1
|
Fu RZ, Cottrell O, Cutillo L, Rowntree A, Zador Z, Wurdak H, Papalopulu N, Marinopoulou E. Identification of genes with oscillatory expression in glioblastoma: the paradigm of SOX2. Sci Rep 2024; 14:2123. [PMID: 38267500 PMCID: PMC10808450 DOI: 10.1038/s41598-024-51340-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
Quiescence, a reversible state of cell-cycle arrest, is an important state during both normal development and cancer progression. For example, in glioblastoma (GBM) quiescent glioblastoma stem cells (GSCs) play an important role in re-establishing the tumour, leading to relapse. While most studies have focused on identifying differentially expressed genes between proliferative and quiescent cells as potential drivers of this transition, recent studies have shown the importance of protein oscillations in controlling the exit from quiescence of neural stem cells. Here, we have undertaken a genome-wide bioinformatic inference approach to identify genes whose expression oscillates and which may be good candidates for controlling the transition to and from the quiescent cell state in GBM. Our analysis identified, among others, a list of important transcription regulators as potential oscillators, including the stemness gene SOX2, which we verified to oscillate in quiescent GSCs. These findings expand on the way we think about gene regulation and introduce new candidate genes as key regulators of quiescence.
Collapse
Affiliation(s)
- Richard Zhiming Fu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, M13 9PL, UK
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Care Organisation, Northern Care Alliance NHS Foundation Trust, Salford Royal, Stott Lane, Salford, M6 8HD, UK
| | - Oliver Cottrell
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Luisa Cutillo
- School of Mathematics, University of Leeds, Woodhouse, Leeds, LS2 9JT, UK
| | - Andrew Rowntree
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Zsolt Zador
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, 36 Queen St E, Toronto, ON, M5B 1W8, Canada
- Department of Surgery, McMaster University, 1280 Mains St W, Hamilton, ON, L8S 4L8, Canada
- Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON, L8S 4L8, Canada
| | - Heiko Wurdak
- Stem Cell and Brain Tumour Group, Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, LS9 7TF, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Elli Marinopoulou
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| |
Collapse
|
2
|
Bose D, Banerjee N, Roy A, Sengupta P, Chatterjee S. Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements. J Biomol Struct Dyn 2024:1-18. [PMID: 38235706 DOI: 10.1080/07391102.2024.2303378] [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: 07/25/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex-forming loci and identified them as binding sites of transcription factors. These segments form either G-quadruplex or i-motif structures, the structural dynamicity of which has been studied in depth via several biophysical techniques. The tetraplexes display high dynamicity and are influenced by both pH and KCl concentrations in vitro. The loci complementary to these sequences form additional non-canonical secondary structures. In the cellular context, the most eminent observation of this study is the binding of hnRNP K to the i-motif forming sequences in its own promoter. We are the first to report a probable transcriptional autoregulatory function of hnRNP K in coordination with higher-order DNA structures. Herein, we also report the positive interaction of the endogenous tetraplexes with Sp1, a well-known transcriptional regulator. Treatment with tetraplex-specific small molecule ligands further uncovered G-quadruplexes' functioning as repressors and i-motifs as activators in this context. Together, our findings strongly indicate the critical regulatory role of the identified tetraplex elements in the hnRNP K promoter.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Debopriya Bose
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Ananya Roy
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Kemihuset (K), Campus, Umeå, Umeå universitet, Umeå, Sweden
| | | |
Collapse
|
3
|
Nordick B, Chae-Yeon Park M, Quaranta V, Hong T. Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports a phenotypic continuum. iScience 2022; 25:105224. [PMID: 36248730 PMCID: PMC9557027 DOI: 10.1016/j.isci.2022.105224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022] Open
Abstract
Multiple intermediate epithelial-mesenchymal transition (EMT) states reflecting hybrid epithelial and mesenchymal phenotypes were observed in physiological and pathological conditions. Previous theoretical models explaining multiple EMT states rely on regulatory loops involving transcriptional feedback, which produce three or four attractors. This is incompatible with the observed continuum-like EMT spectrum. Here, we used mass-action-based models to describe post-transcriptional regulations, finding that cooperative RNA degradation via multiple microRNA binding sites can generate four-attractor systems without transcriptional feedback. Furthermore, the newly identified intermediates-enabling circuits are common in the EMT regulatory network, and they can synergize with transcriptional feedback to support phenotypic continuum. Finally, our model predicted a role of miR-101 in multistate EMT, and we identified evidence from single-cell RNA-sequencing data that support the prediction. Our work reveals a previously unknown role of cooperative RNA degradation and microRNAs in EMT, providing a framework that can bridge the gap between mechanistic models and single-cell experiments.
Collapse
Affiliation(s)
- Benjamin Nordick
- School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37916, USA
| | - Mary Chae-Yeon Park
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37916, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN 37232, USA
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37916, USA
- National Institute for Mathematical and Biological Synthesis, Knoxville, TN 37916, USA
| |
Collapse
|
4
|
Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development 2022; 149:276990. [PMID: 36189829 PMCID: PMC9641661 DOI: 10.1242/dev.200474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/26/2022] [Indexed: 11/06/2022]
Abstract
MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.
Collapse
Affiliation(s)
- Ximena Soto
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK,Authors for correspondence (; )
| | - Joshua Burton
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cerys S. Manning
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Thomas Minchington
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Robert Lea
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Jessica Lee
- Discovery Department, Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK
| | - Jochen Kursawe
- School of Mathematics and Statistics, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK,Authors for correspondence (; )
| |
Collapse
|
5
|
Mehta TK, Penso-Dolfin L, Nash W, Roy S, Di-Palma F, Haerty W. Evolution of miRNA binding sites and regulatory networks in cichlids. Mol Biol Evol 2022; 39:6617238. [PMID: 35748824 PMCID: PMC9260339 DOI: 10.1093/molbev/msac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA and TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.
Collapse
Affiliation(s)
| | - Luca Penso-Dolfin
- Silence Therapeutics GmbH, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | | | - Sushmita Roy
- Dept. of Biostatistics and Medical Informatics, UW Madison, Madison, USA.,Wisconsin Institute for Discovery (WID), Madison, USA.,Dept. of Computer Sciences, UW Madison, Madison, USA
| | - Federica Di-Palma
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Genome British Columbia, Vancouver, Canada
| | - Wilfried Haerty
- Earlham Institute (EI), Norwich, UK.,School of Biological Sciences, University of East Anglia, Norwich, UK
| |
Collapse
|
6
|
Zhang Y, Liang S, Pan Z, Yu Y, Yao H, Liu Y, Liu G. XRE family transcriptional regulator XtrSs modulates Streptococcus suis fitness under hydrogen peroxide stress. Arch Microbiol 2022; 204:244. [PMID: 35386008 DOI: 10.1007/s00203-022-02854-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 12/26/2022]
Abstract
Streptococcus suis is an important emerging zoonosis that causes economic losses in the pig industry and severe threats to public health. Transcriptional regulators play essential roles in bacterial adaptation to host environments. In this study, we identified a novel XRE family transcriptional regulator in S. suis CZ130302, XtrSs, involved in the bacterial fitness to hydrogen peroxide stress. Based on electrophoretic mobility shift and β-galactosidase activity assays, we found that XtrSs auto-regulated its own transcription and repressed the expression of its downstream gene psePs, a surface protein with unknown function in S. suis, by binding to a palindromic sequence from the promoter region. Furthermore, we proved that the deletion of the psePs gene attenuated bacterial antioxidant response. Phylogenetic analysis revealed that XtrSs and PsePs naturally co-existed as a combination in most S. suis genomes. Collectively, we demonstrated the binding characteristics of XtrSs in S. suis and provided a new insight that XtrSs played a critical role in modulating psePs to the hydrogen peroxide resistance of S. suis.
Collapse
Affiliation(s)
- Yumin Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
| | - Song Liang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
| | - Yong Yu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
| | - Yongjie Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
| | - Guangjin Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
- OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China.
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China.
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.
| |
Collapse
|
7
|
Wonnacott A, Denby L, Coward RJM, Fraser DJ, Bowen T. MicroRNAs and their delivery in diabetic fibrosis. Adv Drug Deliv Rev 2022; 182:114045. [PMID: 34767865 DOI: 10.1016/j.addr.2021.114045] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/21/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022]
Abstract
The global prevalence of diabetes mellitus was estimated to be 463 million people in 2019 and is predicted to rise to 700 million by 2045. The associated financial and societal costs of this burgeoning epidemic demand an understanding of the pathology of this disease, and its complications, that will inform treatment to enable improved patient outcomes. Nearly two decades after the sequencing of the human genome, the significance of noncoding RNA expression is still being assessed. The family of functional noncoding RNAs known as microRNAs regulates the expression of most genes encoded by the human genome. Altered microRNA expression profiles have been observed both in diabetes and in diabetic complications. These transcripts therefore have significant potential and novelty as targets for therapy, therapeutic agents and biomarkers.
Collapse
Affiliation(s)
- Alexa Wonnacott
- Wales Kidney Research Unit, Division of Infection & Immunity, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Laura Denby
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard J M Coward
- Bristol Renal, Dorothy Hodgkin Building, Bristol Medical School, University of Bristol, Bristol BS1 3NY, UK
| | - Donald J Fraser
- Wales Kidney Research Unit, Division of Infection & Immunity, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Timothy Bowen
- Wales Kidney Research Unit, Division of Infection & Immunity, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| |
Collapse
|
8
|
Abstract
Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload. So far, no connections between the function of the host genes and the function of their payloads have been reported. Here we investigate whether there is evidence for an association of host gene function or mechanisms with the type of payload. To assess this hypothesis we test whether the miRNA host genes (MIRHGs), snoRNA host genes (SNHGs), and other lncRNA host genes can be distinguished based on sequence and/or structure features unrelated to their payload. A positive answer would imply a functional and mechanistic correlation between host genes and their payload, provided the classification does not depend on the presence and type of the payload. A negative answer would indicate that to the extent that secondary functions are acquired, they are not strongly constrained by the prior, primary function of the payload. We find that the three classes can be distinguished reliably when the classifier is allowed to extract features from the payloads. They become virtually indistinguishable, however, as soon as only sequence and structure of parts of the host gene distal from the snoRNAs or miRNA payload is used for classification. This indicates that the functions of MIRHGs and SNHGs are largely independent of the functions of their payloads. Furthermore, there is no evidence that the MIRHGs and SNHGs form coherent classes of long non-coding RNAs distinguished by features other than their payloads.
Collapse
|