1
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Sakamoto M, Ito A, Wakayama S, Sasaki H, Wakayama T, Ishiuchi T. Detection of newly synthesized RNA reveals transcriptional reprogramming during ZGA and a role of Obox3 in totipotency acquisition. Cell Rep 2024; 43:114118. [PMID: 38619966 DOI: 10.1016/j.celrep.2024.114118] [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: 07/05/2023] [Revised: 02/15/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
Zygotic genome activation (ZGA) after fertilization enables the maternal-to-zygotic transition. However, the global view of ZGA, particularly at initiation, is incompletely understood. Here, we develop a method to capture and sequence newly synthesized RNA in early mouse embryos, providing a view of transcriptional reprogramming during ZGA. Our data demonstrate that major ZGA gene activation begins earlier than previously thought. Furthermore, we identify a set of genes activated during minor ZGA, the promoters of which show enrichment of the Obox factor motif, and find that Obox3 or Obox5 overexpression in mouse embryonic stem cells activates ZGA genes. Notably, the expression of Obox factors is severely impaired in somatic cell nuclear transfer (SCNT) embryos, and restoration of Obox3 expression corrects the ZGA profile and greatly improves SCNT embryo development. Hence, our study reveals dynamic transcriptional reprogramming during ZGA and underscores the crucial role of Obox3 in facilitating totipotency acquisition.
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Affiliation(s)
- Mizuki Sakamoto
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Aoi Ito
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Sayaka Wakayama
- Advanced Biotechnology Center, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Teruhiko Wakayama
- Advanced Biotechnology Center, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Takashi Ishiuchi
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan.
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2
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Gawriyski L, Tan Z, Liu X, Chowdhury I, Malaymar Pinar D, Zhang Q, Weltner J, Jouhilahti EM, Wei GH, Kere J, Varjosalo M. Interaction network of human early embryonic transcription factors. EMBO Rep 2024; 25:1589-1622. [PMID: 38297188 PMCID: PMC10933267 DOI: 10.1038/s44319-024-00074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaonan Liu
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | | | - Dicle Malaymar Pinar
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Qin Zhang
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Markku Varjosalo
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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3
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Onodera W, Kawasaki K, Oishi M, Aoki S, Asahi T. Functional Divergence and Origin of the Vertebrate Praja Family. J Mol Evol 2024; 92:21-29. [PMID: 38158403 DOI: 10.1007/s00239-023-10150-z] [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: 08/27/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
The Praja family is an E3 ubiquitin ligase, promoting polyubiquitination and subsequent degradation of substrates. It comprises two paralogs, praja1 and praja2. Prior research suggests these paralogs have undergone functional divergence, with examples, such as their distinct roles in neurite outgrowth. However, the specific evolutionary trajectories of each paralog remain largely unexplored preventing mechanistic understanding of functional differences between paralogs. Here, we investigated the phylogeny and divergence of the vertebrate Praja family through molecular evolutionary analysis. Phylogenetic examination of the vertebrate praja revealed that praja1 and praja2 originated from the common ancestor of placentals via gene duplication, with praja1 evolving at twice the rate of praja2 shortly after the duplication. Moreover, a unique evolutionary trajectory for praja1 relative to other vertebrate Praja was indicated, as evidenced by principal component analysis on GC content, codon usage frequency, and amino acid composition. Subsequent motif/domain comparison revealed conserved N terminus and C terminus in praja1 and praja2, together with praja1-specific motifs, including nuclear localization signal and Ala-Gly-Ser repeats. The nuclear localization signal was demonstrated to be functional in human neuroblastoma SH-SY5Y cells using deletion mutant, while praja2 was exclusively expressed in the nucleus. These discoveries contribute to a more comprehensive understanding of the Praja family's phylogeny and suggest a functional divergence between praja1 and praja2. Specifically, the shift of praja1 into the nucleus implies the degradation of novel substrates located in the nucleus as an evolutionary consequence.
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Affiliation(s)
- Wataru Onodera
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan.
| | - Kotaro Kawasaki
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan
| | - Mizuho Oishi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan
| | - Shiho Aoki
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan.
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda-Tsurumaki, Shinjuku, Tokyo, 162-0041, Japan.
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4
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Ishiuchi T, Sakamoto M. Molecular mechanisms underlying totipotency. Life Sci Alliance 2023; 6:e202302225. [PMID: 37666667 PMCID: PMC10480501 DOI: 10.26508/lsa.202302225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
Numerous efforts to understand pluripotency in mammals, using pluripotent stem cells in culture, have enabled the generation of artificially induced pluripotent stem cells, which serve as a valuable source for regenerative medicine and the creation of disease models. In contrast to these tremendous successes in the pluripotency field in the past few decades, our understanding of totipotency, which is highlighted by its broader plasticity than pluripotency, is still limited. This is largely attributable to the scarcity of available materials and the lack of in vitro models. However, recent technological advances have unveiled molecular features that characterize totipotent cells. Single-cell or low-input sequencing technologies allow the dissection of pre- and post-fertilization developmental processes at the molecular level with high resolution. In this review, we describe some of the key findings in understanding totipotency and discuss how totipotency is acquired at the beginning of life.
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Affiliation(s)
- Takashi Ishiuchi
- https://ror.org/059x21724 Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Mizuki Sakamoto
- https://ror.org/059x21724 Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
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5
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Morino Y, Yoshikawa H. Role of maternal spiralian-specific homeobox gene SPILE-E in the specification of blastomeres along the animal-vegetal axis during the early cleavage stages of mollusks. Dev Growth Differ 2023; 65:384-394. [PMID: 37392142 DOI: 10.1111/dgd.12874] [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: 03/30/2023] [Revised: 05/24/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Spiralians, one of the major clades of bilaterians, share a unique development known as spiralian development, characterized by the formation of tiers of cells called quartets, which exhibit different developmental potentials along the animal-vegetal axis. Recently, spiralian-specific TALE-type homeobox genes (SPILE) have been identified, some of which show zygotic and staggered expression patterns along the animal-vegetal axis and function in quartet specification in mollusks. However, it is unclear which maternal molecular components control the zygotic expression of these transcription factors. In this study, we focused on SPILE-E, a maternal transcription factor, and investigated its expression and function in mollusks. We found that the maternal and ubiquitous expression of SPILE-E in the cleavage stages is conserved in molluskan species, including limpets, mussels, and chitons. We knocked down SPILE-E in limpets and revealed that the expression of transcription factors specifically expressed in the first quartet (1q2 ; foxj1b) and second quartet (2q; SPILE-B) was abolished, whereas the macromere-quartet marker (SPILE-C) was ectopically expressed in 1q2 in SPILE-E morphants. Moreover, we showed that the expression of SPILE-A, which upregulates SPILE-B but represses SPILE-C expression, decreased in SPILE-E morphants. Consistent with changes in the expression pattern of the above transcription factors, SPILE-E-morphant larvae exhibited patchy or complete loss of expression of marker genes of ciliated cells and shell fields, possibly reflecting incomplete specification of 1q2 and 2q. Our results provide a molecular framework for quartet specification and highlight the importance of maternal lineage-specific transcription factors in the development and evolution of spiralians.
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Affiliation(s)
- Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroki Yoshikawa
- Graduate School of Science and Life Technology, University of Tsukuba, Tsukuba, Japan
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6
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Taubenschmid-Stowers J, Reik W. Human 8-cell embryo-like cells from pluripotent stem cells. Curr Opin Genet Dev 2023; 81:102066. [PMID: 37356343 DOI: 10.1016/j.gde.2023.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/28/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023]
Abstract
The totipotent embryo initiates transcription during zygotic or embryonic genome activation (EGA, ZGA). ZGA occurs at the 8-cell stage in humans and its failure leads to developmental arrest. Understanding the molecular pathways underlying ZGA and totipotency is essential to comprehend human development. Recently, human 8-cell-like cells (8CLCs) have been discovered in vitro that resemble the 8-cell embryo. 8CLCs exist among naive pluripotent stem cells and can be induced genetically or chemically. Their ZGA-like transcriptome, transposable element activation, 8-cell embryo-specific protein expression, and developmental properties make them an exceptional model system to study early embryonic cell-state transitions and human totipotency programs in vitro.
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Affiliation(s)
| | - Wolf Reik
- Altos Labs Cambridge Institute of Science, Cambridge, UK; Babraham Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK. https://twitter.com/@ReikLab
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7
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Ji S, Chen F, Stein P, Wang J, Zhou Z, Wang L, Zhao Q, Lin Z, Liu B, Xu K, Lai F, Xiong Z, Hu X, Kong T, Kong F, Huang B, Wang Q, Xu Q, Fan Q, Liu L, Williams CJ, Schultz RM, Xie W. OBOX regulates mouse zygotic genome activation and early development. Nature 2023; 620:1047-1053. [PMID: 37459895 PMCID: PMC10528489 DOI: 10.1038/s41586-023-06428-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/12/2023] [Indexed: 08/25/2023]
Abstract
Zygotic genome activation (ZGA) activates the quiescent genome to enable the maternal-to-zygotic transition1,2. However, the identity of transcription factors that underlie mammalian ZGA in vivo remains elusive. Here we show that OBOX, a PRD-like homeobox domain transcription factor family (OBOX1-OBOX8)3-5, are key regulators of mouse ZGA. Mice deficient for maternally transcribed Obox1/2/5/7 and zygotically expressed Obox3/4 had a two-cell to four-cell arrest, accompanied by impaired ZGA. The Obox knockout defects could be rescued by restoring either maternal and zygotic OBOX, which suggests that maternal and zygotic OBOX redundantly support embryonic development. Chromatin-binding analysis showed that Obox knockout preferentially affected OBOX-binding targets. Mechanistically, OBOX facilitated the 'preconfiguration' of RNA polymerase II, as the polymerase relocated from the initial one-cell binding targets to ZGA gene promoters and distal enhancers. Impaired polymerase II preconfiguration in Obox mutants was accompanied by defective ZGA and chromatin accessibility transition, as well as aberrant activation of one-cell polymerase II targets. Finally, ectopic expression of OBOX activated ZGA genes and MERVL repeats in mouse embryonic stem cells. These data thus demonstrate that OBOX regulates mouse ZGA and early embryogenesis.
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Affiliation(s)
- Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fengling Chen
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiacheng Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ziming Zhou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qing Zhao
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- College of Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaoyu Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Tianxiang Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Anatomy, Physiology and Cell Biology School of Veterinary Medicine University of California, Davis, Davis, CA, USA.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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8
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Hara Y, Kuraku S. The impact of local genomic properties on the evolutionary fate of genes. eLife 2023; 12:82290. [PMID: 37223962 DOI: 10.7554/elife.82290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Functionally indispensable genes are likely to be retained and otherwise to be lost during evolution. This evolutionary fate of a gene can also be affected by factors independent of gene dispensability, including the mutability of genomic positions, but such features have not been examined well. To uncover the genomic features associated with gene loss, we investigated the characteristics of genomic regions where genes have been independently lost in multiple lineages. With a comprehensive scan of gene phylogenies of vertebrates with a careful inspection of evolutionary gene losses, we identified 813 human genes whose orthologs were lost in multiple mammalian lineages: designated 'elusive genes.' These elusive genes were located in genomic regions with rapid nucleotide substitution, high GC content, and high gene density. A comparison of the orthologous regions of such elusive genes across vertebrates revealed that these features had been established before the radiation of the extant vertebrates approximately 500 million years ago. The association of human elusive genes with transcriptomic and epigenomic characteristics illuminated that the genomic regions containing such genes were subject to repressive transcriptional regulation. Thus, the heterogeneous genomic features driving gene fates toward loss have been in place and may sometimes have relaxed the functional indispensability of such genes. This study sheds light on the complex interplay between gene function and local genomic properties in shaping gene evolution that has persisted since the vertebrate ancestor.
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Affiliation(s)
- Yuichiro Hara
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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9
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Marlétaz F, Couloux A, Poulain J, Labadie K, Da Silva C, Mangenot S, Noel B, Poustka AJ, Dru P, Pegueroles C, Borra M, Lowe EK, Lhomond G, Besnardeau L, Le Gras S, Ye T, Gavriouchkina D, Russo R, Costa C, Zito F, Anello L, Nicosia A, Ragusa MA, Pascual M, Molina MD, Chessel A, Di Carlo M, Turon X, Copley RR, Exposito JY, Martinez P, Cavalieri V, Ben Tabou de Leon S, Croce J, Oliveri P, Matranga V, Di Bernardo M, Morales J, Cormier P, Geneviève AM, Aury JM, Barbe V, Wincker P, Arnone MI, Gache C, Lepage T. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. CELL GENOMICS 2023; 3:100295. [PMID: 37082140 PMCID: PMC10112332 DOI: 10.1016/j.xgen.2023.100295] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 12/24/2022] [Accepted: 03/06/2023] [Indexed: 04/22/2023]
Abstract
Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement.
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Affiliation(s)
- Ferdinand Marlétaz
- Center for Life’s Origin & Evolution, Department of Genetics, Evolution, & Environment, University College London, WC1 6BT London, UK
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Sophie Mangenot
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Albert J. Poustka
- Evolution and Development Group, Max-Planck-Institut für Molekulare Genetik, 14195 Berlin, Germany
- Dahlem Center for Genome Research and Medical Systems Biology (Environmental and Phylogenomics Group), 12489 Berlin, Germany
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Cinta Pegueroles
- Institute for Research on Biodiversity (IRBio), Department of Genetics, Microbiology, and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - Marco Borra
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Elijah K. Lowe
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guy Lhomond
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Lydia Besnardeau
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Stéphanie Le Gras
- Plateforme GenomEast, IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, 67404 Illirch Cedex, France
| | - Tao Ye
- Plateforme GenomEast, IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, 67404 Illirch Cedex, France
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, 904-0495 Onna-son, Japan
| | - Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Caterina Costa
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Letizia Anello
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Aldo Nicosia
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Marta Pascual
- Institute for Research on Biodiversity (IRBio), Department of Genetics, Microbiology, and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - M. Dolores Molina
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
| | - Aline Chessel
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
| | - Marta Di Carlo
- Institute for Biomedical Research and Innovation (CNR), 90146 Palermo, Italy
| | - Xavier Turon
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB, CSIC), 17300 Blanes, Spain
| | - Richard R. Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Jean-Yves Exposito
- Laboratoire de Biologie Tissulaire et d’Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université Lyon 1, 69367 Lyon, France
| | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Smadar Ben Tabou de Leon
- Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, 31095 Haifa, Israel
| | - Jenifer Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Paola Oliveri
- Center for Life’s Origin & Evolution, Department of Genetics, Evolution, & Environment, University College London, WC1 6BT London, UK
| | - Valeria Matranga
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Maria Di Bernardo
- Consiglio Nazionale delle Ricerche, Istituto di Farmacologia Traslazionale, 90146 Palermo, Italy
| | - Julia Morales
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, CNRS, Sorbonne Université, 29680 Roscoff, France
| | - Patrick Cormier
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, CNRS, Sorbonne Université, 29680 Roscoff, France
| | - Anne-Marie Geneviève
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, 66650 Banyuls/Mer, France
| | - Jean Marc Aury
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Christian Gache
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Thierry Lepage
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
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10
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Gawriyski L, Jouhilahti EM, Yoshihara M, Fei L, Weltner J, Airenne TT, Trokovic R, Bhagat S, Tervaniemi MH, Murakawa Y, Salokas K, Liu X, Miettinen S, Bürglin TR, Sahu B, Otonkoski T, Johnson MS, Katayama S, Varjosalo M, Kere J. Comprehensive characterization of the embryonic factor LEUTX. iScience 2023; 26:106172. [PMID: 36876139 PMCID: PMC9978639 DOI: 10.1016/j.isci.2023.106172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/01/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Liangru Fei
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland.,Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 14186 Stockholm, Sweden.,Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden
| | - Tomi T Airenne
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Ras Trokovic
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mari H Tervaniemi
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.,Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,IFOM-ETS, Milan, Italy
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Sini Miettinen
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.,Centre for Molecular Medicine Norway (NCMM), University of Oslo, 0349 Oslo, Norway
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Children's Hospital, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
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11
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Moya-Jódar M, Ullate-Agote A, Barlabé P, Rodríguez-Madoz JR, Abizanda G, Barreda C, Carvajal-Vergara X, Vilas-Zornoza A, Romero JP, Garate L, Agirre X, Coppiello G, Prósper F, Aranguren XL. Revealing cell populations catching the early stages of human embryo development in naive pluripotent stem cell cultures. Stem Cell Reports 2022; 18:64-80. [PMID: 36563688 PMCID: PMC9860119 DOI: 10.1016/j.stemcr.2022.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Naive human pluripotent stem cells (hPSCs) are defined as the in vitro counterpart of the human preimplantation embryo's epiblast and are used as a model system to study developmental processes. In this study, we report the discovery and characterization of distinct cell populations coexisting with epiblast-like cells in 5iLAF naive human induced PSC (hiPSC) cultures. It is noteworthy that these populations closely resemble different cell types of the human embryo at early developmental stages. While epiblast-like cells represent the main cell population, interestingly we detect a cell population with gene and transposable element expression profile closely resembling the totipotent eight-cell (8C)-stage human embryo, and three cell populations analogous to trophectoderm cells at different stages of their maturation process: transition, early, and mature stages. Moreover, we reveal the presence of cells resembling primitive endoderm. Thus, 5iLAF naive hiPSC cultures provide an excellent opportunity to model the earliest events of human embryogenesis, from the 8C stage to the peri-implantation period.
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Affiliation(s)
- Marta Moya-Jódar
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Asier Ullate-Agote
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Paula Barlabé
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Juan Roberto Rodríguez-Madoz
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Gloria Abizanda
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Carolina Barreda
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Xonia Carvajal-Vergara
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Amaia Vilas-Zornoza
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Juan Pablo Romero
- Advanced Genomics Laboratory, Program of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain,10x Genomics, 6230 Stoneridge Mall Road, Pleasanton, CA 94588, USA
| | - Leire Garate
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Giulia Coppiello
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain
| | - Felipe Prósper
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain; Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain; Hemato-Oncology Program, Center for Applied Medical Research (CIMA), IDISNA, University of Navarra, Pamplona, Spain; Hematology Department, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain.
| | - Xabier L. Aranguren
- Program of Regenerative Medicine, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain,Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona 31008, Spain,Corresponding author
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12
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Zou Z, Zhang C, Wang Q, Hou Z, Xiong Z, Kong F, Wang Q, Song J, Liu B, Liu B, Wang L, Lai F, Fan Q, Tao W, Zhao S, Ma X, Li M, Wu K, Zhao H, Chen ZJ, Xie W. Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation. Science 2022; 378:abo7923. [PMID: 36074823 DOI: 10.1126/science.abo7923] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Translational regulation plays a critical role during the oocyte-to-embryo transition (OET) and zygotic genome activation (ZGA). Here, we integrated ultra-low-input Ribo-seq with mRNA-seq to co-profile the translatome and transcriptome in human oocytes and early embryos. Comparison with mouse counterparts identified widespread differentially translated genes functioning in epigenetic reprogramming, transposon defense, and small RNA biogenesis, in part driven by species-specific regulatory elements in 3' untranslated regions. Moreover, PRD-like homeobox transcription factors, including TPRXL, TPRX1, and TPRX2, are highly translated around ZGA. TPRX1/2/L knockdown leads to defective ZGA and preimplantation development. Ectopically expressed TPRXs bind and activate key ZGA genes in human embryonic stem cells. These data reveal the conservation and divergence of translation landscapes during OET and identify critical regulators of human ZGA.
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Affiliation(s)
- Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chuanxin Zhang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Qiuyan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenzhen Hou
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinzhu Song
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Boyang Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Shuai Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Xiaonan Ma
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Miao Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong 250012, China.,Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250012, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China.,Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China.,Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
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13
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Lewin TD, Fouladi-Nashta AA, Holland PWH. PRD-class homeobox genes in bovine early embryos: function, evolution and overlapping roles. Mol Biol Evol 2022; 39:6581424. [PMID: 35512670 PMCID: PMC9117796 DOI: 10.1093/molbev/msac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Eutherian Totipotent Cell Homeobox (ETCHbox) genes are mammalian-specific PRD-class homeobox genes with conserved expression in the preimplantation embryo but fast-evolving and highly divergent sequences. Here, we exploit an ectopic expression approach to examine the role of bovine ETCHbox genes and show that ARGFX and LEUTX homeodomain proteins upregulate genes normally expressed in the blastocyst; the identities of the regulated genes suggest that, in vivo, the ETCHbox genes play a role in coordinating the physical formation of the blastocyst structure. Both genes also downregulate genes expressed earlier during development and genes associated with an undifferentiated cell state, possibly via the JAK/STAT pathway. We find evidence that bovine ARGFX and LEUTX have overlapping functions, in contrast to their antagonistic roles in humans. Finally, we characterize a mutant bovine ARGFX allele which eliminates the homeodomain and show that homozygous mutants are viable. These data support the hypothesis of functional overlap between ETCHbox genes within a species, roles for ETCHbox genes in blastocyst formation and the change of their functions over evolutionary time.
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Affiliation(s)
- Thomas D Lewin
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Ali A Fouladi-Nashta
- Comparative Biomedical Sciences Department, Royal Veterinary College, Hawkshead Campus, North Mymms, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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14
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Mazid MA, Ward C, Luo Z, Liu C, Li Y, Lai Y, Wu L, Li J, Jia W, Jiang Y, Liu H, Fu L, Yang Y, Ibañez DP, Lai J, Wei X, An J, Guo P, Yuan Y, Deng Q, Wang Y, Liu Y, Gao F, Wang J, Zaman S, Qin B, Wu G, Maxwell PH, Xu X, Liu L, Li W, Esteban MA. Rolling back human pluripotent stem cells to an eight-cell embryo-like stage. Nature 2022; 605:315-324. [PMID: 35314832 DOI: 10.1038/s41586-022-04625-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
After fertilization, the quiescent zygote experiences a burst of genome activation that initiates a short-lived totipotent state. Understanding the process of totipotency in human cells would have broad applications. However, in contrast to in mice1,2, demonstration of the time of zygotic genome activation or the eight-cell (8C) stage in in vitro cultured human cells has not yet been reported, and the study of embryos is limited by ethical and practical considerations. Here we describe a transgene-free, rapid and controllable method for producing 8C-like cells (8CLCs) from human pluripotent stem cells. Single-cell analysis identified key molecular events and gene networks associated with this conversion. Loss-of-function experiments identified fundamental roles for DPPA3, a master regulator of DNA methylation in oocytes3, and TPRX1, a eutherian totipotent cell homeobox (ETCHbox) family transcription factor that is absent in mice4. DPPA3 induces DNA demethylation throughout the 8CLC conversion process, whereas TPRX1 is a key executor of 8CLC gene networks. We further demonstrate that 8CLCs can produce embryonic and extraembryonic lineages in vitro or in vivo in the form of blastoids5 and complex teratomas. Our approach provides a resource to uncover the molecular process of early human embryogenesis.
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Affiliation(s)
- Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- BGI-Shenzhen, Shenzhen, China
| | - Liang Wu
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Jinxiu Li
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Jiang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lixin Fu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueli Yang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - David P Ibañez
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoyu Wei
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Juan An
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Pengcheng Guo
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yue Yuan
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Qiuting Deng
- University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Shahriar Zaman
- Department of Genetic Engineering and Biotechnology, Faculty of Life and Earth Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- BGI-Shenzhen, Shenzhen, China.
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
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15
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Morino Y. Dynamic evolutionary history of spiralian-specific TALE homeobox genes in mollusks. Dev Growth Differ 2022; 64:198-209. [PMID: 35441397 DOI: 10.1111/dgd.12779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022]
Abstract
Homeobox genes play essential roles in the early development of many animals. Although the repertoire of most homeobox genes, including three amino acid loop extension (TALE)-type homeobox genes, is conserved in animals, spiralian-TALE (SPILE) genes are a notable exception. In this study, SPILE genes were extracted from the genomic data of 22 mollusk species and classified into four clades (-A/C, -B, -D, and -E) to determine which SPILE genes exhibit dynamic repertoire changes. While SPILE-D and -E duplications were rarely observed, SPILE-B duplication was observed in the bivalve lineage and SPILE-A/C duplication was observed in multiple clades. Conversely, most or all SPILE genes were lost in cephalopods and in some gastropod lineages. SPILE gene expression patterns were also analyzed in multiple mollusk species using publicly available RNA-seq data. The majority of SPILE genes examined, particularly those in the A/C- and B-clades, were specifically expressed during early development, suggesting that most SPILE genes exert specific roles in early development. This comprehensive cataloging and characterization revealed a dynamic evolutionary history, including SPILE-A/C and -B gene duplications and the loss of SPILE genes in several lineages. Furthermore, this study provides a useful resource for studying the molecular mechanism of spiralian early development and the evolution of young and lineage-specific transcription factors.
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Affiliation(s)
- Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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16
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Taubenschmid-Stowers J, Rostovskaya M, Santos F, Ljung S, Argelaguet R, Krueger F, Nichols J, Reik W. 8C-like cells capture the human zygotic genome activation program in vitro. Cell Stem Cell 2022; 29:449-459.e6. [PMID: 35216671 PMCID: PMC8901440 DOI: 10.1016/j.stem.2022.01.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/26/2021] [Accepted: 01/28/2022] [Indexed: 01/12/2023]
Abstract
The activation of the embryonic genome marks the first major wave of transcription in the developing organism. Zygotic genome activation (ZGA) in mouse 2-cell embryos and 8-cell embryos in humans is crucial for development. Here, we report the discovery of human 8-cell-like cells (8CLCs) among naive embryonic stem cells, which transcriptionally resemble the 8-cell human embryo. They express ZGA markers, including ZSCAN4 and LEUTX, and transposable elements, such as HERVL and MLT2A1. 8CLCs show reduced SOX2 levels and can be identified using TPRX1 and H3.Y marker proteins in vitro. Overexpression of the transcription factor DUX4 and spliceosome inhibition increase human ZGA-like transcription. Excitingly, the 8CLC markers TPRX1 and H3.Y are also expressed in ZGA-stage 8-cell human embryos and may thus be relevant in vivo. 8CLCs provide a unique opportunity to characterize human ZGA-like transcription and might provide critical insights into early events in embryogenesis in humans. ZGA genes and transposable elements are expressed in 8CLCs but not in naive stem cells DUX4 overexpression and spliceosome inhibition induce ZGA-like transcription 8CLC marker proteins TPRX1 and H3.Y are expressed in 8-cell human embryos 8CLCs can be used to study human ZGA-like programs in vitro
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Affiliation(s)
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Sebastian Ljung
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Felix Krueger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Jennifer Nichols
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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17
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Lewin TD, Royall AH, Holland PWH. Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires. J Mol Evol 2021; 89:396-414. [PMID: 34097121 PMCID: PMC8208926 DOI: 10.1007/s00239-021-10012-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2021] [Indexed: 11/21/2022]
Abstract
The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.
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Affiliation(s)
- Thomas D Lewin
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Amy H Royall
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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18
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Yamazaki A, Morino Y, Urata M, Yamaguchi M, Minokawa T, Furukawa R, Kondo M, Wada H. pmar1/ phb homeobox genes and the evolution of the double-negative gate for endomesoderm specification in echinoderms. Development 2020; 147:dev.182139. [PMID: 32001441 DOI: 10.1242/dev.182139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
In several model animals, the earliest phases of embryogenesis are regulated by lineage-specific genes, such as Drosophila bicoid Sea urchin (echinoid) embryogenesis is initiated by zygotic expression of pmar1, a paired-class homeobox gene that has been considered to be present only in the lineage of modern urchins (euechinoids). In euechinoids, Pmar1 promotes endomesoderm specification by repressing the hairy and enhancer of split C (hesC) gene. Here, we have identified the basal echinoid (cidaroid) pmar1 gene, which also promotes endomesoderm specification but not by repressing hesC A further search for related genes demonstrated that other echinoderms have pmar1-related genes named phb Functional analyses of starfish Phb proteins indicated that, similar to cidaroid Pmar1, they promote activation of endomesoderm regulatory gene orthologs via an unknown repressor that is not HesC. Based on these results, we propose that Pmar1 may have recapitulated the regulatory function of Phb during the early diversification of echinoids and that the additional repressor HesC was placed under the control of Pmar1 in the euechinoid lineage. This case provides an exceptional model for understanding how early developmental processes diverge.
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Affiliation(s)
- Atsuko Yamazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Urata
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan.,Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaaki Yamaguchi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Takuya Minokawa
- Research Center for Marine Biology, Tohoku University, Sakamoto 9, Asamushi, Aomori 039-3501, Japan
| | - Ryohei Furukawa
- Department of Biology, Research and Education Center for Natural Sciences, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8521, Japan
| | - Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan
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19
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Royall AH, Frankenberg S, Pask AJ, Holland PWH. Of eyes and embryos: subfunctionalization of the CRX homeobox gene in mammalian evolution. Proc Biol Sci 2019; 286:20190830. [PMID: 31337308 PMCID: PMC6661347 DOI: 10.1098/rspb.2019.0830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
ETCHbox genes are fast-evolving homeobox genes present only in eutherian (placental) mammals which originated by duplication and divergence from a conserved homeobox gene, Cone-rod homeobox (CRX). While expression and function of CRX are restricted to the retina in eutherian mammals, ETCHbox gene expression is specific to preimplantation embryos. This dramatic difference could reflect the acquisition of new functions by duplicated genes or subfunctionalization of pleiotropic roles between CRX and ETCHbox genes. To resolve between these hypotheses, we compared expression, sequence and inferred function between CRX of metatherian (marsupial) mammals and ETCHbox genes of eutherians. We find the metatherian CRX homeobox gene is expressed in early embryos and in eyes, unlike eutherian CRX, and distinct amino acid substitutions were fixed in the metatherian and eutherian evolutionary lineages consistent with altered transcription factor specificity. We find that metatherian CRX is capable of regulating embryonically expressed genes in cultured cells in a comparable way to eutherian ETCHbox. The data are consistent with CRX having a dual role in eyes and embryos of metatherians, providing an early embryonic function comparable to that of eutherian ETCHbox genes; we propose that subfunctionalization of pleiotropic functions occurred after gene duplication along the placental lineage, followed by functional elaboration.
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Affiliation(s)
- Amy H Royall
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Stephen Frankenberg
- School of BioSciences, University of Melbourne, Melbourne, 3010 Victoria, Australia
| | - Andrew J Pask
- School of BioSciences, University of Melbourne, Melbourne, 3010 Victoria, Australia
| | - Peter W H Holland
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
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20
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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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21
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Abstract
Establishing the different lineages of the early mammalian embryo takes place over several days and several rounds of cell divisions from the fertilized egg. The resulting blastocyst contains the pluripotent cells of the epiblast, from which embryonic stem cells can be derived, as well as the extraembryonic lineages required for a mammalian embryo to survive in the uterine environment. The dynamics of the cellular and genetic interactions controlling the initiation and maintenance of these lineages in the mouse embryo are increasingly well understood through application of the tools of single-cell genomics, gene editing, and in vivo imaging. Exploring the similarities and differences between mouse and human development will be essential for translation of these findings into new insights into human biology, derivation of stem cells, and improvements in fertility treatments.
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Affiliation(s)
- Janet Rossant
- Program in Stem Cell and Developmental Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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22
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Weltner J, Balboa D, Katayama S, Bespalov M, Krjutškov K, Jouhilahti EM, Trokovic R, Kere J, Otonkoski T. Human pluripotent reprogramming with CRISPR activators. Nat Commun 2018; 9:2643. [PMID: 29980666 PMCID: PMC6035213 DOI: 10.1038/s41467-018-05067-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/13/2018] [Indexed: 02/08/2023] Open
Abstract
CRISPR-Cas9-based gene activation (CRISPRa) is an attractive tool for cellular reprogramming applications due to its high multiplexing capacity and direct targeting of endogenous loci. Here we present the reprogramming of primary human skin fibroblasts into induced pluripotent stem cells (iPSCs) using CRISPRa, targeting endogenous OCT4, SOX2, KLF4, MYC, and LIN28A promoters. The low basal reprogramming efficiency can be improved by an order of magnitude by additionally targeting a conserved Alu-motif enriched near genes involved in embryo genome activation (EEA-motif). This effect is mediated in part by more efficient activation of NANOG and REX1. These data demonstrate that human somatic cells can be reprogrammed into iPSCs using only CRISPRa. Furthermore, the results unravel the involvement of EEA-motif-associated mechanisms in cellular reprogramming.
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Affiliation(s)
- Jere Weltner
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden
| | - Maxim Bespalov
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden
- Competence Centre on Health Technologies, Tartu, 50410, Estonia
| | - Eeva-Mari Jouhilahti
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Ras Trokovic
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Juha Kere
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden.
- School of Basic and Medical Biosciences, Guy's Hospital, King's College London, London, SE1 9RT, UK.
- Folkhälsan Institute of Genetics, Helsinki, 00290, Finland.
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, 00290, Finland.
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23
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Dunwell TL, Paps J, Holland PWH. Novel and divergent genes in the evolution of placental mammals. Proc Biol Sci 2018; 284:rspb.2017.1357. [PMID: 28978728 DOI: 10.1098/rspb.2017.1357] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/04/2017] [Indexed: 01/02/2023] Open
Abstract
Analysis of genome sequences within a phylogenetic context can give insight into the mode and tempo of gene and protein evolution, including inference of gene ages. This can reveal whether new genes arose on particular evolutionary lineages and were recruited for new functional roles. Here, we apply MCL clustering with all-versus-all reciprocal BLASTP to identify and phylogenetically date 'Homology Groups' among vertebrate proteins. Homology Groups include new genes and highly divergent duplicate genes. Focusing on the origin of the placental mammals within the Eutheria, we identify 357 novel Homology Groups that arose on the stem lineage of Placentalia, 87 of which are deduced to play core roles in mammalian biology as judged by extensive retention in evolution. We find the human homologues of novel eutherian genes are enriched for expression in preimplantation embryo, brain, and testes, and enriched for functions in keratinization, reproductive development, and the immune system.
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Affiliation(s)
| | - Jordi Paps
- Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, University of Essex, Colchester, UK
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24
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Mori Y, Sakuraoka M, Suzuki T, Sato S, Sugawara S, Hiraide M, Sato S, Kobayashi M. Exogenous TPRX1 homeoprotein modulates the gene expression of lineage-specific transcription factors in human embryonal carcinoma cells. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1447396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Yuki Mori
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Mizuki Sakuraoka
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Takahiro Suzuki
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Sho Sato
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Saiko Sugawara
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Misuzu Hiraide
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Suguru Sato
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Masayuki Kobayashi
- Laboratory For Advanced Animal Cell Technology, Graduate School of Bioresource Sciences, Akita Prefectural University, Akita, Japan
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25
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Stirparo GG, Boroviak T, Guo G, Nichols J, Smith A, Bertone P. Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast. Development 2018; 145:dev158501. [PMID: 29361568 PMCID: PMC5818005 DOI: 10.1242/dev.158501] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Single-cell profiling techniques create opportunities to delineate cell fate progression in mammalian development. Recent studies have provided transcriptome data from human pre-implantation embryos, in total comprising nearly 2000 individual cells. Interpretation of these data is confounded by biological factors, such as variable embryo staging and cell-type ambiguity, as well as technical challenges in the collective analysis of datasets produced with different sample preparation and sequencing protocols. Here, we address these issues to assemble a complete gene expression time course spanning human pre-implantation embryogenesis. We identify key transcriptional features over developmental time and elucidate lineage-specific regulatory networks. We resolve post-hoc cell-type assignment in the blastocyst, and define robust transcriptional prototypes that capture epiblast and primitive endoderm lineages. Examination of human pluripotent stem cell transcriptomes in this framework identifies culture conditions that sustain a naïve state pertaining to the inner cell mass. Our approach thus clarifies understanding both of lineage segregation in the early human embryo and of in vitro stem cell identity, and provides an analytical resource for comparative molecular embryology.
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Affiliation(s)
- Giuliano G Stirparo
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Thorsten Boroviak
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Ge Guo
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Paul Bertone
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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Royall AH, Maeso I, Dunwell TL, Holland PWH. Mouse Obox and Crxos modulate preimplantation transcriptional profiles revealing similarity between paralogous mouse and human homeobox genes. EvoDevo 2018; 9:2. [PMID: 29423137 PMCID: PMC5787275 DOI: 10.1186/s13227-018-0091-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/07/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND ETCHbox genes are eutherian-specific homeobox genes expressed during preimplantation development at a time when the first cell lineage decisions are being made. The mouse has an unusual repertoire of ETCHbox genes with several gene families lost in evolution and the remaining two, Crxos and Obox, greatly divergent in sequence and number. Each has undergone duplication to give a double homeodomain Crxos locus and a large cluster of over 60 Obox loci. The gene content differences between species raise important questions about how evolution can tolerate loss of genes implicated in key developmental events. RESULTS We find that Crxos internal duplication occurred in the mouse lineage, while Obox duplication was stepwise, generating subgroups with distinct sequence and expression. Ectopic expression of three Obox genes and a Crxos transcript in primary mouse embryonic cells followed by transcriptome sequencing allowed investigation into their functional roles. We find distinct transcriptomic influences for different Obox subgroups and Crxos, including modulation of genes related to zygotic genome activation and preparation for blastocyst formation. Comparison with similar experiments performed using human homeobox genes reveals striking overlap between genes downstream of mouse Crxos and genes downstream of human ARGFX. CONCLUSIONS Mouse Crxos and human ARGFX homeobox genes are paralogous rather than orthologous, yet they have evolved to regulate a common set of genes. This suggests there was compensation of function alongside gene loss through co-option of a different locus. Functional compensation by non-orthologous genes with dissimilar sequences is unusual but may indicate underlying distributed robustness. Compensation may be driven by the strong evolutionary pressure for successful early embryo development.
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Affiliation(s)
- Amy H. Royall
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Thomas L. Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Peter W. H. Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
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Dunwell TL, Holland PWH. A sister of NANOG regulates genes expressed in pre-implantation human development. Open Biol 2018; 7:rsob.170027. [PMID: 28446706 PMCID: PMC5413911 DOI: 10.1098/rsob.170027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/03/2017] [Indexed: 12/19/2022] Open
Abstract
The NANOG homeobox gene plays a pivotal role in self-renewal and maintenance of pluripotency in human, mouse and other vertebrate embryonic stem cells, and in pluripotent cells of the blastocyst inner cell mass. There is a poorly studied and atypical homeobox locus close to the Nanog gene in some mammals which could conceivably be a cryptic paralogue of NANOG, even though the loci share only 20% homeodomain identity. Here we argue that this gene, NANOGNB (NANOG Neighbour), is an extremely divergent duplicate of NANOG that underwent radical sequence change in the mammalian lineage. Like NANOG, the NANOGNB gene is expressed in pre-implantation embryos of human and cow; unlike NANOG, NANOGNB expression is restricted to 8-cell and morula stages, preceding blastocyst formation. When expressed ectopically in adult cells, human NANOGNB elicits gene expression changes, including downregulation of a set of genes that have an expression pulse at the 8-cell stage of pre-implantation development. We conclude that gene duplication and massive sequence divergence in mammals generated a novel homeobox gene that acquired new developmental roles complementary to those of Nanog.
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Affiliation(s)
- Thomas L Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Holland PWH, Marlétaz F, Maeso I, Dunwell TL, Paps J. New genes from old: asymmetric divergence of gene duplicates and the evolution of development. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0480. [PMID: 27994121 DOI: 10.1098/rstb.2015.0480] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 01/10/2023] Open
Abstract
Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such 'asymmetric evolution' seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ferdinand Marlétaz
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Ignacio Maeso
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Thomas L Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Jordi Paps
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,School of Biological Sciences, University of Essex, Colchester, Essex, UK
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Lu C, Wu J, Xiong S, Zhang X, Zhang J, Mei J. MicroRNA-203a regulates fast muscle differentiation by targeting dmrt2a in zebrafish embryos. Gene 2017; 625:49-54. [PMID: 28483596 DOI: 10.1016/j.gene.2017.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/26/2017] [Accepted: 05/04/2017] [Indexed: 01/25/2023]
Abstract
Dmrt2b (doublesex and mab-3 related transcription factor 2b) has been revealed to be involved in zebrafish slow muscle development. However, the function of dmrt2a, a paralogue gene of dmrt2b, remains unclear during zebrafish muscle development. Here, we demonstrated that knockdown of dmrt2a resulted in severe developmental defects, and caused downregulation of fast muscle marker myhz-2 and upregulation of slow muscle marker myhz-5, respectively. It is known that microRNAs (miRNAs) control many biological events including muscle development. Dmrt2a was predicted to be a target gene of miR-203, which was further verified by luciferase reporter assay, since miR-203a was found to directly reduce the expression of dmrt2a by binding to the seed sequence of its 3'UTR. After miR-203a injection into zebrafish embryos, the expression of dmrt2a was significantly inhibited. Similar to the effect of dmrt2a knockdown, miR-203a overexpression led to downregulation of myhz-2 and upregulation of myhz-5. Our studies indicated that miR-203a directly regulated dmrt2a expression to control fast and slow muscle differentiation, while overexpression of miR-203a or knockdown of dmrt2a will impair fast muscle development and promote slow muscle development.
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Affiliation(s)
- Chang Lu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Junjie Wu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuting Xiong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Zhang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin Zhang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Mei
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
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Dunwell TL, Holland PWH. Diversity of human and mouse homeobox gene expression in development and adult tissues. BMC DEVELOPMENTAL BIOLOGY 2016; 16:40. [PMID: 27809766 PMCID: PMC5094009 DOI: 10.1186/s12861-016-0140-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
Background Homeobox genes encode a diverse set of transcription factors implicated in a vast range of biological processes including, but not limited to, embryonic cell fate specification and patterning. Although numerous studies report expression of particular sets of homeobox genes, a systematic analysis of the tissue specificity of homeobox genes is lacking. Results Here we analyse publicly-available transcriptome data from human and mouse developmental stages, and adult human tissues, to identify groups of homeobox genes with similar expression patterns. We calculate expression profiles for 242 human and 278 mouse homeobox loci across a combination of 59 human and 12 mouse adult tissues, early and late developmental stages. This revealed 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes. Most homeobox genes, however, have greater tissue-specificity, allowing us to compile homeobox gene expression lists for neural tissues, immune tissues, reproductive and developmental samples, and for numerous organ systems. In mouse development, we propose four distinct phases of homeobox gene expression: oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The final phase change is marked by expression of ANTP class genes. We also use these data to compare expression specificity between evolutionarily-based gene classes, revealing that ANTP, PRD, LIM and POU homeobox gene classes have highest tissue specificity while HNF, TALE, CUT and CERS are most widely expressed. Conclusions The homeobox genes comprise a large superclass and their expression patterns are correspondingly diverse, although in a broad sense related to an evolutionarily-based classification. The ubiquitous expression of some genes suggests roles in general cellular processes; in contrast, most human homeobox genes have greater tissue specificity and we compile useful homeobox datasets for particular tissues, organs and developmental stages. The identification of a set of eutherian-specific homeobox genes peaking from human 8-cell to morula stages suggests co-option of new genes to new developmental roles in evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0140-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas L Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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