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Schaefer T, Mittal N, Wang H, Ataman M, Candido S, Lötscher J, Velychko S, Tintignac L, Bock T, Börsch A, Baßler J, Rao TN, Zmajkovic J, Roffeis S, Löliger J, Jacob F, Dumlin A, Schürch C, Schmidt A, Skoda RC, Wymann MP, Hess C, Schöler HR, Zaehres H, Hurt E, Zavolan M, Lengerke C. Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate. Cell Rep 2024; 43:114807. [PMID: 39368083 DOI: 10.1016/j.celrep.2024.114807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 01/28/2024] [Accepted: 09/13/2024] [Indexed: 10/07/2024] Open
Abstract
Stemness and pluripotency are mediated by transcriptional master regulators that promote self-renewal and repress cell differentiation, among which is the high-mobility group (HMG) box transcription factor SOX2. Dysregulated SOX2 expression, by contrast, leads to transcriptional aberrations relevant to oncogenic transformation, cancer progression, metastasis, therapy resistance, and relapse. Here, we report a post-transcriptional mechanism by which the cytosolic pool of SOX2 contributes to these events in an unsuspected manner. Specifically, a low-complexity region within SOX2's C-terminal segment connects to the ribosome to modulate the expression of cognate downstream factors. Independent of nuclear structures or DNA, this C-terminal functionality alone changes metabolic properties and induces non-adhesive growth when expressed in the cytosol of SOX2 knockout cells. We thus propose a revised model of SOX2 action where nuclear and cytosolic fractions cooperate to impose cell fate decisions via both transcriptional and translational mechanisms.
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Affiliation(s)
- Thorsten Schaefer
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.
| | | | - Hui Wang
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland; Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Meric Ataman
- Biozentrum, University of Basel, Basel, Switzerland
| | - Silvia Candido
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Jonas Lötscher
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lionel Tintignac
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Thomas Bock
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Anastasiya Börsch
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Jochen Baßler
- Biochemistry Center Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Tata Nageswara Rao
- Medical Research Center, Department of Medical Oncology and Hematology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland; Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Jakub Zmajkovic
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland; Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Sarah Roffeis
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Jordan Löliger
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Francis Jacob
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Alain Dumlin
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Christoph Schürch
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Radek C Skoda
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Matthias P Wymann
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Christoph Hess
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland; CITIID, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Holm Zaehres
- Max Planck Institute for Molecular Biomedicine, Münster, Germany; Institute of Anatomy, Ruhr University Bochum, Bochum, Germany
| | - Ed Hurt
- Biochemistry Center Heidelberg, Heidelberg University, Heidelberg, Germany
| | | | - Claudia Lengerke
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland; Internal Medicine II, University Hospital Tübingen, Tübingen, Germany
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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Ding J, Tang D, Zhang Y, Gao X, Du C, Shen W, Jin S, Zhu J. Transcriptomes of Testes at Different Developmental Stages in the Opsariichthys bidens Predict Key Genes for Testis Development and Spermatogenesis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:123-139. [PMID: 36520355 DOI: 10.1007/s10126-022-10186-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Testis development is a complex process involving multiple genes, and the molecular mechanisms underlying testis development in Opsariichthys bidens remain unclear. We performed transcriptome sequencing analysis on a total of 12 samples of testes from stages II, III, IV, and V of O. bidens and obtained a total of 79.52 Gb clean data, as well as 288,573 transcripts and 116,215 unigenes. Differential expression analysis showed that 22,857 differentially expressed genes (DEGs) were screened in six comparison groups (III vs. II, IV vs. II, V vs. II, IV vs. III, V vs. III, and V vs. IV). Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs showed that six comparison groups were significantly enriched for a total of 20 significantly up- or down-regulated pathways, including six pathways related to signal transduction, three pathways related to energy metabolism, five pathways related to disease, and two pathways related to ribosomes. Furthermore, our investigation revealed that DEGs were enriched in several important functional pathways, such as Huntington's disease signaling pathway, TGF-β signaling pathway, and ribosome signaling pathway. Protein-protein interaction network analysis of DEGs identified 63 up-regulated hub genes, including 9 kinesin genes and 2 cytoplasmic dynein genes, and 39 down-regulated hub genes, including 13 ribosomal protein genes. This result contributes to the knowledge of spermatogenesis and testis development in O. bidens.
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Affiliation(s)
- Jie Ding
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315103, Zhejiang, China
| | - Daojun Tang
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Yibo Zhang
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315103, Zhejiang, China
| | - Xinming Gao
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Chen Du
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Weiliang Shen
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315103, Zhejiang, China
| | - Shan Jin
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China
| | - Junquan Zhu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, College of Marine Sciences, Ningbo University, Ningbo, 315832, Zhejiang, China.
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Hamilton DJ, Hein AE, Holmes ZE, Wuttke DS, Batey RT. The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro. Biochemistry 2022; 61:10.1021/acs.biochem.2c00218. [PMID: 35511045 PMCID: PMC9636074 DOI: 10.1021/acs.biochem.2c00218] [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] [Indexed: 11/29/2022]
Abstract
There is a growing body of evidence that a substantial number of protein domains identified as DNA-binding also interact with RNA to regulate biological processes. Several recent studies have revealed that the Sox2 transcription factor binds RNA through its high-mobility group box (HMGB) domain in vitro and in vivo. A high degree of conservation of this domain among members of the Sox family of transcription factors suggests that RNA-binding activity may be a general feature of these proteins. To address this hypothesis, we examined a subset of HMGB domains from human Sox family of proteins for their ability to bind both DNA and RNA in vitro. We observed selective, high-affinity interactions between Sox family HMGB domains and various model RNA elements, including a four-way junction RNA, a hairpin RNA with an internal bulge, G-quadruplex RNA, and a fragment of long noncoding RNA ES2, which is known to directly interact with Sox2. Importantly, the HMGB domains bind these RNA ligands significantly tighter than nonconsensus dsDNA and in some cases with affinities rivaling those of their consensus dsDNA sequences. These data suggest that RNA binding is a conserved feature of the Sox family of transcription factors with the potential to modulate unappreciated biological functions.
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Affiliation(s)
- Desmond J Hamilton
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Abigail E Hein
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Zachariah E Holmes
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
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The Potential Role of SRY in Epigenetic Gene Regulation During Brain Sexual Differentiation in Mammals. EPIGENETIC SHAPING OF SOCIOSEXUAL INTERACTIONS - FROM PLANTS TO HUMANS 2014; 86:135-65. [DOI: 10.1016/b978-0-12-800222-3.00007-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Mutation of the diamond-blackfan anemia gene Rps7 in mouse results in morphological and neuroanatomical phenotypes. PLoS Genet 2013; 9:e1003094. [PMID: 23382688 PMCID: PMC3561062 DOI: 10.1371/journal.pgen.1003094] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/30/2012] [Indexed: 11/19/2022] Open
Abstract
The ribosome is an evolutionarily conserved organelle essential for cellular function. Ribosome construction requires assembly of approximately 80 different ribosomal proteins (RPs) and four different species of rRNA. As RPs co-assemble into one multi-subunit complex, mutation of the genes that encode RPs might be expected to give rise to phenocopies, in which the same phenotype is associated with loss-of-function of each individual gene. However, a more complex picture is emerging in which, in addition to a group of shared phenotypes, diverse RP gene-specific phenotypes are observed. Here we report the first two mouse mutations (Rps7Mtu and Rps7Zma) of ribosomal protein S7 (Rps7), a gene that has been implicated in Diamond-Blackfan anemia. Rps7 disruption results in decreased body size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations. These phenotypes are reported in other murine RP mutants and, as demonstrated for some other RP mutations, are ameliorated by Trp53 deficiency. Interestingly, Rps7 mutants have additional overt malformations of the developing central nervous system and deficits in working memory, phenotypes that are not reported in murine or human RP gene mutants. Conversely, Rps7 mouse mutants show no anemia or hyperpigmentation, phenotypes associated with mutation of human RPS7 and other murine RPs, respectively. We provide two novel RP mouse models and expand the repertoire of potential phenotypes that should be examined in RP mutants to further explore the concept of RP gene-specific phenotypes. Ribosomes are composed of two subunits that each consist of a large number of proteins, and their function of translating mRNA into protein is essential for cell viability. Naturally occurring or genetically engineered mutations within an individual ribosomal protein provide a valuable resource, since the resulting abnormal phenotypes reveal the function of each ribosomal protein. A number of mutations recently identified in mammalian ribosomal subunit genes have confirmed that homozygous loss of function consistently results in lethality; however, haploinsufficiency causes a variety of tissue-specific phenotypes. In this paper, we describe the first mutant alleles of the gene encoding ribosomal protein S7 (Rps7) in mouse. Rps7 haploinsufficiency causes decreased size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations, phenotypes that also occur with haploinsufficiency for other ribosomal subunits. Additionally, significant apoptosis occurs within the developing central nervous system (CNS) along with subtle behavioral phenotypes, suggesting RPS7 is required for CNS development. Mutation of human RPS7 has been implicated in Diamond-Blackfan anemia (DBA), yet the murine alleles do not present an analogous phenotype. The phenotypes we observe in the Rps7 mouse mutants indicate RPS7 should be considered as a candidate for a broader spectrum of human diseases.
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Jangravi Z, Alikhani M, Arefnezhad B, Sharifi Tabar M, Taleahmad S, Karamzadeh R, Jadaliha M, Mousavi SA, Ahmadi Rastegar D, Parsamatin P, Vakilian H, Mirshahvaladi S, Sabbaghian M, Mohseni Meybodi A, Mirzaei M, Shahhoseini M, Ebrahimi M, Piryaei A, Moosavi-Movahedi AA, Haynes PA, Goodchild AK, Nasr-Esfahani MH, Jabbari E, Baharvand H, Sedighi Gilani MA, Gourabi H, Salekdeh GH. A fresh look at the male-specific region of the human Y chromosome. J Proteome Res 2012; 12:6-22. [PMID: 23253012 DOI: 10.1021/pr300864k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Chromosome-centric Human Proteome Project (C-HPP) aims to systematically map the entire human proteome with the intent to enhance our understanding of human biology at the cellular level. This project attempts simultaneously to establish a sound basis for the development of diagnostic, prognostic, therapeutic, and preventive medical applications. In Iran, current efforts focus on mapping the proteome of the human Y chromosome. The male-specific region of the Y chromosome (MSY) is unique in many aspects and comprises 95% of the chromosome's length. The MSY continually retains its haploid state and is full of repeated sequences. It is responsible for important biological roles such as sex determination and male fertility. Here, we present the most recent update of MSY protein-encoding genes and their association with various traits and diseases including sex determination and reversal, spermatogenesis and male infertility, cancers such as prostate cancers, sex-specific effects on the brain and behavior, and graft-versus-host disease. We also present information available from RNA sequencing, protein-protein interaction, post-translational modification of MSY protein-coding genes and their implications in biological systems. An overview of Human Y chromosome Proteome Project is presented and a systematic approach is suggested to ensure that at least one of each predicted protein-coding gene's major representative proteins will be characterized in the context of its major anatomical sites of expression, its abundance, and its functional relevance in a biological and/or medical context. There are many technical and biological issues that will need to be overcome in order to accomplish the full scale mapping.
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Affiliation(s)
- Zohreh Jangravi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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