus, we challenged the activity of CMPl by two distinct experimental strategies. First we expressed in the developing embryo a chimeric protein, containing the DNA-binding domain of CMPl, which efficiently compete with the endogenous CMPl for the binding to the boxB sequence. Second, to titrate the embryonic CMPl protein, we microinjected an affinity-purified CMPl antibody. In both the experimental assays we congruently observed the loss of the enhancer-blocking function of sns5, as indicated by the specific increase of the H1 expression level. Furthermore, microinjection of the CMPl antiserum in combination with a synthetic mRNA encoding a forced repressor of the H2A enhancer-bound MBF1 factor restores the normal H1 mRNA abundance. Altogether, these results strongly support the conclusion that the recruitment of CMPl on sns5 is required for buffering the H1 promoter from the H2A enhancer activity, and this, in turn, accounts for the different level of accumulation of early linker and nucleosomal transcripts. Mounting evidence in several model organisms collectively demonstrates a role for the DNA-protein complexes known as chromatin insulators in orchestrating the functional domain organization of the eukaryotic genome. Several DNA elements displaying features of insulators, viz barrier and/or directional enhancer-blocking activity, have been identified in yeast, Drosophila, sea urchin, vertebrates and plants; however, proteins that bind these DNA sequences eliciting insulator activities are far less known. Here we identify a novel protein, COMPASS-like (CMPl), which is expressed exclusively by the ambulacrarian group of metazoans and interacts directly with the sea urchin sns5 insulator. Sns5 lies within the early histone gene cluster, basically between the H2A enhancer and H1 promoter, where it acts buffering the H1 promoter from the H2A enhancer influence. Intriguingly, we find that CMPl role is absolutely required for the sns5 activity, therefore imposing the different level of accumulation of the linker and nucleosomal transcripts. Overall, our findings add an interesting and novel facet to the chromatin insulator field, highlighting the surprisingly low evolutionary conservation of trans-acting factors binding to chromatin insulators. This opens the possibility that multiple lineage-specific factors modulate chromatin organization in different metazoans.
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Affiliation(s)
- Vincenzo Cavalieri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
- * E-mail: (VC); (GS)
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
| | - Giovanni Spinelli
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
- * E-mail: (VC); (GS)
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Kagoshima H, Cassata G, Tong YG, Pujol N, Niklaus G, Bürglin TR. The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth. Dev Biol 2013; 380:314-23. [PMID: 23608457 DOI: 10.1016/j.ydbio.2013.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/29/2013] [Accepted: 04/04/2013] [Indexed: 11/29/2022]
Abstract
Transcription factors play key roles in cell fate specification and cell differentiation. Previously, we showed that the LIM homeodomain factor CEH-14 is expressed in the AFD neurons where it is required for thermotaxis behavior in Caenorhabditis elegans. Here, we show that ceh-14 is expressed in the phasmid sensory neurons, PHA and PHB, a number of neurons in the tail, i.e., PHC, DVC, PVC, PVN, PVQ, PVT, PVW and PVR, as well as the touch neurons. Analysis of the promoter region shows that important regulatory elements for the expression in most neurons reside from -4kb to -1.65kb upstream of the start codon. Further, within the first introns are elements for expression in the hypodermis. Phylogenetic footprinting revealed numerous conserved motifs in these regions. In addition to the existing deletion mutation ceh-14(ch3), we isolated a new allele, ceh-14(ch2), in which only one LIM domain is disrupted. The latter mutant allele is partially defective for thermosensation. Analysis of both mutant alleles showed that they are defective in phasmid dye-filling. However, the cell body, dendritic outgrowth and ciliated endings of PHA and PHB appear normal, indicating that ceh-14 is not required for growth. The loss of a LIM domain in the ceh-14(ch2) allele causes a partial loss-of-function phenotype. Examination of the neurites of ALA and tail neurons using a ceh-14::GFP reporter shows abnormal axonal outgrowth and pathfinding.
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Affiliation(s)
- Hiroshi Kagoshima
- Biozentrum, Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JSC, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol 2013; 14:R11. [PMID: 23375108 PMCID: PMC4053784 DOI: 10.1186/gb-2013-14-2-r11] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 02/01/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan. RESULTS Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms. CONCLUSIONS Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.
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Antal Z, Rascle C, Cimerman A, Viaud M, Billon-Grand G, Choquer M, Bruel C. The homeobox BcHOX8 gene in Botrytis cinerea regulates vegetative growth and morphology. PLoS One 2012; 7:e48134. [PMID: 23133556 PMCID: PMC3485016 DOI: 10.1371/journal.pone.0048134] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/27/2012] [Indexed: 11/19/2022] Open
Abstract
Filamentous growth and the capacity at producing conidia are two critical aspects of most fungal life cycles, including that of many plant or animal pathogens. Here, we report on the identification of a homeobox transcription factor encoding gene that plays a role in these two particular aspects of the development of the phytopathogenic fungus Botrytis cinerea. Deletion of the BcHOX8 gene in both the B. cinerea B05-10 and T4 strains causes similar phenotypes, among which a curved, arabesque-like, hyphal growth on hydrophobic surfaces; the mutants were hence named Arabesque. Expression of the BcHOX8 gene is higher in conidia and infection cushions than in developing appressorium or mycelium. In the Arabesque mutants, colony growth rate is reduced and abnormal infection cushions are produced. Asexual reproduction is also affected with abnormal conidiophore being formed, strongly reduced conidia production and dramatic changes in conidial morphology. Finally, the mutation affects the fungus ability to efficiently colonize different host plants. Analysis of the B. cinerea genome shows that BcHOX8 is one member of a nine putative homeobox genes family. Available gene expression data suggest that these genes are functional and sequence comparisons indicate that two of them would be specific to B. cinerea and its close relative Sclerotinia sclerotiorum.
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Affiliation(s)
- Zsuzsanna Antal
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Christine Rascle
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Agnès Cimerman
- Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des Plantes, INRA 1290, Thiverval-Grignon, France
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des Plantes, INRA 1290, Thiverval-Grignon, France
| | - Geneviève Billon-Grand
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Mathias Choquer
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
| | - Christophe Bruel
- Unité Mixte de Recherche 5240 - Microbiologie, Adaptation et Pathogénie; Université Lyon 1, CNRS, Bayer CropScience, Villeurbanne, France
- * E-mail:
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Zou C, Levine EM. Vsx2 controls eye organogenesis and retinal progenitor identity via homeodomain and non-homeodomain residues required for high affinity DNA binding. PLoS Genet 2012; 8:e1002924. [PMID: 23028343 PMCID: PMC3447932 DOI: 10.1371/journal.pgen.1002924] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/05/2012] [Indexed: 12/26/2022] Open
Abstract
The homeodomain and adjacent CVC domain in the visual system homeobox (VSX) proteins are conserved from nematodes to humans. Humans with missense mutations in these regions of VSX2 have microphthalmia, suggesting both regions are critical for function. To assess this, we generated the corresponding mutations in mouse Vsx2. The homeodomain mutant protein lacked DNA binding activity and the knock-in mutant phenocopied the null mutant, ocular retardation J. The CVC mutant protein exhibited weakened DNA binding; and, although the corresponding knock-in allele was recessive, it unexpectedly caused the strongest phenotype, as indicated by severe microphthalmia and hyperpigmentation of the neural retina. This occurred through a cryptic transcriptional feedback loop involving the transcription factors Mitf and Otx1 and the Cdk inhibitor p27Kip1. Our data suggest that the phenotypic severity of the CVC mutant depends on the weakened DNA binding activity elicited by the CVC mutation and a previously unknown protein interaction between Vsx2 and its regulatory target Mitf. Our data also suggest that an essential function of the CVC domain is to assist the homeodomain in high-affinity DNA binding, which is required for eye organogenesis and unhindered execution of the retinal progenitor program in mammals. Finally, the genetic and phenotypic behaviors of the CVC mutation suggest it has the characteristics of a recessive neomorph, a rare type of genetic allele. Problems with the early development of the mammalian retina can cause congenital eye defects such as microphthalmia, in which the eye is dramatically smaller and functionally compromised. Severe microphthalmia is associated with mutations in the retinal-expressed visual system homeobox 2 (Vsx2) gene, but how Vsx2 controls retinal development, and ultimately eye formation, has remained unclear. We assessed the impact of two missense mutations, discovered in humans, on Vsx2 function and eye development in mice. One mutation altered a highly conserved residue of the homeodomain, and the other altered a highly conserved residue in the CVC domain, a region of unresolved function. Both mutations impacted the DNA binding properties of the protein, although to differing extents. Likewise, both mutations caused microphthalmia and disruptions in retinal development, also to differing extents and by distinct mechanisms. Our data suggest that Vsx2 acts as a gatekeeper of the retinal gene expression program by preventing the activation of interfering or competing gene expression programs. We propose that the evolutionary stable association between the VSX-class homeodomain and CVC domain set the stage for Vsx2 or its archetype to assume a gatekeeper function for retinal development and ultimately eye organogenesis.
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Affiliation(s)
- Changjiang Zou
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward M. Levine
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Holland PWH. Evolution of homeobox genes. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:31-45. [DOI: 10.1002/wdev.78] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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