1
|
Boštjančić LL, Dragičević P, Bonassin L, Francesconi C, Tarandek A, Schardt L, Rutz C, Hudina S, Schwenk K, Lecompte O, Theissinger K. Expression of C/EBP and Kr-h1 transcription factors under immune stimulation in the noble crayfish. Gene 2024; 929:148813. [PMID: 39094714 DOI: 10.1016/j.gene.2024.148813] [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: 04/09/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Transcription factors (TFs) have an important role in the regulation of the gene expression network. The role of TFs in the immune response of freshwater crayfish is poorly understood, but leveraging the regulatory mechanisms of immune response could augment the resistance against the invasive oomycete pathogen, Aphanomyces astaci. Previous studies indicated that the TFs CCAAT/enhancer-binding protein (C/EBP) and putative Krüppel homolog-1 protein (Kr-h1) might play a role in immune and stress response of the noble crayfish (Astacus astacus). Here, we aimed to further characterise these two gene products to gain a better understanding of their evolutionary origin, domain organisation and expression patterns across different crayfish tissues. Furthermore, we conducted an immune stimulation experiment to observe the potential changes in the gene expression of C/EBP and Kr-h1 under immune challenge in different crayfish tissues. Our results showed that both C/EBP and Kr-h1 are closely related to other C/EBPs and Kr-h1s in Malacostraca. Gene expression analysis revealed that both TFs are present in all analysed tissues, with higher expression of C/EBP in the gills and Kr-h1 in the abdominal muscle. Immune stimulation with laminarin (mimicking β-1-3-glucan in the oomycete cell wall) showed an activation of the crayfish immune system, with an overall increase in the total haemocyte count (THC) compared to untreated control and crayfish buffered saline (CBS) treatment. On the gene expression level, an up-regulation of the C/EBP gene was detected in the laminarin treated group in hepatopancreas and heart, while no changes were observed for the Kr-h1 gene. Our results indicate an early change in C/EBP expression in multiple tissues during immune stimulation and suggest its involvement in the immune response of the noble crayfish.
Collapse
Affiliation(s)
- Ljudevit Luka Boštjančić
- Institute of Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26, 35392 Gießen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000 Strasbourg, France; iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Fortstraße 7, 76829 Landau, Germany.
| | - Paula Dragičević
- Depatment of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Lena Bonassin
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000 Strasbourg, France; iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Fortstraße 7, 76829 Landau, Germany
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Fortstraße 7, 76829 Landau, Germany
| | - Anita Tarandek
- Depatment of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Leonie Schardt
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000 Strasbourg, France
| | - Sandra Hudina
- Depatment of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Klaus Schwenk
- iES - Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Fortstraße 7, 76829 Landau, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000 Strasbourg, France
| | - Kathrin Theissinger
- Institute of Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26, 35392 Gießen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| |
Collapse
|
2
|
Wu Y, Li Y, Zhou Y, Bai X, Liu Y. Bioinformatics and systems-biology approach to identify common pathogenic mechanisms for COVID-19 and systemic lupus erythematosus. Autoimmunity 2024; 57:2304826. [PMID: 38332666 DOI: 10.1080/08916934.2024.2304826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/07/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The Coronavirus disease 2019 (COVID-19) pandemic has brought a heavy burden to the world, interestingly, it shares many clinical symptoms with systemic lupus erythematosus (SLE). It is unclear whether there is a similar pathological process between COVID-9 and SLE. In addition, we don't know how to treat SLE patients with COVID-19. In this study, we analyse the potential similar pathogenesis between SLE and COVID-19 and explore their possible drug regimens using bioinformatics and systems biology approaches. METHODS The common differentially expressed genes (DEGs) were extracted from the COVID-19 datasets and the SLE datasets for functional enrichment, pathway analysis and candidate drug analysis. RESULT Based on the two transcriptome datasets between COVID-19 and SLE, 325 common DEGs were selected. Hub genes were identified by protein-protein interaction (PPI) analysis. few found a variety of similar functional changes between COVID-19 and SLE, which may be related to the pathogenesis of COVID-19. Besides, we explored the related regulatory networks. Then, through drug target matching, we found many candidate drugs for patients with COVID-19 only or COVID-19 combined with SLE. CONCLUSION COVID-19 and SLE patients share many common hub genes, related pathways and regulatory networks. Based on these common targets, we found many potential drugs that could be used in treating patient with COVID-19 or COVID-19 combined with SLE.
Collapse
Affiliation(s)
- Yinlan Wu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
- Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhong Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
- Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Zhou
- Department of Respiratory and Critical Care Medicine, Chengdu First People's Hospital, Chengdu, China
| | - Xiufeng Bai
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
- Rare Diseases Center, West China Hospital, Sichuan University, Chengdu, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
3
|
Zhang J, Zhu H, Li L, Gao Y, Yu B, Ma G, Jin X, Sun Y. New mechanism of LncRNA: In addition to act as a ceRNA. Noncoding RNA Res 2024; 9:1050-1060. [PMID: 39022688 PMCID: PMC11254507 DOI: 10.1016/j.ncrna.2024.06.002] [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: 04/07/2024] [Revised: 05/20/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Long non-coding RNAs (LncRNAs) are a class of RNA molecules with nucleic acid lengths ranging from 200 bp to 100 kb that cannot code for proteins, which are diverse and widely expressed in both animals and plants. Scholars have found that lncRNAs can regulate human physiological processes at the gene and protein levels, mainly through the regulation of epigenetic, transcriptional and post-transcriptional levels of genes and proteins, as well as in the immune response by regulating the expression of immune cells and inflammatory factors, and thus participate in the occurrence and development of a variety of diseases. From the downstream targets of lncRNAs, we summarize the new research progress of lncRNA mechanisms other than miRNA sponges in recent years, aiming to provide new ideas and directions for the study of lncRNA mechanisms.
Collapse
Affiliation(s)
- Jiahao Zhang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Huike Zhu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Linjing Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Gao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Life Sciences, Northwest Normal University, Gansu Province, Lanzhou, 730070, China
| | - Boyi Yu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guorong Ma
- The First Clinical Medical College of Gansu University of Chinese Medicine Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Xiaodong Jin
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| |
Collapse
|
4
|
Raditsa V, Tsukanov A, Bogomolov A, Levitsky V. Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data. NAR Genom Bioinform 2024; 6:lqae090. [PMID: 39071850 PMCID: PMC11282361 DOI: 10.1093/nargab/lqae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/03/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Efficient de novo motif discovery from the results of wide-genome mapping of transcription factor binding sites (ChIP-seq) is dependent on the choice of background nucleotide sequences. The foreground sequences (ChIP-seq peaks) represent not only specific motifs of target transcription factors, but also the motifs overrepresented throughout the genome, such as simple sequence repeats. We performed a massive comparison of the 'synthetic' and 'genomic' approaches to generate background sequences for de novo motif discovery. The 'synthetic' approach shuffled nucleotides in peaks, while in the 'genomic' approach selected sequences from the reference genome randomly or only from gene promoters according to the fraction of A/T nucleotides in each sequence. We compiled the benchmark collections of ChIP-seq datasets for mouse, human and Arabidopsis, and performed de novo motif discovery. We showed that the genomic approach has both more robust detection of the known motifs of target transcription factors and more stringent exclusion of the simple sequence repeats as possible non-specific motifs. The advantage of the genomic approach over the synthetic approach was greater in plants compared to mammals. We developed the AntiNoise web service (https://denovosea.icgbio.ru/antinoise/) that implements a genomic approach to extract genomic background sequences for twelve eukaryotic genomes.
Collapse
Affiliation(s)
- Vladimir V Raditsa
- Department of System Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Anton V Tsukanov
- Department of System Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Anton G Bogomolov
- Department of Cell Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Victor G Levitsky
- Department of System Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia
| |
Collapse
|
5
|
Inge MM, Miller R, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. Nucleic Acids Res 2024:gkae706. [PMID: 39166482 DOI: 10.1093/nar/gkae706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/14/2024] [Accepted: 08/19/2024] [Indexed: 08/23/2024] Open
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here, we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced histone 3 lysine 27 acetylation (H3K27ac). Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data support clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
Collapse
Affiliation(s)
- Melissa M Inge
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Rebekah Miller
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Heather Hook
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - David Bray
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Jessica L Keenan
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Rose Zhao
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| |
Collapse
|
6
|
Huang Y, Liu Y, Pu M, Zhang Y, Cao Q, Li S, Wei Y, Hou L. SOX2 interacts with hnRNPK to modulate alternative splicing in mouse embryonic stem cells. Cell Biosci 2024; 14:102. [PMID: 39160617 PMCID: PMC11331657 DOI: 10.1186/s13578-024-01284-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
BACKGROUND SOX2 is a determinant transcription factor that governs the balance between stemness and differentiation by influencing transcription and splicing programs. The role of SOX2 is intricately shaped by its interactions with specific partners. In the interactome of SOX2 in mouse embryonic stem cells (mESCs), there is a cohort of heterogeneous nuclear ribonucleoproteins (hnRNPs) that contributes to multiple facets of gene expression regulation. However, the cross-talk between hnRNPs and SOX2 in gene expression regulation remains unclear. RESULTS Here we demonstrate the indispensable role of the co-existence of SOX2 and heterogeneous nuclear ribonucleoprotein K (hnRNPK) in the maintenance of pluripotency in mESCs. While hnRNPK directly interacts with the SOX2-HMG DNA-binding domain and induces the collapse of the transcriptional repressor 7SK small nuclear ribonucleoprotein (7SK snRNP), hnRNPK does not influence SOX2-mediated transcription, either by modulating the interaction between SOX2 and its target cis-regulatory elements or by facilitating transcription elongation as indicated by the RNA-seq analysis. Notably, hnRNPK enhances the interaction of SOX2 with target pre-mRNAs and collaborates with SOX2 in regulating the alternative splicing of a subset of pluripotency genes. CONCLUSIONS These data reveal that SOX2 and hnRNPK have a direct protein-protein interaction, and shed light on the molecular mechanisms by which hnRNPK collaborates with SOX2 in alternative splicing in mESCs.
Collapse
Affiliation(s)
- Yanlan Huang
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
| | - Yuxuan Liu
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
| | - Mingyi Pu
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
| | - Yuli Zhang
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
| | - Qiang Cao
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
| | - Senru Li
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China
| | - Yuanjie Wei
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany.
| | - Linlin Hou
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, People's Republic of China.
| |
Collapse
|
7
|
Wang X, Guan X, Zhu X, Zhang L, Ma C, He S, Bai J, Mei J, Li Q, Sun N, Wu B, Zhu D. CircNAP1L4 regulates pulmonary artery smooth muscle cell proliferation via the NAP1L4-mediated super-enhancer-driven glycolysis gene hexokinase II (HK II) in pulmonary hypertension. FASEB J 2024; 38:e23868. [PMID: 39102213 DOI: 10.1096/fj.202400585rrr] [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: 03/15/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Glycolysis is a major determinant of pulmonary artery smooth muscle cell (PASMC) proliferation in pulmonary hypertension (PH). Circular RNAs (circRNAs) are powerful regulators of glycolysis in multiple diseases; however, the role of circRNAs in glycolysis in PH has been poorly characterized. The aim of this study was to uncover the regulatory mechanism of a new circRNA, circNAP1L4, in human pulmonary artery smooth muscle cell (HPASMC) proliferation through the host protein NAP1L4 to regulate the super-enhancer-driven glycolysis gene hexokinase II (HK II). CircNAP1L4 was downregulated in hypoxic HPASMCs and plasma of PH patients. Functionally, circNAP1L4 overexpression inhibited glycolysis and proliferation in hypoxic HPASMCs. Mechanistically, circNAP1L4 directly bound to its host protein NAP1L4 and affected the ability of NAP1L4 to move into the nucleus to regulate the epigenomic signals of the super-enhancer of HK II. Intriguingly, circNAP1L4 overexpression inhibited the proliferation but not the migration of human pulmonary arterial endothelial cells (HPAECs) cocultured with HPASMCs. Furthermore, pre-mRNA-processing-splicing Factor 8 (PRP8) was found to regulate the production ratio of circNAP1L4 and linear NAP1L4. In vivo, targeting circNAP1L4 alleviates SU5416 combined with hypoxia (SuHx)-induced PH. Overall, these findings reveal a new circRNA that inhibits PASMC proliferation and serves as a therapeutic target for PH.
Collapse
MESH Headings
- Humans
- Hexokinase/metabolism
- Hexokinase/genetics
- Cell Proliferation
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/genetics
- Glycolysis
- Myocytes, Smooth Muscle/metabolism
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Animals
- Mice
- Male
- Cells, Cultured
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/cytology
Collapse
Affiliation(s)
- Xiaoying Wang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Xiaoyu Guan
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
| | - Xiangrui Zhu
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Cui Ma
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Siyu He
- Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, Shenzhen, P. R. China
| | - June Bai
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
| | - Jian Mei
- College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, P. R. China
| | - Qian Li
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
| | - Na Sun
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Myocardial Ischemia, Ministry Education, Harbin Medical University, Harbin, P. R. China
| | - Bingxiang Wu
- Department of Cardiology, the Second Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Myocardial Ischemia, Ministry Education, Harbin Medical University, Harbin, P. R. China
| | - Daling Zhu
- Central Laboratory of Harbin Medical University (Daqing), Daqing, P. R. China
- College of Pharmacy, Harbin Medical University, Harbin, P. R. China
- Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, Harbin, P. R. China
| |
Collapse
|
8
|
Abe K. Dynamic activity changes in transcription factors: Unlocking the mechanisms regulating physiological changes in the brain. Neurosci Res 2024:S0168-0102(24)00101-9. [PMID: 39134224 DOI: 10.1016/j.neures.2024.08.001] [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: 08/03/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/18/2024]
Abstract
Transcription factors (TFs) regulate the establishment and modulation of the transcriptome within cells, thereby playing a crucial role in various aspects of cellular physiology throughout the body. Quantitative measurement of TF activity during the development, function, and dysfunction of the brain is essential for gaining a deeper understanding of the regulatory mechanisms governing gene expression during these processes. Due to their role as regulators of gene expression, assessing and modulating detailed TF activity contributes to the development of practical methods to intervene in these processes, potentially offering more efficient treatments for diseases. Recent methodologies have revealed that TF activity is dynamically regulated within cells and organisms, including the adult brain. This review summarizes the regulatory mechanisms of TF activities and the methodologies used to assess them, emphasizing their importance in both fundamental research and clinical applications.
Collapse
Affiliation(s)
- Kentaro Abe
- Lab of Brain Development, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| |
Collapse
|
9
|
Li T, Liu X, Qian H, Zhang S, Hou Y, Zhang Y, Luo G, Zhu X, Tao Y, Fan M, Wang H, Sha C, Lin A, Qin J, Gu K, Chen W, Fu T, Wang Y, Wei Y, Wu Q, Tan W. Blocker-SELEX: a structure-guided strategy for developing inhibitory aptamers disrupting undruggable transcription factor interactions. Nat Commun 2024; 15:6751. [PMID: 39117705 PMCID: PMC11310338 DOI: 10.1038/s41467-024-51197-w] [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: 01/11/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Despite the well-established significance of transcription factors (TFs) in pathogenesis, their utilization as pharmacological targets has been limited by the inherent challenges in modulating their protein interactions. The lack of defined small-molecule binding pockets and the nuclear localization of TFs do not favor the use of traditional tools. Aptamers possess large molecular weights, expansive blocking surfaces and efficient cellular internalization, making them compelling tools for modulating TF interactions. Here, we report a structure-guided design strategy called Blocker-SELEX to develop inhibitory aptamers (iAptamers) that selectively block TF interactions. Our approach leads to the discovery of iAptamers that cooperatively disrupt SCAF4/SCAF8-RNAP2 interactions, dysregulating RNAP2-dependent gene expression, which impairs cell proliferation. This approach is further applied to develop iAptamers blocking WDR5-MYC interactions. Overall, our study highlights the potential of iAptamers in disrupting pathogenic TF interactions, implicating their potential utility in studying the biological functions of TF interactions and in nucleic acids drug discovery.
Collapse
Affiliation(s)
- Tongqing Li
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Xueying Liu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Haifeng Qian
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Sheyu Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yu Hou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Yuchao Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Guoyan Luo
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Xun Zhu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Yanxin Tao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- Shanghai Institute of Material Medica, Chinese Academy of Sciences, Shanghai, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Mengyang Fan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Hong Wang
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Chulin Sha
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Ailan Lin
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Jingjing Qin
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
- School of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Kedan Gu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Weichang Chen
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Ting Fu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Yajun Wang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China
| | - Yong Wei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
| | - Qin Wu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Weihong Tan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| |
Collapse
|
10
|
Xu C, Kleinschmidt H, Yang J, Leith EM, Johnson J, Tan S, Mahony S, Bai L. Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1. Mol Cell 2024; 84:2838-2855.e10. [PMID: 39019045 PMCID: PMC11334613 DOI: 10.1016/j.molcel.2024.06.022] [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: 01/09/2024] [Revised: 04/23/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024]
Abstract
Despite the unique ability of pioneer factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called chromatin immunoprecipitation with integrated synthetic oligonucleotides (ChIP-ISO) to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1, in human A549 cells. Combining ChIP-ISO with in vitro and neural network analyses, we find that (1) FOXA1 binding is strongly affected by co-binding transcription factors (TFs) AP-1 and CEBPB; (2) FOXA1 and AP-1 show binding cooperativity in vitro; (3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin; and (4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
Collapse
Affiliation(s)
- Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianyu Yang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik M Leith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jenna Johnson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
11
|
LaRue-Nolan KC, Arul GLR, Sigafoos AN, Shi J, Fernandez-Zapico ME. Insights into the mechanisms driven by H3K4 KMTs in pancreatic cancer. Biochem J 2024; 481:983-997. [PMID: 39078225 PMCID: PMC11332384 DOI: 10.1042/bcj20230374] [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: 02/12/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/31/2024]
Abstract
Pancreatic cancer is a malignancy arising from the endocrine or exocrine compartment of this organ. Tumors from exocrine origin comprise over 90% of all pancreatic cancers diagnosed. Of these, pancreatic ductal adenocarcinoma (PDAC) is the most common histological subtype. The five-year survival rate for PDAC ranged between 5 and 9% for over four decades, and only recently saw a modest increase to ∼12-13%, making this a severe and lethal disease. Like other cancers, PDAC initiation stems from genetic changes. However, therapeutic targeting of PDAC genetic drivers has remained relatively unsuccessful, thus the focus in recent years has expanded to the non-genetic factors underlying the disease pathogenesis. Specifically, it has been proposed that dynamic changes in the epigenetic landscape promote tumor growth and metastasis. Emphasis has been given to the re-organization of enhancers, essential regulatory elements controlling oncogenic gene expression, commonly marked my histone 3 lysine 4 monomethylation (H3K4me1). H3K4me1 is typically deposited by histone lysine methyltransferases (KMTs). While well characterized as oncogenes in other cancer types, recent work has expanded the role of KMTs as tumor suppressor in pancreatic cancer. Here, we review the role and translational significance for PDAC development and therapeutics of KMTs.
Collapse
Affiliation(s)
- Kayla C. LaRue-Nolan
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Ashley N. Sigafoos
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Jiaqi Shi
- Department of Pathology and Clinical Labs, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, U.S.A
| | | |
Collapse
|
12
|
Mitra R, Li J, Sagendorf JM, Jiang Y, Cohen AS, Chiu TP, Glasscock CJ, Rohs R. Geometric deep learning of protein-DNA binding specificity. Nat Methods 2024:10.1038/s41592-024-02372-w. [PMID: 39103447 DOI: 10.1038/s41592-024-02372-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 06/14/2024] [Indexed: 08/07/2024]
Abstract
Predicting protein-DNA binding specificity is a challenging yet essential task for understanding gene regulation. Protein-DNA complexes usually exhibit binding to a selected DNA target site, whereas a protein binds, with varying degrees of binding specificity, to a wide range of DNA sequences. This information is not directly accessible in a single structure. Here, to access this information, we present Deep Predictor of Binding Specificity (DeepPBS), a geometric deep-learning model designed to predict binding specificity from protein-DNA structure. DeepPBS can be applied to experimental or predicted structures. Interpretable protein heavy atom importance scores for interface residues can be extracted. When aggregated at the protein residue level, these scores are validated through mutagenesis experiments. Applied to designed proteins targeting specific DNA sequences, DeepPBS was demonstrated to predict experimentally measured binding specificity. DeepPBS offers a foundation for machine-aided studies that advance our understanding of molecular interactions and guide experimental designs and synthetic biology.
Collapse
Affiliation(s)
- Raktim Mitra
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Jinsen Li
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Jared M Sagendorf
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Yibei Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Ari S Cohen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Cameron J Glasscock
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
13
|
Jia C, Grima R. Holimap: an accurate and efficient method for solving stochastic gene network dynamics. Nat Commun 2024; 15:6557. [PMID: 39095346 PMCID: PMC11297302 DOI: 10.1038/s41467-024-50716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Gene-gene interactions are crucial to the control of sub-cellular processes but our understanding of their stochastic dynamics is hindered by the lack of simulation methods that can accurately and efficiently predict how the distributions of gene product numbers vary across parameter space. To overcome these difficulties, here we present Holimap (high-order linear-mapping approximation), an approach that approximates the protein or mRNA number distributions of a complex gene regulatory network by the distributions of a much simpler reaction system. We demonstrate Holimap's computational advantages over conventional methods by applying it to predict the stochastic time-dependent dynamics of various gene networks, including transcriptional networks ranging from simple autoregulatory loops to complex randomly connected networks, post-transcriptional networks, and post-translational networks. Holimap is ideally suited to study how the intricate network of gene-gene interactions results in precise coordination and control of gene expression.
Collapse
Affiliation(s)
- Chen Jia
- Applied and Computational Mathematics Division, Beijing Computational Science Research Center, Beijing, China
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
14
|
Xu Z, Zhang G, Chen J, Ying Y, Yao L, Li X, Teixeira da Silva JA, Yu Z. Role of Rubus chingii BBX gene family in anthocyanin accumulation during fruit ripening. FRONTIERS IN PLANT SCIENCE 2024; 15:1427359. [PMID: 39157519 PMCID: PMC11327127 DOI: 10.3389/fpls.2024.1427359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/17/2024] [Indexed: 08/20/2024]
Abstract
The B-box (BBX) family, which is a class of zinc finger transcription factors, exhibits special roles in plant growth and development as well as in plants' ability to cope with various stresses. Even though Rubus chingii is an important traditional medicinally edible plant in east Asia, there are no comprehensive studies of BBX members in R. chingii. In this study, 32 RcBBX members were identified, and these were divided into five groups. A collinearity analysis showed that gene duplication events were common, and when combined with a motif analysis of the RcBBX genes, it was concluded that group V genes might have undergone deletion of gene fragments or mutations. Analysis of cis-acting elements revealed that each RcBBX gene contained hormone-, light-, and stress-related elements. Expression patterns of the 32 RcBBX genes during fruit ripening revealed that highest expression occurred at the small green fruit stage. Of note, the expression of several RcBBX genes increased rapidly as fruit developed. These findings, combined with the expression profiles of anthocyanin biosynthetic genes during fruit ripening, allowed us to identify the nuclear-targeted RcBBX26, which positively promoted anthocyanin production in R. chingii. The collective findings of this study shed light on the function of RcBBX genes in different tissues, developmental stages, and in response to two abiotic stresses.
Collapse
Affiliation(s)
- Zhangting Xu
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | | | - Junyu Chen
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuxin Ying
- College of Food and Health, Zhejiang A & F University, Hangzhou, China
| | - Lingtiao Yao
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaoxian Li
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | | | - Zhenming Yu
- School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Songyang Institute of Zhejiang Chinese Medical University, Lishui, China
| |
Collapse
|
15
|
Aziz M, Jandeleit-Dahm KA, Khan AW. Interplay between epigenetic mechanisms and transcription factors in atherosclerosis. Atherosclerosis 2024; 395:117615. [PMID: 38917706 DOI: 10.1016/j.atherosclerosis.2024.117615] [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: 12/03/2023] [Revised: 05/26/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024]
Abstract
Cardiovascular diseases (CVD), including coronary heart disease and stroke, comprise the number one cause of mortality worldwide. A major contributor to CVD is atherosclerosis, which is a low-grade inflammatory disease of vasculature that involves a pathological build-up of plaque within the arterial walls. Studies have shown that regulation of gene expression via transcription factors and epigenetic mechanisms play a fundamental role in transcriptomic changes linked to the development of atherosclerosis. Chromatin remodeling is a reversible phenomenon and studies have supported the clinical application of chromatin-modifying agents for the prevention and treatment of CVD. In addition, pre-clinical studies have identified multiple transcription factors as potential therapeutic targets in combating atherosclerotic CVD. Although interaction between transcription factors and epigenetic mechanisms facilitate gene regulation, a limited number of studies appreciate this crosstalk in the context of CVD. Here, we reviewed this gene regulatory mechanism underappreciated in atherosclerosis, which will highlight the mechanisms underlying novel therapeutics targeting epigenetic modifiers and transcription factors in atherosclerosis.
Collapse
Affiliation(s)
- Misbah Aziz
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Karin Am Jandeleit-Dahm
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia; German Diabetes Centre, Leibniz Centre for Diabetes Research at the Heinrich Heine University, Dusseldorf, Germany
| | - Abdul Waheed Khan
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia.
| |
Collapse
|
16
|
Ding N, Yuan Z, Ma Z, Wu Y, Yin L. AI-Assisted Rational Design and Activity Prediction of Biological Elements for Optimizing Transcription-Factor-Based Biosensors. Molecules 2024; 29:3512. [PMID: 39124917 PMCID: PMC11313831 DOI: 10.3390/molecules29153512] [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: 06/27/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The rational design, activity prediction, and adaptive application of biological elements (bio-elements) are crucial research fields in synthetic biology. Currently, a major challenge in the field is efficiently designing desired bio-elements and accurately predicting their activity using vast datasets. The advancement of artificial intelligence (AI) technology has enabled machine learning and deep learning algorithms to excel in uncovering patterns in bio-element data and predicting their performance. This review explores the application of AI algorithms in the rational design of bio-elements, activity prediction, and the regulation of transcription-factor-based biosensor response performance using AI-designed elements. We discuss the advantages, adaptability, and biological challenges addressed by the AI algorithms in various applications, highlighting their powerful potential in analyzing biological data. Furthermore, we propose innovative solutions to the challenges faced by AI algorithms in the field and suggest future research directions. By consolidating current research and demonstrating the practical applications and future potential of AI in synthetic biology, this review provides valuable insights for advancing both academic research and practical applications in biotechnology.
Collapse
Affiliation(s)
- Nana Ding
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Zenan Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China;
| | - Yefei Wu
- Zhejiang Qianjiang Biochemical Co., Ltd., Haining 314400, China;
| | - Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| |
Collapse
|
17
|
Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [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: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
Collapse
Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
18
|
Hemphill WO, Steiner HR, Kominsky JR, Wuttke DS, Cech TR. Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms. RNA (NEW YORK, N.Y.) 2024; 30:1089-1105. [PMID: 38760076 PMCID: PMC11251522 DOI: 10.1261/rna.080027.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024]
Abstract
Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here, we use biophysical assays to interrogate the k on, k off, and K d for DNA and RNA binding of two model human TFs, ERα and Sox2. Unexpectedly, we found that both proteins exhibit multiphasic nucleic acid-binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics can be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, in which two apparent binding transitions are separated by a 10-20 min "lag" phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid-binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product "feedback" on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.
Collapse
Affiliation(s)
- Wayne O Hemphill
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Halley R Steiner
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Jackson R Kominsky
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| |
Collapse
|
19
|
Wang H, Ma B, Stevens T, Knapp J, Lu J, Prochownik EV. MYC Binding Near Transcriptional End Sites Regulates Basal Gene Expression, Read-Through Transcription and Intragenic Contacts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603118. [PMID: 39071289 PMCID: PMC11275772 DOI: 10.1101/2024.07.11.603118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The MYC oncoprotein regulates numerous genes involved in cellular processes such as cell cycle and mitochondrial and ribosomal structure and function. This requires heterodimerization with its partner, MAX, and binding to specific promoter and enhancer elements. Here, we show that MYC and MAX also bind near transcriptional end sites (TESs) of over one-sixth of all annotated genes. These interactions are dose-dependent, evolutionarily conserved, stabilize the normally short-lived MYC protein and regulate expression both in concert with and independent of MYC's binding elsewhere. MYC's TES binding occurs in association with other transcription factors, alters the chromatin landscape, increases nuclease susceptibility and can alter transcriptional read-through, particularly in response to certain stresses. MYC-bound TESs can directly contact promoters and may fine-tune gene expression in response to both physiologic and pathologic stimuli. Collectively, these findings support a previously unrecognized role for MYC in regulating transcription and its read-through via direct intragenic contacts between TESs and promoters.
Collapse
|
20
|
Su J, Wang J, Tang J, Yu W, Liu J, Dong X, Dong J, Chai X, Ji P, Zhang L. Zinc finger transcription factor ZFP1 is associated with growth, conidiation, osmoregulation, and virulence in the Polygonatum kingianum pathogen Fusarium oxysporum. Sci Rep 2024; 14:16061. [PMID: 38992190 PMCID: PMC11239662 DOI: 10.1038/s41598-024-67040-7] [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: 01/26/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024] Open
Abstract
Rhizome rot is a destructive soil-borne disease of Polygonatum kingianum and adversely affects the yield and sustenance of the plant. Understanding how the causal fungus Fusarium oxysporum infects P. kingianum may suggest effective control measures against rhizome rot. In germinating conidia of infectious F. oxysporum, expression of the zinc finger transcription factor gene Zfp1, consisting of two C2H2 motifs, was up-regulated. To characterize the critical role of ZFP1, we generated independent deletion mutants (zfp1) and complemented one mutant with a transgenic copy of ZFP1 (zfp1 tZFP1). Mycelial growth and conidial production of zfp1 were slower than those of wild type (ZFP1) and zfp1 tZFP1. Additionally, a reduced inhibition of growth suggested zfp1 was less sensitive to conditions promoting cell wall and osmotic stresses than ZFP1 and zfp1 tZFP1. Furthermore pathogenicity tests suggested a critical role for growth of zfp1 in infected leaves and rhizomes of P. kingianum. Thus ZFP1 is important for mycelial growth, conidiation, osmoregulation, and pathogenicity in P. kingianum.
Collapse
Affiliation(s)
- Jianyun Su
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jingyi Wang
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jingying Tang
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Weimei Yu
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jiajia Liu
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xian Dong
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jiahong Dong
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xia Chai
- Yunnan Normal University, Kunming, 650500, China.
| | - Pengzhang Ji
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Lei Zhang
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| |
Collapse
|
21
|
Gopalan SS, Perry BW, Francioli YZ, Schield DR, Guss HD, Bernstein JM, Ballard K, Smith CF, Saviola AJ, Adams RH, Mackessy SP, Castoe TA. Diverse Gene Regulatory Mechanisms Alter Rattlesnake Venom Gene Expression at Fine Evolutionary Scales. Genome Biol Evol 2024; 16:evae110. [PMID: 38753011 PMCID: PMC11243404 DOI: 10.1093/gbe/evae110] [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] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole-genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.
Collapse
Affiliation(s)
- Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yannick Z Francioli
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Hannah D Guss
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Justin M Bernstein
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kaas Ballard
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Richard H Adams
- Department of Entomology and Plant Pathology, University of Arkansas Agricultural Experimental Station, University of Arkansas, Fayetteville, AR 72701, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| |
Collapse
|
22
|
Ambrosio L, Schol J, Ruiz-Fernández C, Tamagawa S, Joyce K, Nomura A, de Rinaldis E, Sakai D, Papalia R, Vadalà G, Denaro V. Getting to the Core: Exploring the Embryonic Development from Notochord to Nucleus Pulposus. J Dev Biol 2024; 12:18. [PMID: 39051200 PMCID: PMC11270426 DOI: 10.3390/jdb12030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/12/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
The intervertebral disc (IVD) is the largest avascular organ of the human body and plays a fundamental role in providing the spine with its unique structural and biomechanical functions. The inner part of the IVD contains the nucleus pulposus (NP), a gel-like tissue characterized by a high content of type II collagen and proteoglycans, which is crucial for the disc's load-bearing and shock-absorbing properties. With aging and IVD degeneration (IDD), the NP gradually loses its physiological characteristics, leading to low back pain and additional sequelae. In contrast to surrounding spinal tissues, the NP presents a distinctive embryonic development since it directly derives from the notochord. This review aims to explore the embryology of the NP, emphasizing the pivotal roles of key transcription factors, which guide the differentiation and maintenance of the NP cellular components from the notochord and surrounding sclerotome. Through an understanding of NP development, we sought to investigate the implications of the critical developmental aspects in IVD-related pathologies, such as IDD and the rare malignant chordomas. Moreover, this review discusses the therapeutic strategies targeting these pathways, including the novel regenerative approaches leveraging insights from NP development and embryology to potentially guide future treatments.
Collapse
Affiliation(s)
- Luca Ambrosio
- Operative Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (L.A.); (R.P.); (V.D.)
- Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 01128 Rome, Italy;
- Department of Orthopaedic Surgery, Tokai University School of Medicine, Isehara 259-1143, Japan; (J.S.); (C.R.-F.); (A.N.); (D.S.)
| | - Jordy Schol
- Department of Orthopaedic Surgery, Tokai University School of Medicine, Isehara 259-1143, Japan; (J.S.); (C.R.-F.); (A.N.); (D.S.)
| | - Clara Ruiz-Fernández
- Department of Orthopaedic Surgery, Tokai University School of Medicine, Isehara 259-1143, Japan; (J.S.); (C.R.-F.); (A.N.); (D.S.)
| | - Shota Tamagawa
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan;
| | - Kieran Joyce
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, H91 W2TY Galway, Ireland;
- School of Medicine, University of Galway, H91 W2TY Galway, Ireland
| | - Akira Nomura
- Department of Orthopaedic Surgery, Tokai University School of Medicine, Isehara 259-1143, Japan; (J.S.); (C.R.-F.); (A.N.); (D.S.)
| | - Elisabetta de Rinaldis
- Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 01128 Rome, Italy;
| | - Daisuke Sakai
- Department of Orthopaedic Surgery, Tokai University School of Medicine, Isehara 259-1143, Japan; (J.S.); (C.R.-F.); (A.N.); (D.S.)
| | - Rocco Papalia
- Operative Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (L.A.); (R.P.); (V.D.)
- Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 01128 Rome, Italy;
| | - Gianluca Vadalà
- Operative Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (L.A.); (R.P.); (V.D.)
- Research Unit of Orthopaedic and Trauma Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 01128 Rome, Italy;
| | - Vincenzo Denaro
- Operative Research Unit of Orthopaedic and Trauma Surgery, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy; (L.A.); (R.P.); (V.D.)
| |
Collapse
|
23
|
Jores T, Tonnies J, Mueth NA, Romanowski A, Fields S, Cuperus JT, Queitsch C. Plant enhancers exhibit both cooperative and additive interactions among their functional elements. THE PLANT CELL 2024; 36:2570-2586. [PMID: 38513612 PMCID: PMC11218779 DOI: 10.1093/plcell/koae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Enhancers are cis-regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed to explain how enhancers integrate the activity of multiple transcription factors. However, it remains largely unclear how plant enhancers integrate transcription factor activity. Here, we use Plant STARR-seq to characterize 3 light-responsive plant enhancers-AB80, Cab-1, and rbcS-E9-derived from genes associated with photosynthesis. Saturation mutagenesis revealed mutations, many of which clustered in short regions, that strongly reduced enhancer activity in the light, in the dark, or in both conditions. When tested in the light, these mutation-sensitive regions did not function on their own; rather, cooperative interactions with other such regions were required for full activity. Epistatic interactions occurred between mutations in adjacent mutation-sensitive regions, and the spacing and order of mutation-sensitive regions in synthetic enhancers affected enhancer activity. In contrast, when tested in the dark, mutation-sensitive regions acted independently and additively in conferring enhancer activity. Taken together, this work demonstrates that plant enhancers show evidence for both cooperative and additive interactions among their functional elements. This knowledge can be harnessed to design strong, condition-specific synthetic enhancers.
Collapse
Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Synthetic Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biology, University of Washington, Seattle, WA 98195, USA
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrés Romanowski
- Molecular Biology Group, Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
24
|
Nocente MC, Mesihovic Karamitsos A, Drouineau E, Soleil M, Albawardi W, Dulary C, Ribierre F, Picaud H, Alibert O, Acker J, Kervella M, Aude JC, Gilbert N, Ochsenbein F, Chantalat S, Gérard M. cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers. Nat Struct Mol Biol 2024:10.1038/s41594-024-01344-0. [PMID: 38956169 DOI: 10.1038/s41594-024-01344-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
The canonical BRG/BRM-associated factor (cBAF) complex is essential for chromatin opening at enhancers in mammalian cells. However, the nature of the open chromatin remains unclear. Here, we show that, in addition to producing histone-free DNA, cBAF generates stable hemisome-like subnucleosomal particles containing the four core histones associated with 50-80 bp of DNA. Our genome-wide analysis indicates that cBAF makes these particles by targeting and splitting fragile nucleosomes. In mouse embryonic stem cells, these subnucleosomes become an in vivo binding substrate for the master transcription factor OCT4 independently of the presence of OCT4 DNA motifs. At enhancers, the OCT4-subnucleosome interaction increases OCT4 occupancy and amplifies the genomic interval bound by OCT4 by up to one order of magnitude compared to the region occupied on histone-free DNA. We propose that cBAF-dependent subnucleosomes orchestrate a molecular mechanism that projects OCT4 function in chromatin opening beyond its DNA motifs.
Collapse
Affiliation(s)
- Marina C Nocente
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anida Mesihovic Karamitsos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Emilie Drouineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Manon Soleil
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Waad Albawardi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Cécile Dulary
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Florence Ribierre
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Hélène Picaud
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Olivier Alibert
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Joël Acker
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marie Kervella
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean-Christophe Aude
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Françoise Ochsenbein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sophie Chantalat
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Matthieu Gérard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| |
Collapse
|
25
|
Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 DOI: 10.1038/s41580-024-00710-6] [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] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
Collapse
Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
| |
Collapse
|
26
|
Loupe JM, Anderson AG, Rizzardi LF, Rodriguez-Nunez I, Moyers B, Trausch-Lowther K, Jain R, Bunney WE, Bunney BG, Cartagena P, Sequeira A, Watson SJ, Akil H, Cooper GM, Myers RM. Multiomic profiling of transcription factor binding and function in human brain. Nat Neurosci 2024; 27:1387-1399. [PMID: 38831039 DOI: 10.1038/s41593-024-01658-8] [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: 06/20/2023] [Accepted: 04/19/2024] [Indexed: 06/05/2024]
Abstract
Transcription factors (TFs) orchestrate gene expression programs crucial for brain function, but we lack detailed information about TF binding in human brain tissue. We generated a multiomic resource (ChIP-seq, ATAC-seq, RNA-seq, DNA methylation) on bulk tissues and sorted nuclei from several postmortem brain regions, including binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of high TF occupancy regions. Further, predictive TF binding models demonstrate a bias for these high-occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Binding sites for TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. This work, titled BrainTF, is a powerful resource for future studies seeking to understand the roles of specific TFs in regulating gene expression in the human brain.
Collapse
Affiliation(s)
- Jacob M Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Lindsay F Rizzardi
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Biochemistry and Molecular Biology, The University of Alabama in Birmingham, Birmingham, AL, USA
| | | | - Belle Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Rashmi Jain
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - William E Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Blynn G Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Preston Cartagena
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | - Stanley J Watson
- The Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Huda Akil
- The Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| |
Collapse
|
27
|
McDonnell AF, Plech M, Livesey BJ, Gerasimavicius L, Owen LJ, Hall HN, FitzPatrick DR, Marsh JA, Kudla G. Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants. Mol Syst Biol 2024; 20:825-844. [PMID: 38849565 PMCID: PMC11219921 DOI: 10.1038/s44320-024-00043-8] [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] [Received: 09/04/2023] [Revised: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Nonsense and missense mutations in the transcription factor PAX6 cause a wide range of eye development defects, including aniridia, microphthalmia and coloboma. To understand how changes of PAX6:DNA binding cause these phenotypes, we combined saturation mutagenesis of the paired domain of PAX6 with a yeast one-hybrid (Y1H) assay in which expression of a PAX6-GAL4 fusion gene drives antibiotic resistance. We quantified binding of more than 2700 single amino-acid variants to two DNA sequence elements. Mutations in DNA-facing residues of the N-terminal subdomain and linker region were most detrimental, as were mutations to prolines and to negatively charged residues. Many variants caused sequence-specific molecular gain-of-function effects, including variants in position 71 that increased binding to the LE9 enhancer but decreased binding to a SELEX-derived binding site. In the absence of antibiotic selection, variants that retained DNA binding slowed yeast growth, likely because such variants perturbed the yeast transcriptome. Benchmarking against known patient variants and applying ACMG/AMP guidelines to variant classification, we obtained supporting-to-moderate evidence that 977 variants are likely pathogenic and 1306 are likely benign. Our analysis shows that most pathogenic mutations in the paired domain of PAX6 can be explained simply by the effects of these mutations on PAX6:DNA association, and establishes Y1H as a generalisable assay for the interpretation of variant effects in transcription factors.
Collapse
Affiliation(s)
- Alexander F McDonnell
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Marcin Plech
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Benjamin J Livesey
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Lukas Gerasimavicius
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Liusaidh J Owen
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hildegard Nikki Hall
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| |
Collapse
|
28
|
Gao ZX, He T, Zhang P, Hu X, Ge M, Xu YQ, Wang P, Pan HF. Epigenetic regulation of immune cells in systemic lupus erythematosus: insight from chromatin accessibility. Expert Opin Ther Targets 2024; 28:637-649. [PMID: 38943564 DOI: 10.1080/14728222.2024.2375372] [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: 03/19/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Systemic Lupus Erythematosus (SLE) is a multi-dimensional autoimmune disease involving numerous tissues throughout the body. The chromatin accessibility landscapes in immune cells play a pivotal role in governing their activation, function, and differentiation. Aberrant modulation of chromatin accessibility in immune cells is intimately associated with the onset and progression of SLE. AREAS COVERED In this review, we described the chromatin accessibility landscapes in immune cells, summarized the recent evidence of chromatin accessibility related to the pathogenesis of SLE, and discussed the potential of chromatin accessibility as a valuable option to identify novel therapeutic targets for this disease. EXPERT OPINION Dynamic changes in chromatin accessibility are intimately related to the pathogenesis of SLE and have emerged as a new direction for exploring its epigenetic mechanisms. The differently accessible chromatin regions in immune cells often contain binding sites for transcription factors (TFs) and cis-regulatory elements such as enhancers and promoters, which may be potential therapeutic targets for SLE. Larger scale cohort studies and integrating epigenomic, transcriptomic, and metabolomic data can provide deeper insights into SLE chromatin biology in the future.
Collapse
Affiliation(s)
- Zhao-Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Tian He
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiao Hu
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Man Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Qing Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Wang
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| |
Collapse
|
29
|
Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [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] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
Collapse
Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| |
Collapse
|
30
|
Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [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: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
Collapse
Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
31
|
Wang J, Pu Z, Zhang W, Qu M, Gao L, Pan W, Sun Y, Fu C, Zhang L, Huang M, Hu Y. Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq. PLANTS (BASEL, SWITZERLAND) 2024; 13:1708. [PMID: 38931140 PMCID: PMC11207949 DOI: 10.3390/plants13121708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Interaction between transcription factors (TFs) and motifs is essential for gene regulation and the subsequent phenotype formation. Soybean (Glycine max) JAGGEED 1 (GmJAG1) is a key TF that controls leaf shape, seed number and flower size. To understand the GmJAG1 binding motifs, in this study, we performed the GmJAG1 DNA affinity purification sequencing (DAP-seq) experiment, which is a powerful tool for the de novo motif prediction method. Two new significant GmJAG1 binding motifs were predicted and the EMSA experiments further verified the ability of GmJAG1 bound to these motifs. The potential binding sites in the downstream gene promoter were identified through motif scanning and a potential regulatory network mediated by GmJAG1 was constructed. These results served as important genomic resources for further understanding the regulatory mechanism of GmJAG1.
Collapse
Affiliation(s)
- Jinxing Wang
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Zigang Pu
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
- Heilongjiang Longke Seed Industry Group Co., Ltd., Harbin 150000, China
| | - Weiyao Zhang
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Mengnan Qu
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Lusi Gao
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Wenjing Pan
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Yanan Sun
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Chunxu Fu
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Ling Zhang
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
| | - Mingkun Huang
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
| | - Yufang Hu
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
| |
Collapse
|
32
|
Falo-Sanjuan J, Diaz-Tirado Y, Turner MA, Davis J, Medrano C, Haines J, McKenna J, Eisen MB, Garcia HG. Targeted mutagenesis of specific genomic DNA sequences in animals for the in vivo generation of variant libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598328. [PMID: 38915503 PMCID: PMC11195090 DOI: 10.1101/2024.06.10.598328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Understanding how the number, placement and affinity of transcription factor binding sites dictates gene regulatory programs remains a major unsolved challenge in biology, particularly in the context of multicellular organisms. To uncover these rules, it is first necessary to find the binding sites within a regulatory region with high precision, and then to systematically modulate this binding site arrangement while simultaneously measuring the effect of this modulation on output gene expression. Massively parallel reporter assays (MPRAs), where the gene expression stemming from 10,000s of in vitro-generated regulatory sequences is measured, have made this feat possible in high-throughput in single cells in culture. However, because of lack of technologies to incorporate DNA libraries, MPRAs are limited in whole organisms. To enable MPRAs in multicellular organisms, we generated tools to create a high degree of mutagenesis in specific genomic loci in vivo using base editing. Targeting GFP integrated in genome of Drosophila cell culture and whole animals as a case study, we show that the base editor AIDevoCDA1 stemming from sea lamprey fused to nCas9 is highly mutagenic. Surprisingly, longer gRNAs increase mutation efficiency and expand the mutating window, which can allow the introduction of mutations in previously untargetable sequences. Finally, we demonstrate arrays of >20 gRNAs that can efficiently introduce mutations along a 200bp sequence, making it a promising tool to test enhancer function in vivo in a high throughput manner.
Collapse
Affiliation(s)
- Julia Falo-Sanjuan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Yuliana Diaz-Tirado
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Meghan A. Turner
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Julian Davis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Claudia Medrano
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jenna Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Joey McKenna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Hernan G. Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| |
Collapse
|
33
|
Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
Collapse
Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| |
Collapse
|
34
|
Liu B, He Y, Wu X, Lin Z, Ma J, Qiu Y, Xiang Y, Kong F, Lai F, Pal M, Wang P, Ming J, Zhang B, Wang Q, Wu J, Xia W, Shen W, Na J, Torres-Padilla ME, Li J, Xie W. Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators. Nat Cell Biol 2024; 26:962-974. [PMID: 38839978 DOI: 10.1038/s41556-024-01422-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/11/2024] [Indexed: 06/07/2024]
Abstract
Dynamic epigenomic reprogramming occurs during mammalian oocyte maturation and early development. However, the underlying transcription circuitry remains poorly characterized. By mapping cis-regulatory elements using H3K27ac, we identified putative enhancers in mouse oocytes and early embryos distinct from those in adult tissues, enabling global transitions of regulatory landscapes around fertilization and implantation. Gene deserts harbour prevalent putative enhancers in fully grown oocytes linked to oocyte-specific genes and repeat activation. Embryo-specific enhancers are primed before zygotic genome activation and are restricted by oocyte-inherited H3K27me3. Putative enhancers in oocytes often manifest H3K4me3, bidirectional transcription, Pol II binding and can drive transcription in STARR-seq and a reporter assay. Finally, motif analysis of these elements identified crucial regulators of oogenesis, TCF3 and TCF12, the deficiency of which impairs activation of key oocyte genes and folliculogenesis. These data reveal distinctive regulatory landscapes and their interacting transcription factors that underpin the development of mammalian oocytes and early embryos.
Collapse
Affiliation(s)
- Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuanlin He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Innovation Center of Suzhou Nanjing Medical University, Suzhou, China
| | - Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jing Ma
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuexin Qiu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yunlong Xiang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Mrinmoy Pal
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany
| | - Peizhe Wang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Jia Ming
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Bingjie Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jingyi Wu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Weimin Shen
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | | | - Jing Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China.
- Innovation Center of Suzhou Nanjing Medical University, Suzhou, China.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| |
Collapse
|
35
|
Orsetti A, van Oosten D, Vasarhelyi RG, Dănescu TM, Huertas J, van Ingen H, Cojocaru V. Structural dynamics in chromatin unraveling by pioneer transcription factors. Biophys Rev 2024; 16:365-382. [PMID: 39099839 PMCID: PMC11297019 DOI: 10.1007/s12551-024-01205-6] [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: 03/29/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Pioneer transcription factors are proteins with a dual function. First, they regulate transcription by binding to nucleosome-free DNA regulatory elements. Second, they bind to DNA while wrapped around histone proteins in the chromatin and mediate chromatin opening. The molecular mechanisms that connect the two functions are yet to be discovered. In recent years, pioneer factors received increased attention mainly because of their crucial role in promoting cell fate transitions that could be used for regenerative therapies. For example, the three factors required to induce pluripotency in somatic cells, Oct4, Sox2, and Klf4 were classified as pioneer factors and studied extensively. With this increased attention, several structures of complexes between pioneer factors and chromatin structural units (nucleosomes) have been resolved experimentally. Furthermore, experimental and computational approaches have been designed to study two unresolved, key scientific questions: First, do pioneer factors induce directly local opening of nucleosomes and chromatin fibers upon binding? And second, how do the unstructured tails of the histones impact the structural dynamics involved in such conformational transitions? Here we review the current knowledge about transcription factor-induced nucleosome dynamics and the role of the histone tails in this process. We discuss what is needed to bridge the gap between the static views obtained from the experimental structures and the key structural dynamic events in chromatin opening. Finally, we propose that integrating nuclear magnetic resonance spectroscopy with molecular dynamics simulations is a powerful approach to studying pioneer factor-mediated dynamics of nucleosomes and perhaps small chromatin fibers using native DNA sequences.
Collapse
Affiliation(s)
- Andrea Orsetti
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Daphne van Oosten
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | | | - Theodor-Marian Dănescu
- Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Jan Huertas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Vlad Cojocaru
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| |
Collapse
|
36
|
Li L, Lai F, Liu L, Lu X, Hu X, Liu B, Lin Z, Fan Q, Kong F, Xu Q, Xie W. Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos. Nat Struct Mol Biol 2024; 31:950-963. [PMID: 38243114 DOI: 10.1038/s41594-023-01199-x] [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: 03/23/2023] [Accepted: 12/05/2023] [Indexed: 01/21/2024]
Abstract
During the first lineage segregation, a mammalian totipotent embryo differentiates into the inner cell mass (ICM) and trophectoderm (TE). However, how transcription factors (TFs) regulate this earliest cell-fate decision in vivo remains elusive, with their regulomes primarily inferred from cultured cells. Here, we investigated the TF regulomes during the first lineage specification in early mouse embryos, spanning the pre-initiation, initiation, commitment, and maintenance phases. Unexpectedly, we found that TFAP2C, a trophoblast regulator, bound and activated both early TE and inner cell mass (ICM) genes at the totipotent (two- to eight-cell) stages ('bipotency activation'). Tfap2c deficiency caused downregulation of early ICM genes, including Nanog, Nr5a2, and Tdgf1, and early TE genes, including Tfeb and Itgb5, in eight-cell embryos. Transcription defects in both ICM and TE lineages were also found in blastocysts, accompanied by increased apoptosis and reduced cell numbers in ICMs. Upon trophoblast commitment, TFAP2C left early ICM genes but acquired binding to late TE genes in blastocysts, where it co-bound with CDX2, and later to extra-embryonic ectoderm (ExE) genes, where it cooperatively co-occupied with the former ICM regulator SOX2. Finally, 'bipotency activation' in totipotent embryos also applied to a pluripotency regulator NR5A2, which similarly bound and activated both ICM and TE lineage genes at the eight-cell stage. These data reveal a unique transcription circuity of totipotency underpinned by highly adaptable lineage regulators.
Collapse
Affiliation(s)
- Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Fangnong Lai
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xukun Lu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiaoyu Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- College of Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| |
Collapse
|
37
|
Wu S, Huang J, Li Y. Antiviral effect of miR-206 in rainbow trout (Oncorhynchus mykiss) against infectious hematopoietic necrosis virus infection. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109552. [PMID: 38599364 DOI: 10.1016/j.fsi.2024.109552] [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: 01/30/2024] [Revised: 03/12/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Infectious hematopoietic necrosis (IHN), caused by IHN virus, is a highly contagious and lethal disease that seriously hampers the development of rainbow trout (Oncorhynchus mykiss) aquaculture. However, the immune response mechanism of rainbow trout underlying IHNV infection remains largely unknown. MicroRNAs act as post-transcriptional regulators of gene expression and perform a crucial role in fish immune response. Herein, the regulatory mechanism and function of miR-206 in rainbow trout resistance to IHNV were investigated by overexpression and silencing. The expression analysis showed that miR-206 and its potential target receptor-interacting serine/threonine-protein kinase 2 (RIP2) exhibited significant time-dependent changes in headkidney, spleen and rainbow trout primary liver cells infected with IHNV and their expression displayed a negative correlation. In vitro, the interaction between miR-206 and RIP2 was verified by luciferase reporter assay, and miR-206 silencing in rainbow trout primary liver cells markedly increased RIP2 and interferon (IFN) expression but significantly decreased IHNV copies, and opposite results were obtained after miR-206 overexpression or RIP2 knockdown. In vivo, overexpressed miR-206 with agomiR resulted in a decrease in the expression of RIP2 and IFN in liver, headkidney and spleen. This study revealed the key role of miR-206 in anti-IHNV, which provided potential for anti-viral drug screening in rainbow trout.
Collapse
Affiliation(s)
- Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| |
Collapse
|
38
|
Wu PC, McGowan EC, Lee YQ, Ghosh S, Hansson J, Olsson ML. Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci. Transfusion 2024; 64:1083-1096. [PMID: 38644556 DOI: 10.1111/trf.17840] [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: 12/30/2023] [Revised: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Blood typing is essential for safe transfusions and is performed serologically or genetically. Genotyping predominantly focuses on coding regions, but non-coding variants may affect gene regulation, as demonstrated in the ABO, FY and XG systems. To uncover regulatory loci, we expanded a recently developed bioinformatics pipeline for discovery of non-coding variants by including additional epigenetic datasets. METHODS Multiple datasets including ChIP-seq with erythroid transcription factors (TFs), histone modifications (H3K27ac, H3K4me1), and chromatin accessibility (ATAC-seq) were analyzed. Candidate regulatory regions were investigated for activity (luciferase assays) and TF binding (electrophoretic mobility shift assay, EMSA, and mass spectrometry, MS). RESULTS In total, 814 potential regulatory sites in 47 blood-group-related genes were identified where one or more erythroid TFs bound. Enhancer candidates in CR1, EMP3, ABCB6, and ABCC4 indicated by ATAC-seq, histone markers, and co-occupancy of 4 TFs (GATA1/KLF1/RUNX1/NFE2) were investigated but only CR1 and ABCC4 showed increased transcription. Co-occupancy of GATA1 and KLF1 was observed in the KEL promoter, previously reported to contain GATA1 and Sp1 sites. TF binding energy scores decreased when three naturally occurring variants were introduced into GATA1 and KLF1 motifs. Two of three GATA1 sites and the KLF1 site were confirmed functionally. EMSA and MS demonstrated increased GATA1 and KLF1 binding to the wild-type compared to variant motifs. DISCUSSION This combined bioinformatics and experimental approach revealed multiple candidate regulatory regions and predicted TF co-occupancy sites. The KEL promoter was characterized in detail, indicating that two adjacent GATA1 and KLF1 motifs are most crucial for transcription.
Collapse
Affiliation(s)
- Ping Chun Wu
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Eunike C McGowan
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yan Quan Lee
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sudip Ghosh
- Department of Experimental Medical Science and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jenny Hansson
- Department of Experimental Medical Science and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Sweden
| |
Collapse
|
39
|
Oka H, Kojima T, Kato R, Ihara K, Nakano H. Construction of transcript regulation mechanism prediction models based on binding motif environment of transcription factor AoXlnR in Aspergillus oryzae. J Bioinform Comput Biol 2024; 22:2450017. [PMID: 39051143 DOI: 10.1142/s0219720024500173] [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] [Indexed: 07/27/2024]
Abstract
DNA-binding transcription factors (TFs) play a central role in transcriptional regulation mechanisms, mainly through their specific binding to target sites on the genome and regulation of the expression of downstream genes. Therefore, a comprehensive analysis of the function of these TFs will lead to the understanding of various biological mechanisms. However, the functions of TFs in vivo are diverse and complicated, and the identified binding sites on the genome are not necessarily involved in the regulation of downstream gene expression. In this study, we investigated whether DNA structural information around the binding site of TFs can be used to predict the involvement of the binding site in the regulation of the expression of genes located downstream of the binding site. Specifically, we calculated the structural parameters based on the DNA shape around the DNA binding motif located upstream of the gene whose expression is directly regulated by one TF AoXlnR from Aspergillus oryzae, and showed that the presence or absence of expression regulation can be predicted from the sequence information with high accuracy ([Formula: see text]-1.0) by machine learning incorporating these parameters.
Collapse
Affiliation(s)
- Hiroya Oka
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Takaaki Kojima
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, Shiogamaguchi, Tempaku Nagoya 468-8502, Japan
| | - Ryuji Kato
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hideo Nakano
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| |
Collapse
|
40
|
Böttcher J, Fuchs JE, Mayer M, Kahmann J, Zak KM, Wunberg T, Woehrle S, Kessler D. Ligandability assessment of the C-terminal Rel-homology domain of NFAT1. Arch Pharm (Weinheim) 2024; 357:e2300649. [PMID: 38396281 DOI: 10.1002/ardp.202300649] [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: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024]
Abstract
Transcription factors are generally considered challenging, if not "undruggable", targets but they promise new therapeutic options due to their fundamental involvement in many diseases. In this study, we aim to assess the ligandability of the C-terminal Rel-homology domain of nuclear factor of activated T cells 1 (NFAT1), a TF implicated in T-cell regulation. Using a combination of experimental and computational approaches, we demonstrate that small molecule fragments can indeed bind to this protein domain. The newly identified binder is the first small molecule binder to NFAT1 validated with biophysical methods and an elucidated binding mode by X-ray crystallography. The reported eutomer/distomer pair provides a strong basis for potential exploration of higher potency binders on the path toward degrader or glue modalities.
Collapse
Affiliation(s)
- Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simon Woehrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| |
Collapse
|
41
|
Ali MZ, Guharajan S, Parisutham V, Brewster RC. Regulatory properties of transcription factors with diverse mechanistic function. PLoS Comput Biol 2024; 20:e1012194. [PMID: 38857275 PMCID: PMC11192337 DOI: 10.1371/journal.pcbi.1012194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/21/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
Transcription factors (TFs) regulate the process of transcription through the modulation of different kinetic steps. Although models can often describe the observed transcriptional output of a measured gene, predicting a TFs role on a given promoter requires an understanding of how the TF alters each step of the transcription process. In this work, we use a simple model of transcription to assess the role of promoter identity, and the degree to which TFs alter binding of RNAP (stabilization) and initiation of transcription (acceleration) on three primary characteristics: the range of steady-state regulation, cell-to-cell variability in expression, and the dynamic response time of a regulated gene. We find that steady state regulation and the response time of a gene behave uniquely for TFs that regulate incoherently, i.e that speed up one step but slow the other. We also find that incoherent TFs have dynamic implications, with one type of incoherent mode configuring the promoter to respond more slowly at intermediate TF concentrations. We also demonstrate that the noise of gene expression for these TFs is sensitive to promoter strength, with a distinct non-monotonic profile that is apparent under stronger promoters. Taken together, our work uncovers the coupling between promoters and TF regulatory modes with implications for understanding natural promoters and engineering synthetic gene circuits with desired expression properties.
Collapse
Affiliation(s)
- Md Zulfikar Ali
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Geology, Physics and Environmental Science, University of Southern Indiana, Evansville, Indiana, United States of America
| | - Sunil Guharajan
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Vinuselvi Parisutham
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert C. Brewster
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| |
Collapse
|
42
|
Park SJ, Nakai K. A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response. NAR Genom Bioinform 2024; 6:lqae050. [PMID: 38711859 PMCID: PMC11071120 DOI: 10.1093/nargab/lqae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/08/2024] Open
Abstract
Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The present study aimed to develop a computational method for accurately modeling the spatial proximal and distal regulatory interactions. Our method combined regression-based models to identify key regulators through gene expression prediction and a graph-embedding approach to detect coregulated genes. This approach enabled a detailed investigation of the gene regulatory mechanisms for germinal center B cells, accompanied by dramatic rearrangements of the genome structure. We found that while the promoter-proximal regulatory elements were the principal regulators of gene expression, the distal regulators fine-tuned transcription. Moreover, our approach unveiled the presence of modular regulators, such as cofactors and proximal/distal transcription factors, which were co-expressed with their target genes. Some of these modules exhibited abnormal expression patterns in lymphoma. These findings suggest that the dysregulation of interactions between transcriptional and architectural factors is associated with chromatin reorganization failure, which may increase the risk of malignancy. Therefore, our computational approach helps decipher the transcriptional cis-regulatory code spatially interacting.
Collapse
Affiliation(s)
- Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| |
Collapse
|
43
|
Hu B, Zhang X, Fan H, Jin X, Qi Y, Liu R, Li X, Duan M, Zhang C, Li S, Yao W, Hao C. FOXF1 reverses lung fibroblasts transdifferentiation via inhibiting TGF-β/SMAD2/3 pathway in silica-induced pulmonary fibrosis. Int Immunopharmacol 2024; 133:112067. [PMID: 38608444 DOI: 10.1016/j.intimp.2024.112067] [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: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Silicosis is one of the most common and severe types of pneumoconiosis and is characterized by lung dysfunction, persistent lung inflammation, pulmonary nodule formation, and irreversible pulmonary fibrosis. The transdifferentiation of fibroblasts into myofibroblasts is one of the main reasons for the exacerbation of silicosis. However, the underlying mechanism of transcription factors regulating silicosis fibrosis has not been clarified. The aim of this study was to investigate the potential mechanism of transcription factor FOXF1 in fibroblast transdifferentiation in silica-induced pulmonary fibrosis. Therefore, a silicosis mouse model was established, and we found that FOXF1 expression level was significantly down-regulated in the silicosis group, and after overexpression of FOXF1 by adeno-associated virus (AAV), FOXF1 expression level was up-regulated, and silicosis fibrosis was alleviated. In order to further explore the specific regulatory mechanism of FOXF1 in silicosis, we established a fibroblasts transdifferentiation model induced by TGF-β in vitro. In the model, the expression levels of SMAD2/3 and P-SMAD2/3 were up-regulated, but the expression levels of SMAD2/3 and P-SMAD2/3 were down-regulated, inhibiting transdifferentiation and accumulation of extracellular matrix after the overexpressed FOXF1 plasmid was constructed. However, after silencing FOXF1, the expression levels of SMAD2/3 and P-SMAD2/3 were further up-regulated, aggravating transdifferentiation and accumulation of extracellular matrix. These results indicate that the activation of FOXF1 in fibroblasts can slow down the progression of silicosis fibrosis by inhibiting TGF-β/SMAD2/3 classical pathway, which provides a new idea for further exploration of silicosis treatment.
Collapse
Affiliation(s)
- Botao Hu
- School of Public Health, Zhengzhou University, Henan, China
| | - Xuesong Zhang
- School of Public Health, Zhengzhou University, Henan, China
| | - Hui Fan
- Department of Ultrasound, The Third Affiliated Hospital of Zhengzhou University, Henan, China
| | - Xiaofei Jin
- Department of Ultrasound, The Third Affiliated Hospital of Zhengzhou University, Henan, China
| | - Yuanmeng Qi
- School of Public Health, Zhengzhou University, Henan, China
| | - Ruimin Liu
- School of Public Health, Zhengzhou University, Henan, China
| | - Xiaoying Li
- School of Public Health, Zhengzhou University, Henan, China
| | - Meixiu Duan
- School of Public Health, Zhengzhou University, Henan, China
| | | | - Shiyu Li
- School of Public Health, Zhengzhou University, Henan, China
| | - Wu Yao
- School of Public Health, Zhengzhou University, Henan, China
| | - Changfu Hao
- School of Public Health, Zhengzhou University, Henan, China.
| |
Collapse
|
44
|
Rottenberg JT, Taslim TH, Soto-Ugaldi LF, Martinez-Cuesta L, Martinez-Calejman C, Fuxman Bass JI. Viral cis-regulatory elements as sensors of cellular states and environmental cues. Trends Genet 2024:S0168-9525(24)00108-2. [PMID: 38821843 DOI: 10.1016/j.tig.2024.05.004] [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: 03/26/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
To withstand a hostile cellular environment and replicate, viruses must sense, interpret, and respond to many internal and external cues. Retroviruses and DNA viruses can intercept these cues impinging on host transcription factors via cis-regulatory elements (CREs) in viral genomes, allowing them to sense and coordinate context-specific responses to varied signals. Here, we explore the characteristics of viral CREs, the classes of signals and host transcription factors that regulate them, and how this informs outcomes of viral replication, immune evasion, and latency. We propose that viral CREs constitute central hubs for signal integration from multiple pathways and that sequence variation between viral isolates can rapidly rewire sensing mechanisms, contributing to the variability observed in patient outcomes.
Collapse
Affiliation(s)
| | - Tommy H Taslim
- Department of Biology, Boston University, Boston, MA, USA; Molecular and Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Lucia Martinez-Cuesta
- Department of Biology, Boston University, Boston, MA, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA; Molecular and Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA.
| |
Collapse
|
45
|
Gautam P, Sinha SK. The Blueprint of Logical Decisions in a NF-κB Signaling System. ACS OMEGA 2024; 9:22625-22634. [PMID: 38826544 PMCID: PMC11137707 DOI: 10.1021/acsomega.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 06/04/2024]
Abstract
Nearly identical cells can exhibit substantially different responses to the same stimulus that causes phenotype diversity. Such interplay between phenotype diversity and the architecture of regulatory circuits is crucial since it determines the state of a biological cell. Here, we theoretically analyze how the circuit blueprints of NF-κB in cellular environments are formed and their role in determining the cells' metabolic state. The NF-κB is a collective name for a developmental conserved family of five different transcription factors that can form homodimers or heterodimers and often promote DNA looping to reprogram the inflammatory gene response. The NF-κB controls many biological functions, including cellular differentiation, proliferation, migration, and survival. Our model shows that nuclear localization of NF-κB differentially promotes logic operations such as AND, NAND, NOR, and OR in its regulatory network. Through the quantitative thermodynamic model of transcriptional regulation and systematic variation of promoter-enhancer interaction modes, we can account for the origin of various logic gates as formed in the NF-κB system. We further show that the interconversion or switching of logic gates yielded under systematic variations of the stimuli activity and DNA looping parameters. Such computation occurs in regulatory and signaling pathways in individual cells at a molecular scale, which one can exploit to design a biomolecular computer.
Collapse
Affiliation(s)
- Pankaj Gautam
- Theoretical and Computational
Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Sudipta Kumar Sinha
- Theoretical and Computational
Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| |
Collapse
|
46
|
Qi T, Zhou Y, Sheng Y, Li Z, Yang Y, Liu Q, Ge Q. Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning. J Chem Inf Model 2024; 64:4002-4008. [PMID: 38798191 DOI: 10.1021/acs.jcim.4c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transcription factors (TFs) are important regulatory elements for vital cellular activities, and the identification of transcription factor binding sites (TFBS) can help to explore gene regulatory mechanisms. Research studies have proved that cfDNA (cell-free DNA) shows relatively higher coverage at TFBS due to the protection by TF from degradation by nucleases and short fragments of cfDNA are enriched in TFBS. However, there are still great difficulties in the noninvasive identification of TFBSs from experimental techniques. In this study, we propose a deep learning-based approach that can noninvasively predict TFBSs of cfDNA by learning sequence information from known TFBSs through convolutional neural networks. Under the addition of long short-term memory, our model achieved an area under the curve of 84%. Based on this model to predict cfDNA, we found consistent motifs in cfDNA fragments and lower coverage occurred upstream and downstream of these cfDNA fragments, which is consistent with a previous study. We also found that the binding sites of the same TF differ in different cell lines. TF-specific target genes were detected from cfDNA and were enriched in cancer-related pathways. In summary, our method of locating TFBSs from plasma has the potential to reflect the intrinsic regulatory mechanism from a noninvasive perspective and provide technical guidance for dynamic monitoring of disease in clinical practice.
Collapse
Affiliation(s)
- Ting Qi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Ying Zhou
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Yuqi Sheng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Zhihui Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Yuwei Yang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Quanjun Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People's Republic of China
| |
Collapse
|
47
|
Bower G, Hollingsworth EW, Jacinto S, Clock B, Cao K, Liu M, Dziulko A, Alcaina-Caro A, Xu Q, Skowronska-Krawczyk D, Lopez-Rios J, Dickel DE, Bardet AF, Pennacchio LA, Visel A, Kvon EZ. Conserved Cis-Acting Range Extender Element Mediates Extreme Long-Range Enhancer Activity in Mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595809. [PMID: 38826394 PMCID: PMC11142232 DOI: 10.1101/2024.05.26.595809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
While most mammalian enhancers regulate their cognate promoters over moderate distances of tens of kilobases (kb), some enhancers act over distances in the megabase range. The sequence features enabling such extreme-distance enhancer-promoter interactions remain elusive. Here, we used in vivo enhancer replacement experiments in mice to show that short- and medium-range enhancers cannot initiate gene expression at extreme-distance range. We uncover a novel conserved cis-acting element, Range EXtender (REX), that confers extreme-distance regulatory activity and is located next to a long-range enhancer of Sall1. The REX element itself has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of the REX increased the range of an enhancer by an order of magnitude, from its native 71kb to 840kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs. These motifs are enriched around long-range limb enhancers genome-wide, including the ZRS, a benchmark long-range limb enhancer of Shh. Mutating the [C/T]AATTA motifs within the ZRS does not affect its limb-specific enhancer activity at short range, but selectively abolishes its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature globally associated with long-range enhancer-promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer extreme-distance gene activation by remote enhancers.
Collapse
Affiliation(s)
- Grace Bower
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
- Medical Scientist Training Program, University of California, Irvine, CA 92967, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Kaitlyn Cao
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Mandy Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| | - Adam Dziulko
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Qianlan Xu
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, 41013, Spain
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anaïs F. Bardet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U1258, 67400 Illkirch, France
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92967, USA
| |
Collapse
|
48
|
Dorans E, Jagadeesh K, Dey K, Price AL. Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307813. [PMID: 38826240 PMCID: PMC11142273 DOI: 10.1101/2024.05.24.24307813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown great promise in linking regulatory elements to genes. However, existing methods differ in their modeling assumptions and approaches to account for biological and technical noise-leading to low concordance in their linking scores-and do not capture the effects of genomic distance. We propose pgBoost, an integrative modeling framework that trains a non-linear combination of existing linking strategies (including genomic distance) on fine-mapped eQTL data to assign a probabilistic score to each candidate SNP-gene link. We applied pgBoost to single-cell multiome data from 85k cells representing 6 major immune/blood cell types. pgBoost attained higher enrichment for fine-mapped eSNP-eGene pairs (e.g. 21x at distance >10kb) than existing methods (1.2-10x; p-value for difference = 5e-13 vs. distance-based method and < 4e-35 for each other method), with larger improvements at larger distances (e.g. 35x vs. 0.89-6.6x at distance >100kb; p-value for difference < 0.002 vs. each other method). pgBoost also outperformed existing methods in enrichment for CRISPR-validated links (e.g. 4.8x vs. 1.6-4.1x at distance >10kb; p-value for difference = 0.25 vs. distance-based method and < 2e-5 for each other method), with larger improvements at larger distances (e.g. 15x vs. 1.6-2.5x at distance >100kb; p-value for difference < 0.009 for each other method). Similar improvements in enrichment were observed for links derived from Activity-By-Contact (ABC) scores and GWAS data. We further determined that restricting pgBoost to features from a focal cell type improved the identification of SNP-gene links relevant to that cell type. We highlight several examples where pgBoost linked fine-mapped GWAS variants to experimentally validated or biologically plausible target genes that were not implicated by other methods. In conclusion, a non-linear combination of linking strategies, including genomic distance, improves power to identify target genes underlying GWAS associations.
Collapse
|
49
|
He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell 2024; 187:2746-2766.e25. [PMID: 38631355 DOI: 10.1016/j.cell.2024.03.023] [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: 06/09/2023] [Revised: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
Collapse
Affiliation(s)
- Jinnan He
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiangru Huo
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Zeran Jia
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yiming Yan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Yu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haozhi Qu
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yunxin Xie
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Junsong Yuan
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Zheng
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yanyan Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Minglei Shi
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Michael Q Zhang
- Bioinformatics Division, National Research Center for Information Science and Technology, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Yinqing Li
- The IDG/McGovern Institute for Brain Research, MOE Key Laboratory of Bioinformatics, State Key Lab of Molecular Oncology, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
50
|
Peng Z, Kan Q, Wang K, Deng T, Wang S, Wu R, Yao C. Deciphering smooth muscle cell heterogeneity in atherosclerotic plaques and constructing model: a multi-omics approach with focus on KLF15/IGFBP4 axis. BMC Genomics 2024; 25:490. [PMID: 38760675 PMCID: PMC11102212 DOI: 10.1186/s12864-024-10379-y] [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: 12/11/2023] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Ruptured atherosclerotic plaques often precipitate severe ischemic events, such as stroke and myocardial infarction. Unraveling the intricate molecular mechanisms governing vascular smooth muscle cell (VSMC) behavior in plaque stabilization remains a formidable challenge. METHODS In this study, we leveraged single-cell and transcriptomic datasets from atherosclerotic plaques retrieved from the gene expression omnibus (GEO) database. Employing a combination of single-cell population differential analysis, weighted gene co-expression network analysis (WGCNA), and transcriptome differential analysis techniques, we identified specific genes steering the transformation of VSMCs in atherosclerotic plaques. Diagnostic models were developed and validated through gene intersection, utilizing the least absolute shrinkage and selection operator (LASSO) and random forest (RF) methods. Nomograms for plaque assessment were constructed. Tissue localization and expression validation were performed on specimens from animal models, utilizing immunofluorescence co-localization, western blot, and reverse-transcription quantitative-polymerase chain reaction (RT-qPCR). Various online databases were harnessed to predict transcription factors (TFs) and their interacting compounds, with determination of the cell-specific localization of TF expression using single-cell data. RESULTS Following rigorous quality control procedures, we obtained a total of 40,953 cells, with 6,261 representing VSMCs. The VSMC population was subsequently clustered into 5 distinct subpopulations. Analyzing inter-subpopulation cellular communication, we focused on the SMC2 and SMC5 subpopulations. Single-cell subpopulation and WGCNA analyses revealed significant module enrichments, notably in collagen-containing extracellular matrix and cell-substrate junctions. Insulin-like growth factor binding protein 4 (IGFBP4), apolipoprotein E (APOE), and cathepsin C (CTSC) were identified as potential diagnostic markers for early and advanced plaques. Notably, gene expression pattern analysis suggested that IGFBP4 might serve as a protective gene, a hypothesis validated through tissue localization and expression analysis. Finally, we predicted TFs capable of binding to IGFBP4, with Krüppel-like family 15 (KLF15) emerging as a prominent candidate showing relative specificity within smooth muscle cells. Predictions about compounds associated with affecting KLF15 expression were also made. CONCLUSION Our study established a plaque diagnostic and assessment model and analyzed the molecular interaction mechanisms of smooth muscle cells within plaques. Further analysis revealed that the transcription factor KLF15 may regulate the biological behaviors of smooth muscle cells through the KLF15/IGFBP4 axis, thereby influencing the stability of advanced plaques via modulation of the PI3K-AKT signaling pathway. This could potentially serve as a target for plaque stability assessment and therapy, thus driving advancements in the management and treatment of atherosclerotic plaques.
Collapse
MESH Headings
- Animals
- Humans
- Male
- Gene Expression Profiling
- Gene Regulatory Networks
- Insulin-Like Growth Factor Binding Protein 4/metabolism
- Insulin-Like Growth Factor Binding Protein 4/genetics
- Kruppel-Like Transcription Factors/metabolism
- Kruppel-Like Transcription Factors/genetics
- Multiomics
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/cytology
- Myocytes, Smooth Muscle/metabolism
- Plaque, Atherosclerotic/metabolism
- Plaque, Atherosclerotic/genetics
- Plaque, Atherosclerotic/pathology
- Single-Cell Analysis
- Transcriptome
- Rats
Collapse
Affiliation(s)
- Zhanli Peng
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Qinghui Kan
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Kangjie Wang
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Tang Deng
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shenming Wang
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ridong Wu
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China.
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.
| | - Chen Yao
- Division of Vascular Surgery, The First Affiliated Hospital, Sun Yat-sen University, No. 58 Zhongshan Er Road, Guangzhou, 510080, P.R. China.
- National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.
| |
Collapse
|