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Osanai Y, Xing YL, Mochizuki S, Kobayashi K, Homman-Ludiye J, Cooray A, Poh J, Inutsuka A, Ohno N, Merson TD. 5' Transgenes drive leaky expression of 3' transgenes in Cre-inducible bi-cistronic vectors. Mol Ther Methods Clin Dev 2024; 32:101288. [PMID: 39104576 PMCID: PMC11298883 DOI: 10.1016/j.omtm.2024.101288] [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] [Received: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 08/07/2024]
Abstract
Molecular cloning techniques enabling contemporaneous expression of two or more protein-coding sequences provide an invaluable tool for understanding the molecular regulation of cellular functions. The Cre-lox system is used for inducing the expression of recombinant proteins encoded within a bi-/poly-cistronic cassette. However, leak expression of transgenes is often observed in the absence of Cre recombinase activity, compromising the utility of this approach. To investigate the mechanism of leak expression, we generated Cre-inducible bi-cistronic vectors to monitor the expression of transgenes positioned either 5' or 3' of a 2A peptide or internal ribosomal entry site (IRES) sequence. Cells transfected with these bi-cistronic vectors exhibited Cre-independent leak expression specifically of transgenes positioned 3' of the 2A peptide or IRES sequence. Similarly, AAV-FLEX vectors encoding bi-cistronic cassettes or fusion proteins revealed the selective Cre-independent leak expression of transgenes positioned at the 3' end of the open reading frame. Our data demonstrate that 5' transgenes confer promoter-like activity that drives the expression of 3' transgenes. An additional lox-STOP-lox cassette between the 2A sequence and 3' transgene dramatically decreased Cre-independent transgene expression. Our findings highlight the need for appropriate experimental controls when using Cre-inducible bi-/poly-cistronic constructs and inform improved design of vectors for more tightly regulated inducible transgene expression.
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Affiliation(s)
- Yasuyuki Osanai
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0431, Japan
| | - Yao Lulu Xing
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Shinya Mochizuki
- Department of Anatomy, Bioimaging and Neuro-cell Science, Jichi Medical University, Shimotsuke, Tochigi 329-0431, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Myodaiji, Okazaki 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Shonan Village, Hayama, Kanagawa 240-0193, Japan
| | - Jihane Homman-Ludiye
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Amali Cooray
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Jasmine Poh
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Ayumu Inutsuka
- Division of Brain and Neurophysiology, Department of Physiology, Jichi Medical University, Shimotsuke, Tochigi 329-0431, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0431, Japan
- Division of Ultrastructure Research, National Institute for Physiological Sciences, Myodaiji, Okazaki 444-8585, Japan
| | - Tobias D. Merson
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
- Oligodendroglial Interactions Group, Systems Neurodevelopment Laboratory, National Institute of Mental Health, Bethesda, MD 20892, USA
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2
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Sun R, Fisher RP. The CDK9-SPT5 Axis in Control of Transcription Elongation by RNAPII. J Mol Biol 2024:168746. [PMID: 39147127 DOI: 10.1016/j.jmb.2024.168746] [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: 06/21/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
The RNA polymerase II (RNAPII) transcription cycle is regulated at every stage by a network of cyclin-dependent protein kinases (CDKs) and protein phosphatases. Progression of RNAPII from initiation to termination is marked by changing patterns of phosphorylation on the highly repetitive carboxy-terminal domain (CTD) of RPB1, its largest subunit, suggesting the existence of a CTD code. In parallel, the conserved transcription elongation factor SPT5, large subunit of the DRB sensitivity-inducing factor (DSIF), undergoes spatiotemporally regulated changes in phosphorylation state that may be directly linked to the transitions between transcription-cycle phases. Here we review insights gained from recent structural, biochemical, and genetic analyses of human SPT5, which suggest that two of its phosphorylated regions perform distinct functions at different points in transcription. Phosphorylation within a flexible, RNA-binding linker promotes release from the promoter-proximal pause-frequently a rate-limiting step in gene expression-whereas modifications in a repetitive carboxy-terminal region are thought to favor processive elongation, and are removed just prior to termination. Phosphorylations in both motifs depend on CDK9, catalytic subunit of positive transcription elongation factor b (P-TEFb); their different timing of accumulation on chromatin and function during the transcription cycle might reflect their removal by different phosphatases, different kinetics of phosphorylation by CDK9, or both. Perturbations of SPT5 regulation have profound impacts on viability and development in model organisms through largely unknown mechanisms, while enzymes that modify SPT5 have emerged as potential therapeutic targets in cancer; elucidating a putative SPT5 code is therefore a high priority.
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Affiliation(s)
- Rui Sun
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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3
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Ng BW, Kaukonen MK, McClements ME, Shamsnajafabadi H, MacLaren RE, Cehajic-Kapetanovic J. Genetic therapies and potential therapeutic applications of CRISPR activators in the eye. Prog Retin Eye Res 2024; 102:101289. [PMID: 39127142 DOI: 10.1016/j.preteyeres.2024.101289] [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: 06/06/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Conventional gene therapy involving supplementation only treats loss-of-function diseases and is limited by viral packaging sizes, precluding therapy of large genes. The discovery of CRISPR/Cas has led to a paradigm shift in the field of genetic therapy, with the promise of precise gene editing, thus broadening the range of diseases that can be treated. The initial uses of CRISPR/Cas have focused mainly on gene editing or silencing of abnormal variants via utilising Cas endonuclease to trigger the target cell endogenous non-homologous end joining. Subsequently, the technology has evolved to modify the Cas enzyme and even its guide RNA, leading to more efficient editing tools in the form of base and prime editing. Further advancements of this CRISPR/Cas technology itself have expanded its functional repertoire from targeted editing to programmable transactivation, shifting the therapeutic focus to precise endogenous gene activation or upregulation with the potential for epigenetic modifications. In vivo experiments using this platform have demonstrated the potential of CRISPR-activators (CRISPRa) to treat various loss-of-function diseases, as well as in regenerative medicine, highlighting their versatility to overcome limitations associated with conventional strategies. This review summarises the molecular mechanisms of CRISPRa platforms, the current applications of this technology in vivo, and discusses potential solutions to translational hurdles for this therapy, with a focus on ophthalmic diseases.
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Affiliation(s)
- Benjamin Wj Ng
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maria K Kaukonen
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Hoda Shamsnajafabadi
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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4
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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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Cao H, Zhang X, Li F, Han Z, Ding B. A point mutation in the IAA14 promoter enhances callus formation and regeneration. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1253-1263. [PMID: 39184564 PMCID: PMC11341521 DOI: 10.1007/s12298-024-01493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/27/2024]
Abstract
Callus formation induced by auxin accumulation is considered the first step of in vitro plant regeneration. In Arabidopsis, degradation of the Aux/IAA protein, IAA14, in response to auxin signaling, which activates the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 along with a series of downstream transcription factors, also plays a critical role in this process. However, the specific mechanism by which auxin regulates callus formation remains unclear. By screening mutant library in the solitary root 1 (iaa14/slr) Arabidopsis background we obtained the callus formation related 2 (cfr2) mutant. The cfr2 mutant exhibited a stronger capacity for callus formation, as well as lateral root and adventitious root regeneration from leaf explants than wild type (WT) seedlings, but did not recover gravitropism capability. The auxin signal in cfr2 was significantly enhanced, and the expression of some downstream transcription factors was increased. Map-based cloning, whole genome resequencing, and phenotypic complementation experiments showed that the phenotypes observed in the cfr2 mutant were caused by a point mutation in the IAA14 promoter region. This mutation, which is predicted to disrupt the binding of LBD16, LBD19, and LBD30 to the IAA14 promoter, changed the expression pattern of IAA14 in cfr2. Taken together, our results identified a new mutation in the IAA14 promoter region, which affects the expression pattern of IAA14 and in turn its ability to control plant regeneration. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01493-y.
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Affiliation(s)
- Huifen Cao
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Xiao Zhang
- Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Feng Li
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Zhiping Han
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Baopeng Ding
- Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Shanxi Datong University, Datong, 037009 Shanxi Province China
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6
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Lu Z, Xiao X, Zheng Q, Wang X, Xu L. Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets. Brief Bioinform 2024; 25:bbae366. [PMID: 39082650 PMCID: PMC11289684 DOI: 10.1093/bib/bbae366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/21/2024] [Accepted: 07/18/2024] [Indexed: 08/03/2024] Open
Abstract
This article provides an in-depth review of computational methods for predicting transcriptional regulators (TRs) with query gene sets. Identification of TRs is of utmost importance in many biological applications, including but not limited to elucidating biological development mechanisms, identifying key disease genes, and predicting therapeutic targets. Various computational methods based on next-generation sequencing (NGS) data have been developed in the past decade, yet no systematic evaluation of NGS-based methods has been offered. We classified these methods into two categories based on shared characteristics, namely library-based and region-based methods. We further conducted benchmark studies to evaluate the accuracy, sensitivity, coverage, and usability of NGS-based methods with molecular experimental datasets. Results show that BART, ChIP-Atlas, and Lisa have relatively better performance. Besides, we point out the limitations of NGS-based methods and explore potential directions for further improvement.
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Affiliation(s)
- Zeyu Lu
- Department of Statistics and Data Science, Moody School of Graduate and Advanced Studies, Southern Methodist University, 3225 Daniel Ave., P.O. Box 750332, Dallas, TX, United States
| | - Xue Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, United States
| | - Qiang Zheng
- Division of Data Science, College of Science, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, United States
| | - Xinlei Wang
- Division of Data Science, College of Science, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, United States
- Department of Mathematics, University of Texas at Arlington, 411 S. Nedderman Dr., Arlington, TX 76019, United States
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, United States
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, United States
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7
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Wang L, Pan H, Ping Z, Ma N, Wang Q, Huang Z. Genome-wide identification and expression analysis revealed key transcription factors as potential regulators of high-temperature adaptation of Coriolopsis trogii. Arch Microbiol 2024; 206:357. [PMID: 39028428 DOI: 10.1007/s00203-024-04081-6] [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: 06/03/2024] [Revised: 06/30/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Abstract
Transcription factors (TFs) play a crucial role in gene expression, and studying them can lay the foundation for future research on the functional characterization of TFs involved in various biological processes. In this study, we conducted a genome-wide identification and analysis of TFs in the thermotolerant basidiomycete fungus, Coriolopsis trogii. The TF repertoire of C. trogii consisted of 350 TFs, with C2H2 and Zn2C6 being the largest TF families. When the mycelia of C. trogii were cultured on PDA and transferred from 25 to 35 °C, 14 TFs were up-regulated and 14 TFs were down-regulated. By analyzing RNA-seq data from mycelia cultured at different temperatures and under different carbon sources, we identified 22 TFs that were differentially expressed in more than three comparisons. Co-expression analysis revealed that seven differentially expressed TFs, including four Zn2C6s, one Hap4_Hap_bind, one HMG_box, and one Zinc_knuckle, showed significant correlation with 729 targeted genes. Overall, this study provides a comprehensive characterization of the TF family and systematically screens TFs involved in the high-temperature adaptation of C. trogii, laying the groundwork for further research into the specific roles of TFs in the heat tolerance mechanisms of filamentous fungi.
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Affiliation(s)
- Lining Wang
- Guangdong Engineering Laboratory of Biomass Value-added Utilization, Guangdong Engineering Research and Development Center for Comprehensive Utilization of Plant Fiber, Guangzhou Key Laboratory for Comprehensive Utilization of Plant Fiber, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Hengyu Pan
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zhaohua Ping
- Guangdong Engineering Laboratory of Biomass Value-added Utilization, Guangdong Engineering Research and Development Center for Comprehensive Utilization of Plant Fiber, Guangzhou Key Laboratory for Comprehensive Utilization of Plant Fiber, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Nianfang Ma
- Guangdong Engineering Laboratory of Biomass Value-added Utilization, Guangdong Engineering Research and Development Center for Comprehensive Utilization of Plant Fiber, Guangzhou Key Laboratory for Comprehensive Utilization of Plant Fiber, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Qingfu Wang
- Guangdong Engineering Laboratory of Biomass Value-added Utilization, Guangdong Engineering Research and Development Center for Comprehensive Utilization of Plant Fiber, Guangzhou Key Laboratory for Comprehensive Utilization of Plant Fiber, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China.
| | - Zhihai Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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8
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [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: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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9
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Ning YN, Liang X, Shen X, Tian D, Li WT, Luo XM, Feng JX, Zhao S. A RsrC-RsrA-RsrB transcriptional circuit positively regulates polysaccharide-degrading enzyme biosynthesis and development in Penicillium oxalicum. Commun Biol 2024; 7:848. [PMID: 38992164 PMCID: PMC11239660 DOI: 10.1038/s42003-024-06536-4] [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: 01/04/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024] Open
Abstract
Filamentous fungi produce polysaccharide-degrading enzymes, which is controlled by poorly understood transcriptional circuits. Here we show that a circuit comprising RsrC-RsrA-RsrB (Rsr: production of raw-starch-degrading enzyme regulator) that positively regulates production of raw starch-degrading enzymes in Penicillium oxalicum. Transcription factor (TF) RsrA is essential for biosynthesis of raw starch-degrading enzymes. RsrB and RsrC containing Zn2Cys6- and C2H2-zinc finger domains, act downstream and upstream of RsrA, respectively. RsrA activates rsrB transcription, and three nucleotides (G-286, G-287 and G-292) of rsrB promoter region are required for RsrA, in terms of TF, for binding. RsrB165-271 binds to DNA sequence 5'-TCGATCAGGCACGCC-3' in the promoter region of the gene encoding key raw-starch-degrading enzyme PoxGA15A. RsrC specifically binds rsrA promoter, but not amylase genes, to positively regulate the expression of rsrA and the production of raw starch-degrading enzymes. These findings expand complex regulatory network of fungal raw starch-degrading enzyme biosynthesis.
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Affiliation(s)
- Yuan-Ni Ning
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Xue Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Xin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Di Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Wen-Tong Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Xue-Mei Luo
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
- Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
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10
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Li X, Tang P, Pang X, Song X, Xiong J, Yu L, Liu H, Pang C. The features analysis of hemoglobin expression on visual information transmission pathway in early stage of Alzheimer's disease. Sci Rep 2024; 14:15636. [PMID: 38972885 PMCID: PMC11228039 DOI: 10.1038/s41598-024-64099-0] [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: 03/06/2024] [Accepted: 06/05/2024] [Indexed: 07/09/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized primarily by cognitive impairment. The motivation of this paper is to explore the impact of the visual information transmission pathway (V-H pathway) on AD, and the following feature were observed: Hemoglobin expression on the V-H pathway becomes dysregulated as AD occurs so as to the pathway becomes dysfunctional. According to the feature, the following conclusion was proposed: As AD occurs, abnormal tau proteins penetrate bloodstream and arrive at the brain regions of the pathway. Then the tau proteins or other toxic substances attack hemoglobin molecules. Under the attack, hemoglobin expression becomes more dysregulated. The dysfunction of V-H pathway has an impact on early symptoms of AD, such as spatial recognition disorder and face recognition disorder.
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Affiliation(s)
- Xuehui Li
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Pan Tang
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xinping Pang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xianghu Song
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Jing Xiong
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Lei Yu
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China
| | - Hui Liu
- School of Information and Software Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Chaoyang Pang
- College of Computer Science, Sichuan Normal University, Chengdu, 610101, China.
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11
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Li J, Fu L, Li Y, Sun W, Yi Y, Jia W, Li H, Liu H, Guo P, Wang Y, Shen Y, Zhang X, Lv Y, Qin B, Li W, Liu C, Liu L, Mazid MA, Lai Y, Esteban MA, Jiang Y, Wu L. A single-cell chromatin accessibility dataset of human primed and naïve pluripotent stem cell-derived teratoma. Sci Data 2024; 11:725. [PMID: 38956385 PMCID: PMC11220047 DOI: 10.1038/s41597-024-03558-9] [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: 02/28/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
Teratoma, due to its remarkable ability to differentiate into multiple cell lineages, is a valuable model for studying human embryonic development. The similarity of the gene expression and chromatin accessibility patterns in these cells to those observed in vivo further underscores its potential as a research tool. Notably, teratomas derived from human naïve (pre-implantation epiblast-like) pluripotent stem cells (PSCs) have larger embryonic cell diversity and contain extraembryonic lineages, making them more suitable to study developmental processes. However, the cell type-specific epigenetic profiles of naïve PSC teratomas have not been yet characterized. Using single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), we analyzed 66,384 cell profiles from five teratomas derived from human naïve PSCs and their post-implantation epiblast-like (primed) counterparts. We observed 17 distinct cell types from both embryonic and extraembryonic lineages, resembling the corresponding cell types in human fetal tissues. Additionally, we identified key transcription factors specific to different cell types. Our dataset provides a resource for investigating gene regulatory programs in a relevant model of human embryonic development.
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Affiliation(s)
- Jinxiu Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Lixin Fu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Wei Sun
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yao Yi
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Wenqi Jia
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Haiwei Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou, Guangdong, 510530, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Pengcheng Guo
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Yang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Hangzhou, 310030, China
| | - Yue Shen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Changzhou, 213299, China
| | - Xiuqing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
| | - Yuan Lv
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Baoming Qin
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chuanyu Liu
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
| | - Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yiwei Lai
- BGI Research, Shenzhen, 518083, China
- BGI Research, Hangzhou, 310030, China
- 3DCStar lab, BGI, Shenzhen, 518083, China
| | - Miguel A Esteban
- BGI Research, Shenzhen, 518083, China
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- 3DCStar lab, BGI, Shenzhen, 518083, China
| | - Yu Jiang
- BGI Research, Shenzhen, 518083, China.
- BGI Research, Hangzhou, 310030, China.
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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12
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Abdul-Rahman T, Lizano-Jubert I, Bliss ZSB, Garg N, Meale E, Roy P, Crino SA, Deepak BL, Miteu GD, Wireko AA, Qadeer A, Condurat A, Tanasa AD, Pyrpyris N, Sikora K, Horbas V, Sood A, Gupta R, Lavie CJ. RNA in cardiovascular disease: A new frontier of personalized medicine. Prog Cardiovasc Dis 2024; 85:93-102. [PMID: 38253161 DOI: 10.1016/j.pcad.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024]
Abstract
Personalized medicine has witnessed remarkable progress with the emergence of RNA therapy, offering new possibilities for the treatment of various diseases, and in particular in the context of cardiovascular disease (CVD). The ability to target the human genome through RNA manipulation offers great potential not only in the treatment of cardiac pathologies but also in their diagnosis and prevention, notably in cases of hyperlipidemia and myocardial infarctions. While only a few RNA-based treatments have entered clinical trials or obtained approval from the US Food and Drug Administration, the growing body of research on this subject is promising. However, the development of RNA therapies faces several challenges that must be overcome. These include the efficient delivery of drugs into cells, the potential for immunogenic responses, and safety. Resolving these obstacles is crucial to advance the development of RNA therapies. This review explores the newest developments in medical studies, treatment plans, and results related to RNA therapies for heart disease. Furthermore, it discusses the exciting possibilities and difficulties in this innovative area of research.
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Affiliation(s)
| | | | | | - Neil Garg
- Rowan-Virtua School of osteopathic medicine, Stratford, NJ, USA
| | - Emily Meale
- Rowan-Virtua School of osteopathic medicine, Stratford, NJ, USA
| | - Poulami Roy
- Department of Medicine, North Bengal Medical College and Hospital, Siliguri, India
| | | | | | - Goshen David Miteu
- School of Biosciences, University of Nottingham, Nottingham, England, United Kingdom
| | | | - Abdul Qadeer
- Hospital Internal Medicine Department, Scottsdale Campus, Mayo Clinic, AZ, USA
| | | | | | - Nikolaos Pyrpyris
- First Department of Cardiology, School of Medicine, National and Kapodistrian University of Athens, Hippokration General Hospital, Athens, Greece
| | | | | | - Aayushi Sood
- Department of Medicine, The Wright Center for Graduate Medical Education, Scranton, PA, USA
| | - Rahul Gupta
- Lehigh Valley Heart and Vascular Institute, Lehigh Valley Health Network, Allentown, PA, USA.
| | - Carl J Lavie
- Department of Cardiology, Ochsner Clinic Foundation, New Orleans, LA, United States; The University of Queensland Medical School, Ochsner Clinical School, New Orleans, LA, United States
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13
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van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 DOI: 10.1042/bst20230770] [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: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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14
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4. Cell Rep 2024; 43:114242. [PMID: 38768033 PMCID: PMC11264335 DOI: 10.1016/j.celrep.2024.114242] [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: 11/08/2023] [Revised: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
Terminal differentiation requires massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4,000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identify dynamic occupancy of RNA polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II occupancy and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of-function, chromatin immunoprecipitation sequencing (ChIP-seq), and immunoprecipitation (IP) mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II occupancy at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms that drive differentiation gene expression and find that pause-release of Pol II and post-transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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15
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [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: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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16
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Callan-Sidat A, Zewdu E, Cavallaro M, Liu J, Hebenstreit D. N-terminal tagging of RNA Polymerase II shapes transcriptomes more than C-terminal alterations. iScience 2024; 27:109914. [PMID: 38799575 PMCID: PMC11126984 DOI: 10.1016/j.isci.2024.109914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 02/14/2024] [Accepted: 05/03/2024] [Indexed: 05/29/2024] Open
Abstract
RNA polymerase II (Pol II) has a C-terminal domain (CTD) that is unstructured, consisting of a large number of heptad repeats, and whose precise function remains unclear. Here, we investigate how altering the CTD's length and fusing it with protein tags affects transcriptional output on a genome-wide scale in mammalian cells at single-cell resolution. While transcription generally appears to occur in burst-like fashion, where RNA is predominantly made during short bursts of activity that are interspersed with periods of transcriptional silence, the CTD's role in shaping these dynamics seems gene-dependent; global patterns of bursting appear mostly robust to CTD alterations. Introducing protein tags with defined structures to the N terminus cause transcriptome-wide effects, however. We find the type of tag to dominate characteristics of the resulting transcriptomes. This is possibly due to Pol II-interacting factors, including non-coding RNAs, whose expression correlates with the tags. Proteins involved in liquid-liquid phase separation appear prominently.
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Affiliation(s)
- Adam Callan-Sidat
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Emmanuel Zewdu
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Massimo Cavallaro
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- School of Computing and Mathematical Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Juntai Liu
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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17
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Kong D, Zhou Y, Wei Y, Wang X, Huang Q, Gao X, Wan H, Liu M, Kang L, Yu G, Yin J, Guan N, Ye H. Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals. Nat Commun 2024; 15:4894. [PMID: 38849338 PMCID: PMC11161646 DOI: 10.1038/s41467-024-49254-5] [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: 01/04/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
Synthetic biology applications require finely tuned gene expression, often mediated by synthetic transcription factors (sTFs) compatible with the human genome and transcriptional regulation mechanisms. While various DNA-binding and activation domains have been developed for different applications, advanced artificially controllable sTFs with improved regulatory capabilities are required for increasingly sophisticated applications. Here, in mammalian cells and mice, we validate the transactivator function and homo-/heterodimerization activity of the plant-derived phytochrome chaperone proteins, FHY1 and FHL. Our results demonstrate that FHY1/FHL form a photosensing transcriptional regulation complex (PTRC) through interaction with the phytochrome, ΔPhyA, that can toggle between active and inactive states through exposure to red or far-red light, respectively. Exploiting this capability, we develop a light-switchable platform that allows for orthogonal, modular, and tunable control of gene transcription, and incorporate it into a PTRC-controlled CRISPRa system (PTRCdcas) to modulate endogenous gene expression. We then integrate the PTRC with small molecule- or blue light-inducible regulatory modules to construct a variety of highly tunable systems that allow rapid and reversible control of transcriptional regulation in vitro and in vivo. Validation and deployment of these plant-derived phytochrome chaperone proteins in a PTRC platform have produced a versatile, powerful tool for advanced research and biomedical engineering applications.
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Affiliation(s)
- Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
- Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China
| | - Yu Wei
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Qin Huang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Xianyun Gao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Hang Wan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Mengyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
| | - Jianli Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401120, China
| | - Ningzi Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
- Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China.
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18
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Bayanjargal A, Taslim C, Showpnil IA, Selich-Anderson J, Crow JC, Lessnick SL, Theisen ER. DBD-α4 helix of EWSR1::FLI1 is required for GGAA microsatellite binding that underlies genome regulation in Ewing sarcoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578127. [PMID: 38352344 PMCID: PMC10862889 DOI: 10.1101/2024.01.31.578127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ewing sarcoma is the second most common bone cancer in children and young adults. In 85% of patients, a translocation between chromosomes 11 and 22 results in a potent fusion oncoprotein, EWSR1::FLI1. EWSR1::FLI1 is the only genetic alteration in an otherwise unaltered genome of Ewing sarcoma tumors. The EWSR1 portion of the protein is an intrinsically disordered domain involved in transcriptional regulation by EWSR1::FLI1. The FLI portion of the fusion contains a DNA binding domain shown to bind core GGAA motifs and GGAA repeats. A small alpha-helix in the DNA binding domain of FLI1, DBD-𝛼4 helix, is critical for the transcription function of EWSR1::FLI1. In this study, we aimed to understand the mechanism by which the DBD-𝛼4 helix promotes transcription, and therefore oncogenic transformation. We utilized a multi-omics approach to assess chromatin organization, active chromatinmarks, genome binding, and gene expression in cells expressing EWSR1::FLI1 constructs with and without the DBD-𝛼4 helix. Our studies revealed DBD-𝛼4 helix is crucial for cooperative binding of EWSR1::FLI1 at GGAA microsatellites. This binding underlies many aspects of genome regulation by EWSR1::FLI1 such as formation of TADs, chromatin loops, enhancers and productive transcription hubs.
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19
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Mabe NW, Perry JA, Malone CF, Stegmaier K. Pharmacological targeting of the cancer epigenome. NATURE CANCER 2024; 5:844-865. [PMID: 38937652 DOI: 10.1038/s43018-024-00777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Epigenetic dysregulation is increasingly appreciated as a hallmark of cancer, including disease initiation, maintenance and therapy resistance. As a result, there have been advances in the development and evaluation of epigenetic therapies for cancer, revealing substantial promise but also challenges. Three epigenetic inhibitor classes are approved in the USA, and many more are currently undergoing clinical investigation. In this Review, we discuss recent developments for each epigenetic drug class and their implications for therapy, as well as highlight new insights into the role of epigenetics in cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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20
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Zhang D, Li L, Li M, Cao X. Biological functions and clinic significance of SAF‑A (Review). Biomed Rep 2024; 20:88. [PMID: 38665420 PMCID: PMC11040223 DOI: 10.3892/br.2024.1776] [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] [Received: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
As one member of the heterogeneous ribonucleoprotein (hnRNP) family, scaffold attachment factor A (SAF-A) or hnRNP U, is an abundant nuclear protein. With RNA and DNA binding activities, SAF-A has multiple functions. The present review focused on the biological structure and different roles of SAF-A and SAF-A-related diseases. It was found that SAF-A maintains the higher-order chromatin organization via RNA and DNA, and regulates transcription at the initiation and elongation stages. In addition to regulating pre-mRNA splicing, mRNA transportation and stabilization, SAF-A participates in double-strand breaks and mitosis repair. Therefore, the aberrant expression and mutation of SAF-A results in tumors and impaired neurodevelopment. Moreover, SAF-A may play a role in the anti-virus system. In conclusion, due to its essential biological functions, SAF-A may be a valuable clinical prediction factor or therapeutic target. Since the role of SAF-A in tumors and viral infections may be controversial, more animal experiments and clinical assays are needed.
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Affiliation(s)
- Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Mengni Li
- Department of Pediatrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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21
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Xu JJ, Viny AD. Chromatin organization in myelodysplastic syndrome. Exp Hematol 2024; 134:104216. [PMID: 38582293 DOI: 10.1016/j.exphem.2024.104216] [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: 01/10/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Disordered chromatin organization has emerged as a new aspect of the pathogenesis of myelodysplastic syndrome (MDS). Characterized by lineage dysplasia and a high transformation rate to acute myeloid leukemia (AML), the genetic determinant of MDS is thought to be the main driver of the disease's progression. Among the recurrently mutated pathways, alterations in chromatin organization, such as the cohesin complex, have a profound impact on hematopoietic stem cell (HSC) function and lineage commitment. The cohesin complex is a ring-like structure comprised of structural maintenance of chromosomes (SMC), RAD21, and STAG proteins that involve three-dimensional (3D) genome organization via loop extrusion in mammalian cells. The partial loss of the functional cohesin ring leads to altered chromatin accessibility specific to key hematopoietic transcription factors, which is thought to be the molecular mechanism of cohesin dysfunction. Currently, there are no specific targeting agents for cohesin mutant MDS/AML. Potential therapeutic strategies have been proposed based on the current understanding of cohesin mutant leukemogenesis. Here, we will review the recent advances in investigation and targeting approaches against cohesin mutant MDS/AML.
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Affiliation(s)
- Jane Jialu Xu
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York City, New York
| | - Aaron D Viny
- Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, New York; Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York City, New York.
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22
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Ouyang Z, Wang Y, Wang S, Geng S, Zhao X, Zhang X, Xu Q, Yuan B, Tang S, Li J, Wang F, Yao G, Sun H. Programmable DNA Interphase Layers for High-Performance Anode-Free Lithium Metal Batteries. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401114. [PMID: 38549402 DOI: 10.1002/adma.202401114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Anode-free lithium (Li) metal batteries are promising candidates for advanced energy storage, attributed to their appealing characteristics such as high energy density, low cost, and convenient production. However, their major challenges lie in the poor cycling and rate performance owing to the inferior reversibility and kinetics of Li plating and stripping, which significantly hinder their real-world applications. Here, it is demonstrated that deoxyribonucleic acid (DNA), the most important genetic material in nature, can serve as a highly programmable interphase layer for innovation of anode-free Li metal batteries. It is found that the abundant base pairs in DNA can contribute transient Li-N bonds that facilitate homogeneous Li+ flux, thus resulting in excellent Li plating/stripping kinetics and reversibility even at a harsh areal current of 15 mA cm-2. The anode-free LiFePO4 full batteries based on an ultrathin (0.12 µm) and ultralight (≈0.01 mg cm-2) DNA interphase layer show high CEs (≈99.1%) over 400 cycles, corresponding to an increase of ≈186% compared with bare copper (Cu) foil. These results shed light on the excellent programmability of DNA as a new family of interphase materials for anode-free batteries, and provide a new paradigm for future battery innovation toward high programmability, high sustainability, and remarkable electrochemical performance.
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Affiliation(s)
- Zhaofeng Ouyang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Wang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuo Wang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shitao Geng
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoju Zhao
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiao Zhang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qiuchen Xu
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bin Yuan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shanshan Tang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Li
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guangbao Yao
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Sun
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, and Key Laboratory of Green and High-End Utilization of Salt Lake Resources (Chinese Academy of Sciences), Shanghai Jiao Tong University, Shanghai, 200240, China
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23
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Luo J, Chen Z, Qiao Y, Tien JCY, Young E, Mannan R, Mahapatra S, He T, Eyunni S, Zhang Y, Zheng Y, Su F, Cao X, Wang R, Cheng Y, Seri R, George J, Shahine M, Miner SJ, Vaishampayan U, Wang M, Wang S, Parolia A, Chinnaiyan AM. p300/CBP degradation is required to disable the active AR enhanceosome in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587346. [PMID: 38586029 PMCID: PMC10996709 DOI: 10.1101/2024.03.29.587346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Prostate cancer is an exemplar of an enhancer-binding transcription factor-driven disease. The androgen receptor (AR) enhanceosome complex comprised of chromatin and epigenetic coregulators assembles at enhancer elements to drive disease progression. The paralog lysine acetyltransferases p300 and CBP deposit histone marks that are associated with enhancer activation. Here, we demonstrate that p300/CBP are determinant cofactors of the active AR enhanceosome in prostate cancer. Histone H2B N-terminus multisite lysine acetylation (H2BNTac), which is exclusively reliant on p300/CBP catalytic function, marked active enhancers and was notably elevated in prostate cancer lesions relative to the adjacent benign epithelia. Degradation of p300/CBP rapidly depleted acetylation marks associated with the active AR enhanceosome, which was only partially phenocopied by inhibition of their reader bromodomains. Notably, H2BNTac was effectively abrogated only upon p300/CBP degradation, which led to a stronger suppression of p300/CBP-dependent oncogenic gene programs relative to bromodomain inhibition or the inhibition of its catalytic domain. In vivo experiments using an orally active p300/CBP proteolysis targeting chimera (PROTAC) degrader (CBPD-409) showed that p300/CBP degradation potently inhibited tumor growth in preclinical models of castration-resistant prostate cancer and synergized with AR antagonists. While mouse p300/CBP orthologs were effectively degraded in host tissues, prolonged treatment with the PROTAC degrader was well tolerated with no significant signs of toxicity. Taken together, our study highlights the pivotal role of p300/CBP in maintaining the active AR enhanceosome and demonstrates how target degradation may have functionally distinct effects relative to target inhibition, thus supporting the development of p300/CBP degraders for the treatment of advanced prostate cancer.
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Affiliation(s)
- Jie Luo
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Zhixiang Chen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Interdisciplinary Research Center on Biology and Chemistry, Chinese Academy of Sciences, Shanghai, China
- These authors contributed equally
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Molecular and Cellular Pathology Program, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yunhui Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rithvik Seri
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - James George
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Miriam Shahine
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ulka Vaishampayan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mi Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Shaomeng Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
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24
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Ren L, Ma W, Wang Y. Predicting RNA polymerase II transcriptional elongation pausing and associated histone code. Brief Bioinform 2024; 25:bbae246. [PMID: 38783706 PMCID: PMC11116834 DOI: 10.1093/bib/bbae246] [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: 01/22/2024] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
RNA Polymerase II (Pol II) transcriptional elongation pausing is an integral part of the dynamic regulation of gene transcription in the genome of metazoans. It plays a pivotal role in many vital biological processes and disease progression. However, experimentally measuring genome-wide Pol II pausing is technically challenging and the precise governing mechanism underlying this process is not fully understood. Here, we develop RP3 (RNA Polymerase II Pausing Prediction), a network regularized logistic regression machine learning method, to predict Pol II pausing events by integrating genome sequence, histone modification, gene expression, chromatin accessibility, and protein-protein interaction data. RP3 can accurately predict Pol II pausing in diverse cellular contexts and unveil the transcription factors that are associated with the Pol II pausing machinery. Furthermore, we utilize a forward feature selection framework to systematically identify the combination of histone modification signals associated with Pol II pausing. RP3 is freely available at https://github.com/AMSSwanglab/RP3.
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Affiliation(s)
- Lixin Ren
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Wanbiao Ma
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, 55 Zhongguancun East Road, Haidian District, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Wuhua District, Kunming 650223, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 1 Xiangshan Zhi Nong, West Lake District, Hangzhou 330106, China
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25
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Kilgore HR, Chinn I, Mikhael PG, Mitnikov I, Van Dongen C, Zylberberg G, Afeyan L, Banani S, Wilson-Hawken S, Lee TI, Barzilay R, Young RA. Protein codes promote selective subcellular compartmentalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589616. [PMID: 38659952 PMCID: PMC11042338 DOI: 10.1101/2024.04.15.589616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.
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Affiliation(s)
- Henry R. Kilgore
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Itamar Chinn
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter G. Mikhael
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ilan Mitnikov
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Guy Zylberberg
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lena Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Salman Banani
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Susana Wilson-Hawken
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Program of Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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He X, Tan Y, Feng Y, Sun Y, Ma H. Tracking pairwise genomic loci by the ParB-ParS and Noc-NBS systems in living cells. Nucleic Acids Res 2024; 52:4922-4934. [PMID: 38412314 PMCID: PMC11109969 DOI: 10.1093/nar/gkae134] [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: 11/15/2023] [Revised: 01/23/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
The dynamics of genomic loci pairs and their interactions are essential for transcriptional regulation and genome organization. However, a robust method for tracking pairwise genomic loci in living cells is lacking. Here we developed a multicolor DNA labeling system, mParSpot (multicolor ParSpot), to track pairs of genomic loci and their interactions in living cells. The mParSpot system is derived from the ParB/ParS in the parABS system and Noc/NBS in its paralogous nucleoid occlusion system. The insertion of 16 base-pair palindromic ParSs or NBSs into the genomic locus allows the cognate binding protein ParB or Noc to spread kilobases of DNA around ParSs or NBSs for loci-specific visualization. We tracked two loci with a genomic distance of 53 kilobases and measured their spatial distance over time. Using the mParSpot system, we labeled the promoter and terminator of the MSI2 gene span 423 kb and measured their spatial distance. We also tracked the promoter and terminator dynamics of the MUC4 gene in living cells. In sum, the mParSpot is a robust and sensitive DNA labeling system for tracking genomic interactions in space and time under physiological or pathological contexts.
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Affiliation(s)
- Xiaohui He
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yuxi Tan
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ying Feng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yadong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hanhui Ma
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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27
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Yoon J, Hwang Y, Yun H, Chung JM, Kim S, Kim G, Lee Y, Lee B, Kang HC. LC3B drives transcription-associated homologous recombination via direct interaction with R-loops. Nucleic Acids Res 2024; 52:5088-5106. [PMID: 38412240 PMCID: PMC11109984 DOI: 10.1093/nar/gkae156] [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: 11/09/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
Exploring the connection between ubiquitin-like modifiers (ULMs) and the DNA damage response (DDR), we employed several advanced DNA damage and repair assay techniques and identified a crucial role for LC3B. Notably, its RNA recognition motif (RRM) plays a pivotal role in the context of transcription-associated homologous recombination (HR) repair (TA-HRR), a particular subset of HRR pathways. Surprisingly, independent of autophagy flux, LC3B interacts directly with R-loops at DNA lesions within transcriptionally active sites via its RRM, promoting TA-HRR. Using native RNA immunoprecipitation (nRIP) coupled with high-throughput sequencing (nRIP-seq), we discovered that LC3B also directly interacts with the 3'UTR AU-rich elements (AREs) of BRCA1 via its RRM, influencing its stability. This suggests that LC3B regulates TA-HRR both proximal to and distal from DNA lesions. Data from our LC3B depletion experiments showed that LC3B knockdown disrupts end-resection for TA-HRR, redirecting it towards the non-homologous end joining (NHEJ) pathway and leading to chromosomal instability, as evidenced by alterations in sister chromatid exchange (SCE) and interchromosomal fusion (ICF). Thus, our findings unveil autophagy-independent functions of LC3B in DNA damage and repair pathways, highlighting its importance. This could reshape our understanding of TA-HRR and the interaction between autophagy and DDR.
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Affiliation(s)
- Junghyun Yoon
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Yiseul Hwang
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hansol Yun
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jee Min Chung
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Soyeon Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Gyeongmin Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Yeji Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Byoung Dae Lee
- Department of Neuroscience, Kyung Hee University, Seoul 02447; Department of Physiology, Kyung Hee University School of Medicine, Seoul 02447, Republic of Korea
| | - Ho Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
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28
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression. Proc Natl Acad Sci U S A 2024; 121:e2401494121. [PMID: 38753513 PMCID: PMC11127048 DOI: 10.1073/pnas.2401494121] [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: 01/26/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross-over between two and four at contour lengths on the order of 30 kilo-base pairs. The anomalously high fractal dimension [Formula: see text] is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ([Formula: see text]) longer than tens of minutes to be proportional to [Formula: see text]. We validate our results with hybrid molecular dynamics-Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, NC27708
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, NC27708
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
- Department of Physics, Duke University, Durham, NC27708
- Department of Chemistry, Duke University, Durham, NC27708
- World Premier International Research Center Initiative–Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
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29
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Riera Aroche R, Ortiz García YM, Martínez Arellano MA, Riera Leal A. DNA as a perfect quantum computer based on the quantum physics principles. Sci Rep 2024; 14:11636. [PMID: 38773193 PMCID: PMC11109248 DOI: 10.1038/s41598-024-62539-5] [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: 02/01/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
DNA is a complex multi-resolution molecule whose theoretical study is a challenge. Its intrinsic multiscale nature requires chemistry and quantum physics to understand the structure and quantum informatics to explain its operation as a perfect quantum computer. Here, we present theoretical results of DNA that allow a better description of its structure and the operation process in the transmission, coding, and decoding of genetic information. Aromaticity is explained by the oscillatory resonant quantum state of correlated electron and hole pairs due to the quantized molecular vibrational energy acting as an attractive force. The correlated pairs form a supercurrent in the nitrogenous bases in a single band π -molecular orbital ( π -MO). The MO wave function ( Φ ) is assumed to be the linear combination of the n constituent atomic orbitals. The central Hydrogen bond between Adenine (A) and Thymine (T) or Guanine (G) and Cytosine (C) functions like an ideal Josephson Junction. The approach of a Josephson Effect between two superconductors is correctly described, as well as the condensation of the nitrogenous bases to obtain the two entangled quantum states that form the qubit. Combining the quantum state of the composite system with the classical information, RNA polymerase teleports one of the four Bell states. DNA is a perfect quantum computer.
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Affiliation(s)
- R Riera Aroche
- Department of Research in Physics, University of Sonora, Hermosillo, Sonora, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - Y M Ortiz García
- Research Institute of Dentistry, University of Guadalajara, Guadalajara Jalisco, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - M A Martínez Arellano
- General Hospital of the State of Sonora, Boulevar José María Escrivá de Balaguer 157, Colonia Villa del Palmar, C.P. 83105, Hermosillo, Sonora, Mexico
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico
| | - A Riera Leal
- General Hospital of the State of Sonora, Boulevar José María Escrivá de Balaguer 157, Colonia Villa del Palmar, C.P. 83105, Hermosillo, Sonora, Mexico.
- Research and Higher Education Center of UNEPROP, Hermosillo, Sonora, Mexico.
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Wu Z, Pope SD, Ahmed NS, Leung DL, Hajjar S, Yue Q, Anand DM, Kopp EB, Okin D, Ma W, Kagan JC, Hargreaves DC, Medzhitov R, Zhou X. Control of Inflammatory Response by Tissue Microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.592432. [PMID: 38798655 PMCID: PMC11118380 DOI: 10.1101/2024.05.10.592432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Inflammation is an essential defense response but operates at the cost of normal functions. Whether and how the negative impact of inflammation is monitored remains largely unknown. Acidification of the tissue microenvironment is associated with inflammation. Here we investigated whether macrophages sense tissue acidification to adjust inflammatory responses. We found that acidic pH restructured the inflammatory response of macrophages in a gene-specific manner. We identified mammalian BRD4 as a novel intracellular pH sensor. Acidic pH disrupts the transcription condensates containing BRD4 and MED1, via histidine-enriched intrinsically disordered regions. Crucially, decrease in macrophage intracellular pH is necessary and sufficient to regulate transcriptional condensates in vitro and in vivo, acting as negative feedback to regulate the inflammatory response. Collectively, these findings uncovered a pH-dependent switch in transcriptional condensates that enables environmental sensing to directly control inflammation, with a broader implication for calibrating the magnitude and quality of inflammation by the inflammatory cost.
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Affiliation(s)
- Zhongyang Wu
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Scott D. Pope
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Nasiha S. Ahmed
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Diana L. Leung
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stephanie Hajjar
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Qiuyu Yue
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Diya M. Anand
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Elizabeth B. Kopp
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Daniel Okin
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02115
| | - Weiyi Ma
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonathan C. Kagan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Diana C. Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ruslan Medzhitov
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Tananbaum Center for Theoretical and Analytical Human Biology, Yale University School of Medicine
| | - Xu Zhou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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31
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Hoboth P, Sztacho M, Hozák P. Nuclear patterns of phosphatidylinositol 4,5- and 3,4-bisphosphate revealed by super-resolution microscopy differ between the consecutive stages of RNA polymerase II transcription. FEBS J 2024. [PMID: 38734927 DOI: 10.1111/febs.17136] [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: 08/09/2023] [Revised: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
Abstract
Phosphatidylinositol phosphates are powerful signaling molecules that orchestrate signaling and direct membrane trafficking in the cytosol. Interestingly, phosphatidylinositol phosphates also localize within the membrane-less compartments of the cell nucleus, where they participate in the regulation of gene expression. Nevertheless, current models of gene expression, which include condensates of proteins and nucleic acids, do not include nuclear phosphatidylinositol phosphates. This gap is partly a result of the missing detailed analysis of the subnuclear distribution of phosphatidylinositol phosphates and their relationships with gene expression. Here, we used quantitative dual-color direct stochastic optical reconstruction microscopy to analyze the nanoscale co-patterning between RNA polymerase II transcription initiation and elongation markers with respect to phosphatidylinositol 4,5- or 3,4-bisphosphate in the nucleoplasm and nuclear speckles and compared it with randomized data and cells with inhibited transcription. We found specific co-patterning of the transcription initiation marker P-S5 with phosphatidylinositol 4,5-bisphosphate in the nucleoplasm and with phosphatidylinositol 3,4-bisphosphate at the periphery of nuclear speckles. We showed the specific accumulation of the transcription elongation marker PS-2 and of nascent RNA in the proximity of phosphatidylinositol 3,4-bisphosphate associated with nuclear speckles. Taken together, this shows that the distinct spatial associations between the consecutive stages of RNA polymerase II transcription and nuclear phosphatidylinositol phosphates exhibit specificity within the gene expression compartments. Thus, in analogy to the cellular membranes, where phospholipid composition orchestrates signaling pathways and directs membrane trafficking, we propose a model in which the phospholipid identity of gene expression compartments orchestrates RNA polymerase II transcription.
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Affiliation(s)
- Peter Hoboth
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Viničná Microscopy Core Facility, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Sztacho
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Cancer Cell Architecture, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Hozák
- Laboratory of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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32
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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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DeHaro-Arbona FJ, Roussos C, Baloul S, Townson J, Gómez Lamarca MJ, Bray S. Dynamic modes of Notch transcription hubs conferring memory and stochastic activation revealed by live imaging the co-activator Mastermind. eLife 2024; 12:RP92083. [PMID: 38727722 PMCID: PMC11087053 DOI: 10.7554/elife.92083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Developmental programming involves the accurate conversion of signalling levels and dynamics to transcriptional outputs. The transcriptional relay in the Notch pathway relies on nuclear complexes containing the co-activator Mastermind (Mam). By tracking these complexes in real time, we reveal that they promote the formation of a dynamic transcription hub in Notch ON nuclei which concentrates key factors including the Mediator CDK module. The composition of the hub is labile and persists after Notch withdrawal conferring a memory that enables rapid reformation. Surprisingly, only a third of Notch ON hubs progress to a state with nascent transcription, which correlates with polymerase II and core Mediator recruitment. This probability is increased by a second signal. The discovery that target-gene transcription is probabilistic has far-reaching implications because it implies that stochastic differences in Notch pathway output can arise downstream of receptor activation.
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Affiliation(s)
- F Javier DeHaro-Arbona
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Charalambos Roussos
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Sarah Baloul
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Jonathan Townson
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - María J Gómez Lamarca
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocıo/CSIC/Universidad de Sevilla, Departamento de Biologıa CelularSevilleSpain
| | - Sarah Bray
- Department of Physiology Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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35
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Garcia IS, Silva-Vignato B, Cesar ASM, Petrini J, da Silva VH, Morosini NS, Goes CP, Afonso J, da Silva TR, Lima BD, Clemente LG, Regitano LCDA, Mourão GB, Coutinho LL. Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions. Sci Rep 2024; 14:10094. [PMID: 38698200 PMCID: PMC11066111 DOI: 10.1038/s41598-024-60703-5] [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: 10/19/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.
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Affiliation(s)
- Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Natália Silva Morosini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Thaís Ribeiro da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Beatriz Delcarme Lima
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil.
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Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P. Three-step mechanism of promoter escape by RNA polymerase II. Mol Cell 2024; 84:1699-1710.e6. [PMID: 38604172 DOI: 10.1016/j.molcel.2024.03.016] [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: 10/02/2023] [Revised: 01/04/2024] [Accepted: 03/16/2024] [Indexed: 04/13/2024]
Abstract
The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.
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Affiliation(s)
- Yumeng Zhan
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frauke Grabbe
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Elisa Oberbeckmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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37
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Wang J, Zhu H, Tian R, Zhang Q, Zhang H, Hu J, Wang S. Physiological and pathological effects of phase separation in the central nervous system. J Mol Med (Berl) 2024; 102:599-615. [PMID: 38441598 PMCID: PMC11055734 DOI: 10.1007/s00109-024-02435-7] [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: 05/01/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 04/28/2024]
Abstract
Phase separation, also known as biomolecule condensate, participates in physiological processes such as transcriptional regulation, signal transduction, gene expression, and DNA damage repair by creating a membrane-free compartment. Phase separation is primarily caused by the interaction of multivalent non-covalent bonds between proteins and/or nucleic acids. The strength of molecular multivalent interaction can be modified by component concentration, the potential of hydrogen, posttranslational modification, and other factors. Notably, phase separation occurs frequently in the cytoplasm of mitochondria, the nucleus, and synapses. Phase separation in vivo is dynamic or stable in the normal physiological state, while abnormal phase separation will lead to the formation of biomolecule condensates, speeding up the disease progression. To provide candidate suggestions for the clinical treatment of nervous system diseases, this review, based on existing studies, carefully and systematically represents the physiological roles of phase separation in the central nervous system and its pathological mechanism in neurodegenerative diseases.
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Affiliation(s)
- Jiaxin Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Hongrui Zhu
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China.
- Core Facility Center, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Hefei, China.
| | - Ruijia Tian
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Qian Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Haoliang Zhang
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Jin Hu
- School of Medicine, Xiamen University, Xiamen, Fujian, 361000, People's Republic of China
| | - Sheng Wang
- Department of Anesthesiology, First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, People's Republic of China.
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38
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Chen M, Zou C, Tian Y, Li W, Li Y, Zhang D. An integrated ceRNA network identifies miR-375 as an upregulated miRNA playing a tumor suppressive role in aggressive prostate cancer. Oncogene 2024; 43:1594-1607. [PMID: 38565944 DOI: 10.1038/s41388-024-03011-6] [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: 07/17/2023] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Prostate cancer (PCa) remains a significant cause of morbidity and mortality among men worldwide. A number of genes have been implicated in prostate tumorigenesis, but the mechanisms underlying their dysregulation are still incompletely understood. Evidence has established the competing endogenous RNA (ceRNA) theory as a novel regulatory mechanism for post-transcriptional alterations. Yet, a comprehensive characterization of ceRNA network in PCa lacks. Here we utilize stringent in-silico methods to construct a large ceRNA network across different PCa stages, and provide experimental demonstration for the competing regulation among protumorigenic SEC23A, PHTF2, and their corresponding ceRNA pairs. Using machine learning, we establish a ceRNA-based signature (ceRNA_sig) predictive of androgen receptor (AR) activity, tumor aggressiveness, and patient outcomes. Importantly, we identify miR-375 as a key node in PCa ceRNA network, which is upregulated in PCa relative to normal tissues. Forced expression of miR-375 significantly inhibits, while its inhibition promotes, aggressive behaviors of both AR+ and AR- PCa cells in vitro and in vivo. Mechanistically, we show that miR-375 predominantly targets genes possessing oncogenic roles (e.g., proliferation, DNA repair, and metastasis), and thus release targets with tumor suppressive functions. This action model well clarifies why an upregulated miRNA plays a tumor suppressive role in PCa. Together, our study provides new insights into understanding of transcriptomic aberrations during PCa evolution, and nominates miR-375 as a potential therapeutic target for combating aggressive PCa.
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Affiliation(s)
- Mengjie Chen
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, School of BioMedical Sciences, Hunan University, Changsha, China
| | - Cheng Zou
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, School of BioMedical Sciences, Hunan University, Changsha, China.
| | - Yu Tian
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, School of BioMedical Sciences, Hunan University, Changsha, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yingying Li
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, School of BioMedical Sciences, Hunan University, Changsha, China
| | - Dingxiao Zhang
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, School of BioMedical Sciences, Hunan University, Changsha, China.
- Shenzhen Research Institute, Hunan University, Shenzhen, China.
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Song X, Fang C, Dai Y, Sun Y, Qiu C, Lin X, Xu R. Cyclin-dependent kinase 7 (CDK7) inhibitors as a novel therapeutic strategy for different molecular types of breast cancer. Br J Cancer 2024; 130:1239-1248. [PMID: 38355840 PMCID: PMC11014910 DOI: 10.1038/s41416-024-02589-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Cyclin-dependent kinase (CDK) 7 is aberrantly overexpressed in many types of cancer and is an attractive target for cancer therapy due to its dual role in transcription and cell cycle progression. Moreover, CDK7 can directly modulate the activities of estrogen receptor (ER), which is a major driver in breast cancer. Breast cancer cells have exhibited high sensitivity to CDK7 inhibition in pre-clinical studies. METHODS In this review, we provide a comprehensive summary of the latest insights into CDK7 biology and recent advancements in CDK7 inhibitor development for breast cancer treatment. We also discuss the current application of CDK7 inhibitors in different molecular types of breast cancer to provide potential strategies for the treatment of breast cancer. RESULTS Significant progress has been made in the development of selective CDK7 inhibitors, which show efficacy in both triple-negative breast cancer (TNBC) and hormone receptor-positive breast cancer (HR+). Moreover, combined with other agents, CDK7 inhibitors may provide synergistic effects for endocrine therapy and chemotherapy. Thus, high-quality studies for developing potent CDK7 inhibitors and investigating their applications in breast cancer therapy are rapidly emerging. CONCLUSION CDK7 inhibitors have emerged as a promising therapeutic strategy and have demonstrated significant anti-cancer activity in different subtypes of breast cancer, especially those that have been resistant to current therapies.
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Affiliation(s)
- Xue Song
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Chen Fang
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Yan Dai
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Yang Sun
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Chang Qiu
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Xiaojie Lin
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Rui Xu
- Department of Breast Cancer, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China.
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40
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Fang S, Luo Z, Wei Z, Qin Y, Zheng J, Zhang H, Jin J, Li J, Miao C, Yang S, Li Y, Liang Z, Yu XD, Zhang XM, Xiong W, Zhu H, Gan WB, Huang L, Li B. Sexually dimorphic control of affective state processing and empathic behaviors. Neuron 2024; 112:1498-1517.e8. [PMID: 38430912 DOI: 10.1016/j.neuron.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Recognizing the affective states of social counterparts and responding appropriately fosters successful social interactions. However, little is known about how the affective states are expressed and perceived and how they influence social decisions. Here, we show that male and female mice emit distinct olfactory cues after experiencing distress. These cues activate distinct neural circuits in the piriform cortex (PiC) and evoke sexually dimorphic empathic behaviors in observers. Specifically, the PiC → PrL pathway is activated in female observers, inducing a social preference for the distressed counterpart. Conversely, the PiC → MeA pathway is activated in male observers, evoking excessive self-grooming behaviors. These pathways originate from non-overlapping PiC neuron populations with distinct gene expression signatures regulated by transcription factors and sex hormones. Our study unveils how internal states of social counterparts are processed through sexually dimorphic mechanisms at the molecular, cellular, and circuit levels and offers insights into the neural mechanisms underpinning sex differences in higher brain functions.
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Affiliation(s)
- Shunchang Fang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zhengyi Luo
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zicheng Wei
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yuxin Qin
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jieyan Zheng
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Hongyang Zhang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jianhua Jin
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jiali Li
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Chenjian Miao
- Institute on Aging, Hefei, China and Brain Disorders, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Shana Yang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yonglin Li
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Zirui Liang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiao-Dan Yu
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiao Min Zhang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Wei Xiong
- Institute on Aging, Hefei, China and Brain Disorders, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Hongying Zhu
- Institute on Aging, Hefei, China and Brain Disorders, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | | | - Lianyan Huang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Ministry of Education, Guangzhou 510655, China.
| | - Boxing Li
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China; Advanced Medical Technology Center, the First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-Sen University), Ministry of Education, Guangzhou 510655, China.
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41
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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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42
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Kim KL, Rahme GJ, Goel VY, El Farran CA, Hansen AS, Bernstein BE. Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. Mol Cell 2024; 84:1365-1376.e7. [PMID: 38452764 PMCID: PMC10997458 DOI: 10.1016/j.molcel.2024.02.007] [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: 10/03/2023] [Revised: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 03/09/2024]
Abstract
Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.
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Affiliation(s)
- Kyung Lock Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Gilbert J Rahme
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Viraat Y Goel
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Chadi A El Farran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Anders S Hansen
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA.
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43
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Zhang Z, Zhang Y. Transcriptional regulation of cancer stem cell: regulatory factors elucidation and cancer treatment strategies. J Exp Clin Cancer Res 2024; 43:99. [PMID: 38561775 PMCID: PMC10986082 DOI: 10.1186/s13046-024-03021-y] [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: 12/04/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Cancer stem cells (CSCs) were first discovered in the 1990s, revealing the mysteries of cancer origin, migration, recurrence and drug-resistance from a new perspective. The expression of pluripotent genes and complex signal regulatory networks are significant features of CSC, also act as core factors to affect the characteristics of CSC. Transcription is a necessary link to regulate the phenotype and potential of CSC, involving chromatin environment, nucleosome occupancy, histone modification, transcription factor (TF) availability and cis-regulatory elements, which suffer from ambient pressure. Especially, the expression and activity of pluripotent TFs are deeply affected by both internal and external factors, which is the foundation of CSC transcriptional regulation in the current research framework. Growing evidence indicates that regulating epigenetic modifications to alter cancer stemness is effective, and some special promoters and enhancers can serve as targets to influence the properties of CSC. Clarifying the factors that regulate CSC transcription will assist us directly target key stem genes and TFs, or hinder CSC transcription through environmental and other related factors, in order to achieve the goal of inhibiting CSC and tumors. This paper comprehensively reviews the traditional aspects of transcriptional regulation, and explores the progress and insights of the impact on CSC transcription and status through tumor microenvironment (TME), hypoxia, metabolism and new meaningful regulatory factors in conjunction with the latest research. Finally, we present opinions on omnidirectional targeting CSCs transcription to eliminate CSCs and address tumor resistance.
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Affiliation(s)
- Zhengyue Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, People's Republic of China
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, People's Republic of China
| | - Yanjie Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, People's Republic of China.
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, People's Republic of China.
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44
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Fan S, Zhang Y, Zhu S, Shen L. Plant RNA-binding proteins: Phase separation dynamics and functional mechanisms underlying plant development and stress responses. MOLECULAR PLANT 2024; 17:531-551. [PMID: 38419328 DOI: 10.1016/j.molp.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
RNA-binding proteins (RBPs) accompany RNA from synthesis to decay, mediating every aspect of RNA metabolism and impacting diverse cellular and developmental processes in eukaryotes. Many RBPs undergo phase separation along with their bound RNA to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of RNA metabolism. Increasing evidence suggests that phase-separating RBPs with RNA-binding domains and intrinsically disordered regions play important roles in plant development and stress adaptation. Here, we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions, with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating RNA metabolism. We also discuss roles of multiple factors, such as environmental signals, protein modifications, and N6-methyladenosine RNA methylation, in modulating the phase separation behaviors of RBPs, and highlight the prospects and challenges for future research on phase-separating RBPs in crops.
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Affiliation(s)
- Sheng Fan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Yu Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Shaobo Zhu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
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45
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Lu Z, Xiao X, Zheng Q, Wang X, Xu L. Assessing NGS-based computational methods for predicting transcriptional regulators with query gene sets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578316. [PMID: 38562775 PMCID: PMC10983863 DOI: 10.1101/2024.02.01.578316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This article provides an in-depth review of computational methods for predicting transcriptional regulators with query gene sets. Identification of transcriptional regulators is of utmost importance in many biological applications, including but not limited to elucidating biological development mechanisms, identifying key disease genes, and predicting therapeutic targets. Various computational methods based on next-generation sequencing (NGS) data have been developed in the past decade, yet no systematic evaluation of NGS-based methods has been offered. We classified these methods into two categories based on shared characteristics, namely library-based and region-based methods. We further conducted benchmark studies to evaluate the accuracy, sensitivity, coverage, and usability of NGS-based methods with molecular experimental datasets. Results show that BART, ChIP-Atlas, and Lisa have relatively better performance. Besides, we point out the limitations of NGS-based methods and explore potential directions for further improvement. Key points An introduction to available computational methods for predicting functional TRs from a query gene set.A detailed walk-through along with practical concerns and limitations.A systematic benchmark of NGS-based methods in terms of accuracy, sensitivity, coverage, and usability, using 570 TR perturbation-derived gene sets.NGS-based methods outperform motif-based methods. Among NGS methods, those utilizing larger databases and adopting region-centric approaches demonstrate favorable performance. BART, ChIP-Atlas, and Lisa are recommended as these methods have overall better performance in evaluated scenarios.
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46
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Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 2024; 15:2425. [PMID: 38499544 PMCID: PMC10948791 DOI: 10.1038/s41467-024-46596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Siyan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Wujian Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Qiao Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Ping Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Di Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Simeng He
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jiayi Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China.
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47
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Gan P, Eppert M, De La Cruz N, Lyons H, Shah AM, Veettil RT, Chen K, Pradhan P, Bezprozvannaya S, Xu L, Liu N, Olson EN, Sabari BR. Coactivator condensation drives cardiovascular cell lineage specification. SCIENCE ADVANCES 2024; 10:eadk7160. [PMID: 38489358 PMCID: PMC10942106 DOI: 10.1126/sciadv.adk7160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
During development, cells make switch-like decisions to activate new gene programs specifying cell lineage. The mechanisms underlying these decisive choices remain unclear. Here, we show that the cardiovascular transcriptional coactivator myocardin (MYOCD) activates cell identity genes by concentration-dependent and switch-like formation of transcriptional condensates. MYOCD forms such condensates and activates cell identity genes at critical concentration thresholds achieved during smooth muscle cell and cardiomyocyte differentiation. The carboxyl-terminal disordered region of MYOCD is necessary and sufficient for condensate formation. Disrupting this region's ability to form condensates disrupts gene activation and smooth muscle cell reprogramming. Rescuing condensate formation by replacing this region with disordered regions from functionally unrelated proteins rescues gene activation and smooth muscle cell reprogramming. Our findings demonstrate that MYOCD condensate formation is required for gene activation during cardiovascular differentiation. We propose that the formation of transcriptional condensates at critical concentrations of cell type-specific regulators provides a molecular switch underlying the activation of key cell identity genes during development.
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Affiliation(s)
- Peiheng Gan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mikayla Eppert
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nancy De La Cruz
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Heankel Lyons
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Akansha M. Shah
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Reshma T. Veettil
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Pradhan
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin R. Sabari
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Laboratory of Nuclear Organization, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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48
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Hu Y, Wang Y, He Y, Ye M, Yuan J, Ren C, Wang X, Wang S, Guo Y, Cao Q, Zhou S, Wang B, He A, Hu J, Guo X, Shu W, Huo R. Maternal KLF17 controls zygotic genome activation by acting as a messenger for RNA Pol II recruitment in mouse embryos. Dev Cell 2024; 59:613-626.e6. [PMID: 38325372 DOI: 10.1016/j.devcel.2024.01.013] [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: 10/13/2022] [Revised: 09/01/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Initiation of timely and sufficient zygotic genome activation (ZGA) is crucial for the beginning of life, yet our knowledge of transcription factors (TFs) contributing to ZGA remains limited. Here, we screened the proteome of early mouse embryos after cycloheximide (CHX) treatment and identified maternally derived KLF17 as a potential TF for ZGA genes. Using a conditional knockout (cKO) mouse model, we further investigated the role of maternal KLF17 and found that it promotes embryonic development and full fertility. Mechanistically, KLF17 preferentially binds to promoters and recruits RNA polymerase II (RNA Pol II) in early 2-cell embryos, facilitating the expression of major ZGA genes. Maternal Klf17 knockout resulted in a downregulation of 9% of ZGA genes and aberrant RNA Pol II pre-configuration, which could be partially rescued by introducing exogenous KLF17. Overall, our study provides a strategy for screening essential ZGA factors and identifies KLF17 as a crucial TF in this process.
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Affiliation(s)
- Yue Hu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | | | - Yuanlin He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Maosheng Ye
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Jie Yuan
- Bioinformatics Center of AMMS, Beijing, China
| | - Chao Ren
- Bioinformatics Center of AMMS, Beijing, China
| | - Xia Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Siqi Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Qiqi Cao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Shuai Zhou
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Bing Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Anlan He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | | | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Wenjie Shu
- Bioinformatics Center of AMMS, Beijing, China.
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China; Innovation Center of Suzhou Nanjing Medical University, Suzhou, China.
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49
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Russo M, Gualdrini F, Vallelonga V, Prosperini E, Noberini R, Pedretti S, Borriero C, Di Chiaro P, Polletti S, Imperato G, Marenda M, Ghirardi C, Bedin F, Cuomo A, Rodighiero S, Bonaldi T, Mitro N, Ghisletti S, Natoli G. Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide. Mol Cell 2024; 84:967-980.e10. [PMID: 38242130 PMCID: PMC7615796 DOI: 10.1016/j.molcel.2023.12.033] [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: 03/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Histone-modifying enzymes depend on the availability of cofactors, with acetyl-coenzyme A (CoA) being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA-producing enzymes translocate to the nucleus suggests that high concentrations of locally synthesized metabolites may impact acylation of histones and other nuclear substrates, thereby controlling gene expression. Here, we show that 2-ketoacid dehydrogenases are stably associated with the Mediator complex, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in lipopolysaccharide-stimulated macrophages, inhibited the activity of Mediator-associated 2-ketoacid dehydrogenases. Elevation of NO levels and the disruption of Mediator complex integrity both affected de novo histone acetylation within a shared set of genomic regions. Our findings indicate that the local supply of acetyl-CoA generated by 2-ketoacid dehydrogenases bound to Mediator is required to maximize acetylation of histone tails at sites of elevated HAT activity.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Gabriele Imperato
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; Department of Hematology and Hematology-Oncology (DIPO), Università degli Studi di Milano, Milano 20122, Italy
| | - Nico Mitro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
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50
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Sobański D, Bogdał P, Staszkiewicz R, Sobańska M, Filipowicz M, Czepko RA, Strojny D, Grabarek BO. Evaluation of differences in expression pattern of three isoforms of the transforming growth factor beta in patients with lumbosacral stenosis. Cell Cycle 2024; 23:555-572. [PMID: 38695374 PMCID: PMC11135850 DOI: 10.1080/15384101.2024.2345484] [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: 01/30/2024] [Accepted: 03/30/2024] [Indexed: 05/28/2024] Open
Abstract
The study investigates molecular changes in the lumbosacral (L/S) spine's yellow ligamentum flavum during degenerative stenosis, focusing on the role of transforming growth factor beta 1-3 (TGF-β-1-3). Sixty patients with degenerative stenosis and sixty control participants underwent molecular analysis using real-time quantitative reverse transcription reaction technique (RTqPCR), enzyme-linked immunosorbent assay (ELISA), Western blot, and immunohistochemical analysis (IHC). At the mRNA level, study samples showed reduced expression of TGF-β-1 and TGF-β-3, while TGF-β-2 increased by only 4%. Conversely, at the protein level, the study group exhibited significantly higher concentrations of TGF-β-1, TGF-β-2, and TGF-β-3 compared to controls. On the other hand, at the protein level, a statistically significant higher concentration of TGF-β-1 was observed (2139.33 pg/mL ± 2593.72 pg/mL vs. 252.45 pg/mL ± 83.89 pg/mL; p < 0.0001), TGF-β-2 (3104.34 pg/mL ± 1192.74 pg/mL vs. 258.86 pg/mL ± 82.98 pg/mL; p < 0.0001), TGF-β-3 (512.75 pg/mL ± 107.36 pg/mL vs. 55.06 pg/mL ± 9.83 pg/mL, p < 0.0001) in yellow ligaments obtained from patients of the study group compared to control samples. The study did not establish a significant correlation between TGF-β-1-3 concentrations and pain severity. The findings suggest that molecular therapy aimed at restoring the normal expression pattern of TGF-β-1-3 could be a promising strategy for treating degenerative stenosis of the L/S spine. The study underscores the potential therapeutic significance of addressing molecular changes at the TGF-β isoforms level for better understanding and managing degenerative spinal conditions.
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Affiliation(s)
- Dawid Sobański
- Department of Neurosurgery, Szpital sw. Rafala in Cracow, Cracow, Poland
- Collegium Medicum, WSB University, Dabrowa Gornicza, Poland
| | - Paweł Bogdał
- Department of Orthopedic, Szpital Powiatowy w Zawierciu, Zawiercie, Poland
| | - Rafał Staszkiewicz
- Collegium Medicum, WSB University, Dabrowa Gornicza, Poland
- Department of Neurosurgery, 5th Military Clinical Hospital with the SP ZOZ Polyclinic in Krakow, Krakow, Poland
- Department of Neurosurgery, Faculty of Medicine in Zabrze, Academy of Silesia, Katowice, Poland
| | | | - Michał Filipowicz
- Department of Neurosurgery, Szpital sw. Rafala in Cracow, Cracow, Poland
| | - Ryszard Adam Czepko
- Department of Neurosurgery, Szpital sw. Rafala in Cracow, Cracow, Poland
- Department of Neurosurgery, Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski University in Cracow, Cracow, Poland
| | - Damian Strojny
- Collegium Medicum, WSB University, Dabrowa Gornicza, Poland
- Institute of Health Care, National Academy of Applied Sciences in Przemyśl, Przemyśl, Poland
- Department of Medical Science, New Medical Techniques Specialist Hospital of St. Family in Rudna Mała, Rzeszów, Poland
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