1
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Waite JB, Boytz R, Traeger AR, Lind TM, Lumbao-Conradson K, Torigoe SE. A suboptimal OCT4-SOX2 binding site facilitates the naïve-state specific function of a Klf4 enhancer. PLoS One 2024; 19:e0311120. [PMID: 39348365 DOI: 10.1371/journal.pone.0311120] [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: 02/05/2024] [Accepted: 09/12/2024] [Indexed: 10/02/2024] Open
Abstract
Enhancers have critical functions in the precise, spatiotemporal control of transcription during development. It is thought that enhancer grammar, or the characteristics and arrangements of transcription factor binding sites, underlie the specific functions of developmental enhancers. In this study, we sought to identify grammatical constraints that direct enhancer activity in the naïve state of pluripotency, focusing on the enhancers for the naïve-state specific gene, Klf4. Using a combination of biochemical tests, reporter assays, and endogenous mutations in mouse embryonic stem cells, we have studied the binding sites for the transcription factors OCT4 and SOX2. We have found that the three Klf4 enhancers contain suboptimal OCT4-SOX2 composite binding sites. Substitution with a high-affinity OCT4-SOX2 binding site in Klf4 enhancer E2 rescued enhancer function and Klf4 expression upon loss of the ESRRB and STAT3 binding sites. We also observed that the low-affinity of the OCT4-SOX2 binding site is crucial to drive the naïve-state specific activities of Klf4 enhancer E2. Altogether, our work suggests that the affinity of OCT4-SOX2 binding sites could facilitate enhancer functions in specific states of pluripotency.
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Affiliation(s)
- Jack B Waite
- Biochemistry & Molecular Biology Program, Lewis & Clark College, Portland, Oregon, United States of America
| | - RuthMabel Boytz
- Biology Department, Lewis & Clark College, Portland, Oregon, United States of America
| | - Alexis R Traeger
- Biochemistry & Molecular Biology Program, Lewis & Clark College, Portland, Oregon, United States of America
| | - Torrey M Lind
- Biochemistry & Molecular Biology Program, Lewis & Clark College, Portland, Oregon, United States of America
| | - Koya Lumbao-Conradson
- Biochemistry & Molecular Biology Program, Lewis & Clark College, Portland, Oregon, United States of America
| | - Sharon E Torigoe
- Biochemistry & Molecular Biology Program, Lewis & Clark College, Portland, Oregon, United States of America
- Biology Department, Lewis & Clark College, Portland, Oregon, United States of America
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2
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Khetan S, Bulyk ML. Overlapping binding sites underlie TF genomic occupancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583629. [PMID: 38496549 PMCID: PMC10942454 DOI: 10.1101/2024.03.05.583629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Sequence-specific DNA binding by transcription factors (TFs) is a crucial step in gene regulation. However, current high-throughput in vitro approaches cannot reliably detect lower affinity TF-DNA interactions, which play key roles in gene regulation. Here, we developed PADIT-seq ( p rotein a ffinity to D NA by in vitro transcription and RNA seq uencing) to assay TF binding preferences to all 10-bp DNA sequences at far greater sensitivity than prior approaches. The expanded catalogs of low affinity DNA binding sites for the human TFs HOXD13 and EGR1 revealed that nucleotides flanking high affinity DNA binding sites create overlapping lower affinity sites that together modulate TF genomic occupancy in vivo . Formation of such extended recognition sequences stems from an inherent property of TF binding sites to interweave each other and expands the genomic sequence space for identifying noncoding variants that directly alter TF binding. One-Sentence Summary Overlapping DNA binding sites underlie TF genomic occupancy through their inherent propensity to interweave each other.
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3
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Salomone J, Farrow E, Gebelein B. Homeodomain complex formation and biomolecular condensates in Hox gene regulation. Semin Cell Dev Biol 2024; 152-153:93-100. [PMID: 36517343 PMCID: PMC10258226 DOI: 10.1016/j.semcdb.2022.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Hox genes are a family of homeodomain transcription factors that regulate specialized morphological structures along the anterior-posterior axis of metazoans. Over the past few decades, researchers have focused on defining how Hox factors with similar in vitro DNA binding activities achieve sufficient target specificity to regulate distinct cell fates in vivo. In this review, we highlight how protein interactions with other transcription factors, many of which are also homeodomain proteins, result in the formation of transcription factor complexes with enhanced DNA binding specificity. These findings suggest that Hox-regulated enhancers utilize distinct combinations of homeodomain binding sites, many of which are low-affinity, to recruit specific Hox complexes. However, low-affinity sites can only yield reproducible responses with high transcription factor concentrations. To overcome this limitation, recent studies revealed how transcription factors, including Hox factors, use intrinsically disordered domains (IDRs) to form biomolecular condensates that increase protein concentrations. Moreover, Hox factors with altered IDRs have been associated with altered transcriptional activity and human disease states, demonstrating the importance of IDRs in mediating essential Hox output. Collectively, these studies highlight how Hox factors use their DNA binding domains, protein-protein interaction domains, and IDRs to form specific transcription factor complexes that yield accurate gene expression.
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Affiliation(s)
- Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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4
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Zhao Y, Vartak SV, Conte A, Wang X, Garcia DA, Stevens E, Kyoung Jung S, Kieffer-Kwon KR, Vian L, Stodola T, Moris F, Chopp L, Preite S, Schwartzberg PL, Kulinski JM, Olivera A, Harly C, Bhandoola A, Heuston EF, Bodine DM, Urrutia R, Upadhyaya A, Weirauch MT, Hager G, Casellas R. "Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes. Mol Cell 2022; 82:3398-3411.e11. [PMID: 35863348 PMCID: PMC9481673 DOI: 10.1016/j.molcel.2022.06.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/06/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
Regulatory elements activate promoters by recruiting transcription factors (TFs) to specific motifs. Notably, TF-DNA interactions often depend on cooperativity with colocalized partners, suggesting an underlying cis-regulatory syntax. To explore TF cooperativity in mammals, we analyze ∼500 mouse and human primary cells by combining an atlas of TF motifs, footprints, ChIP-seq, transcriptomes, and accessibility. We uncover two TF groups that colocalize with most expressed factors, forming stripes in hierarchical clustering maps. The first group includes lineage-determining factors that occupy DNA elements broadly, consistent with their key role in tissue-specific transcription. The second one, dubbed universal stripe factors (USFs), comprises ∼30 SP, KLF, EGR, and ZBTB family members that recognize overlapping GC-rich sequences in all tissues analyzed. Knockouts and single-molecule tracking reveal that USFs impart accessibility to colocalized partners and increase their residence time. Mammalian cells have thus evolved a TF superfamily with overlapping DNA binding that facilitate chromatin accessibility.
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Affiliation(s)
- Yongbing Zhao
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA.
| | - Supriya V Vartak
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Andrea Conte
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Xiang Wang
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Evan Stevens
- Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Seol Kyoung Jung
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | | | - Laura Vian
- Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA
| | - Timothy Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Francisco Moris
- EntreChem S.L., Vivero Ciencias de la Salud, 33011 Oviedo, Spain
| | - Laura Chopp
- Laboratory of Immune Cell Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Silvia Preite
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Joseph M Kulinski
- Mast cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ana Olivera
- Mast cell Biology Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Christelle Harly
- Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - David M Bodine
- Genetics and Molecular Biology Branch, NHGRI, NIH, Bethesda, MD 20892, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Matthew T Weirauch
- Divisions of Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Gordon Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20893, USA
| | - Rafael Casellas
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD 20892, USA; Lymphocyte Nuclear Biology, NIAMS-NCI, NIH, Bethesda, MD 20892, USA.
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5
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Cain B, Gebelein B. Mechanisms Underlying Hox-Mediated Transcriptional Outcomes. Front Cell Dev Biol 2021; 9:787339. [PMID: 34869389 PMCID: PMC8635045 DOI: 10.3389/fcell.2021.787339] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Metazoans differentially express multiple Hox transcription factors to specify diverse cell fates along the developing anterior-posterior axis. Two challenges arise when trying to understand how the Hox transcription factors regulate the required target genes for morphogenesis: First, how does each Hox factor differ from one another to accurately activate and repress target genes required for the formation of distinct segment and regional identities? Second, how can a Hox factor that is broadly expressed in many tissues within a segment impact the development of specific organs by regulating target genes in a cell type-specific manner? In this review, we highlight how recent genomic, interactome, and cis-regulatory studies are providing new insights into answering these two questions. Collectively, these studies suggest that Hox factors may differentially modify the chromatin of gene targets as well as utilize numerous interactions with additional co-activators, co-repressors, and sequence-specific transcription factors to achieve accurate segment and cell type-specific transcriptional outcomes.
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Affiliation(s)
- Brittany Cain
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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6
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Kuang Y, Pyo A, Eafergan N, Cain B, Gutzwiller LM, Axelrod O, Gagliani EK, Weirauch MT, Kopan R, Kovall RA, Sprinzak D, Gebelein B. Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor. PLoS Genet 2021; 17:e1009039. [PMID: 34559800 PMCID: PMC8494340 DOI: 10.1371/journal.pgen.1009039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/06/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022] Open
Abstract
Notch signaling controls many developmental processes by regulating gene expression. Notch-dependent enhancers recruit activation complexes consisting of the Notch intracellular domain, the Cbf/Su(H)/Lag1 (CSL) transcription factor (TF), and the Mastermind co-factor via two types of DNA sites: monomeric CSL sites and cooperative dimer sites called Su(H) paired sites (SPS). Intriguingly, the CSL TF can also bind co-repressors to negatively regulate transcription via these same sites. Here, we tested how synthetic enhancers with monomeric CSL sites versus dimeric SPSs bind Drosophila Su(H) complexes in vitro and mediate transcriptional outcomes in vivo. Our findings reveal that while the Su(H)/Hairless co-repressor complex similarly binds SPS and CSL sites in an additive manner, the Notch activation complex binds SPSs, but not CSL sites, in a cooperative manner. Moreover, transgenic reporters with SPSs mediate stronger, more consistent transcription and are more resistant to increased Hairless co-repressor expression compared to reporters with the same number of CSL sites. These findings support a model in which SPS containing enhancers preferentially recruit cooperative Notch activation complexes over Hairless repression complexes to ensure consistent target gene activation. Cell signaling provides a basic means of communication during development. Many signaling pathways, including the Notch pathway, convert extracellular signals into changes in gene expression via transcription factors that bind specific DNA sequences. Importantly, the Notch pathway transcription factor can either form activating complexes upon Notch activation to stimulate gene expression or repression complexes with co-repressors to inhibit gene expression. Prior studies showed that the Notch activation complex binds DNA as either an independent complex on monomer binding sites or as two cooperative complexes (dimer) on paired binding sites. In this study, we used synthetic biology to examine how these two types of DNA sites impact the binding of Notch activation versus repression complexes and the output of Notch target gene expression. Our studies reveal that unlike the Notch activation complex, the repression complex does not cooperatively bind dimer sites. Moreover, our findings support the model that the enhanced stability of the Notch activation complex on dimer sites makes target genes with dimer sites less sensitive to the repression complex than target genes with only monomer sites. Thus, our studies reveal how target genes with different binding sites differ in sensitivity to the ratio of Notch activation to repression complexes.
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Affiliation(s)
- Yi Kuang
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Anna Pyo
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Natanel Eafergan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Lisa M. Gutzwiller
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Ofri Axelrod
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Ellen K. Gagliani
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Divisions of Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Raphael Kopan
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rhett A. Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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7
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Ryan GE, Bohaczuk SC, Cassin J, Witham EA, Shojaei S, Ho EV, Thackray VG, Mellon PL. Androgen receptor positively regulates gonadotropin-releasing hormone receptor in pituitary gonadotropes. Mol Cell Endocrinol 2021; 530:111286. [PMID: 33872733 PMCID: PMC8177864 DOI: 10.1016/j.mce.2021.111286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/29/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022]
Abstract
Within pituitary gonadotropes, the gonadotropin-releasing hormone receptor (GnRHR) receives hypothalamic input from GnRH neurons that is critical for reproduction. Previous studies have suggested that androgens may regulate GnRHR, although the mechanisms remain unknown. In this study, we demonstrated that androgens positively regulate Gnrhr mRNA in mice. We then investigated the effects of androgens and androgen receptor (AR) on Gnrhr promoter activity in immortalized mouse LβT2 cells, which represent mature gonadotropes. We found that AR positively regulates the Gnrhr proximal promoter, and that this effect requires a hormone response element (HRE) half site at -159/-153 relative to the transcription start site. We also identified nonconsensus, full-length HREs at -499/-484 and -159/-144, which are both positively regulated by androgens on a heterologous promoter. Furthermore, AR associates with the Gnrhr promoter in ChIP. Altogether, we report that GnRHR is positively regulated by androgens through recruitment of AR to the Gnrhr proximal promoter.
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Affiliation(s)
- Genevieve E Ryan
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Stephanie C Bohaczuk
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Jessica Cassin
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Emily A Witham
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Shadi Shojaei
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Emily V Ho
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Pamela L Mellon
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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8
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Jindal GA, Farley EK. Enhancer grammar in development, evolution, and disease: dependencies and interplay. Dev Cell 2021; 56:575-587. [PMID: 33689769 PMCID: PMC8462829 DOI: 10.1016/j.devcel.2021.02.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/19/2022]
Abstract
Each language has standard books describing that language's grammatical rules. Biologists have searched for similar, albeit more complex, principles relating enhancer sequence to gene expression. Here, we review the literature on enhancer grammar. We introduce dependency grammar, a model where enhancers encode information based on dependencies between enhancer features shaped by mechanistic, evolutionary, and biological constraints. Classifying enhancers based on the types of dependencies may identify unifying principles relating enhancer sequence to gene expression. Such rules would allow us to read the instructions for development within genomes and pinpoint causal enhancer variants underlying disease and evolutionary changes.
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Affiliation(s)
- Granton A Jindal
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA.
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9
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Salomone J, Qin S, Fufa TD, Cain B, Farrow E, Guan B, Hufnagel RB, Nakafuku M, Lim HW, Campbell K, Gebelein B. Conserved Gsx2/Ind homeodomain monomer versus homodimer DNA binding defines regulatory outcomes in flies and mice. Genes Dev 2020; 35:157-174. [PMID: 33334823 PMCID: PMC7778271 DOI: 10.1101/gad.343053.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022]
Abstract
How homeodomain proteins gain sufficient specificity to control different cell fates has been a long-standing problem in developmental biology. The conserved Gsx homeodomain proteins regulate specific aspects of neural development in animals from flies to mammals, and yet they belong to a large transcription factor family that bind nearly identical DNA sequences in vitro. Here, we show that the mouse and fly Gsx factors unexpectedly gain DNA binding specificity by forming cooperative homodimers on precisely spaced and oriented DNA sites. High-resolution genomic binding assays revealed that Gsx2 binds both monomer and homodimer sites in the developing mouse ventral telencephalon. Importantly, reporter assays showed that Gsx2 mediates opposing outcomes in a DNA binding site-dependent manner: Monomer Gsx2 binding represses transcription, whereas homodimer binding stimulates gene expression. In Drosophila, the Gsx homolog, Ind, similarly represses or stimulates transcription in a site-dependent manner via an autoregulatory enhancer containing a combination of monomer and homodimer sites. Integrating these findings, we test a model showing how the homodimer to monomer site ratio and the Gsx protein levels defines gene up-regulation versus down-regulation. Altogether, these data serve as a new paradigm for how cooperative homeodomain transcription factor binding can increase target specificity and alter regulatory outcomes.
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Affiliation(s)
- Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio 45229, USA.,Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Shenyue Qin
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Temesgen D Fufa
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, Ohio 45219, USA
| | - Edward Farrow
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Bin Guan
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Masato Nakafuku
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Hee-Woong Lim
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Kenneth Campbell
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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10
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Berndt AJ, Othonos KM, Lian T, Flibotte S, Miao M, Bhuiyan SA, Cho RY, Fong JS, Hur SA, Pavlidis P, Allan DW. A low affinity cis-regulatory BMP response element restricts target gene activation to subsets of Drosophila neurons. eLife 2020; 9:59650. [PMID: 33124981 PMCID: PMC7669266 DOI: 10.7554/elife.59650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/29/2020] [Indexed: 11/19/2022] Open
Abstract
Retrograde BMP signaling and canonical pMad/Medea-mediated transcription regulate diverse target genes across subsets of Drosophila efferent neurons, to differentiate neuropeptidergic neurons and promote motor neuron terminal maturation. How a common BMP signal regulates diverse target genes across many neuronal subsets remains largely unresolved, although available evidence implicates subset-specific transcription factor codes rather than differences in BMP signaling. Here we examine the cis-regulatory mechanisms restricting BMP-induced FMRFa neuropeptide expression to Tv4-neurons. We find that pMad/Medea bind at an atypical, low affinity motif in the FMRFa enhancer. Converting this motif to high affinity caused ectopic enhancer activity and eliminated Tv4-neuron expression. In silico searches identified additional motif instances functional in other efferent neurons, implicating broader functions for this motif in BMP-dependent enhancer activity. Thus, differential interpretation of a common BMP signal, conferred by low affinity pMad/Medea binding motifs, can contribute to the specification of BMP target genes in efferent neuron subsets.
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Affiliation(s)
- Anthony Je Berndt
- Department of Food & Fuel for the 21st Century, University of California San Diego, San Diego, United States
| | - Katerina M Othonos
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Tianshun Lian
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Stephane Flibotte
- UBC/LSI Bioinformatics Facility, University of British Columbia, Vancouver, Canada
| | - Mo Miao
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | | | - Raymond Y Cho
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Justin S Fong
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Seo Am Hur
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Paul Pavlidis
- Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Douglas W Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
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Ryan GE, Farley EK. Functional genomic approaches to elucidate the role of enhancers during development. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1467. [PMID: 31808313 PMCID: PMC7027484 DOI: 10.1002/wsbm.1467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/02/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022]
Abstract
Successful development depends on the precise tissue-specific regulation of genes by enhancers, genetic elements that act as switches to control when and where genes are expressed. Because enhancers are critical for development, and the majority of disease-associated mutations reside within enhancers, it is essential to understand which sequences within enhancers are important for function. Advances in sequencing technology have enabled the rapid generation of genomic data that predict putative active enhancers, but functionally validating these sequences at scale remains a fundamental challenge. Herein, we discuss the power of genome-wide strategies used to identify candidate enhancers, and also highlight limitations and misconceptions that have arisen from these data. We discuss the use of massively parallel reporter assays to test enhancers for function at scale. We also review recent advances in our ability to study gene regulation during development, including CRISPR-based tools to manipulate genomes and single-cell transcriptomics to finely map gene expression. Finally, we look ahead to a synthesis of complementary genomic approaches that will advance our understanding of enhancer function during development. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Developmental Biology > Developmental Processes in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Genevieve E. Ryan
- Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
- Division of Biological Sciences, Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
| | - Emma K. Farley
- Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
- Division of Biological Sciences, Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
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12
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Trefflich S, Dalmolin RJS, Ortega JM, Castro MAA. Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194472. [PMID: 31825805 DOI: 10.1016/j.bbagrm.2019.194472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/06/2019] [Accepted: 11/30/2019] [Indexed: 01/06/2023]
Abstract
Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity, TFs are highly conserved and recognize the same DNA sequences in different organisms. One of the main factors that confer regulatory specificity is the distribution of the binding sites of the TFs along the genome, allowing the configuration of different transcriptional regulatory networks (TRNs) from the same regulator. A similar scenario occurs between tissues of the same organism, where a TRN can be rewired by epigenetic factors, modulating the accessibility of the TF to its binding sites. In this article we discuss concepts that can help to formulate testable hypotheses about the construction of regulons, exploring the presence and absence of the elements that form a TRN throughout the evolution of an ancestral lineage. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Sheyla Trefflich
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - José Miguel Ortega
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil.
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13
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Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. Annu Rev Cell Dev Biol 2019; 35:357-379. [PMID: 31283382 DOI: 10.1146/annurev-cellbio-100617-062719] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell partly resolves this specificity paradox through combinatorial strategies and the use of low-affinity binding sites, which are better able to distinguish between similar TFs. However, because these sites have low affinity, it is challenging to understand how TFs recognize them in vivo. Here, we summarize recent findings and technological advancements that allow for the quantification and mechanistic interpretation of TF recognition across a wide range of affinities. We propose a model that integrates insights from the fields of genetics and cell biology to provide further conceptual understanding of TF binding specificity. We argue that in eukaryotes, target specificity is driven by an inhomogeneous 3D nuclear distribution of TFs and by variation in DNA binding affinity such that locally elevated TF concentration allows low-affinity binding sites to be functional.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Richard S Mann
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA; .,Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10031, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
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Zandvakili A, Uhl JD, Campbell I, Salomone J, Song YC, Gebelein B. The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila. Dev Biol 2018; 445:226-236. [PMID: 30468713 DOI: 10.1016/j.ydbio.2018.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/12/2018] [Indexed: 11/19/2022]
Abstract
During development diverse transcription factor inputs are integrated by cis-regulatory modules (CRMs) to yield cell-specific gene expression. Defining how CRMs recruit the appropriate combinations of factors to either activate or repress gene expression remains a challenge. In this study, we compare and contrast the ability of two CRMs within the Drosophila embryo to recruit functional Hox transcription factor complexes. The DCRE CRM recruits Ultrabithorax (Ubx) and Abdominal-A (Abd-A) Hox complexes that include the Extradenticle (Exd) and Homothorax (Hth) transcription factors to repress the Distal-less leg selector gene, whereas the RhoA CRM selectively recruits Abd-A/Exd/Hth complexes to activate rhomboid and stimulate Epidermal Growth Factor secretion in sensory cell precursors. By swapping binding sites between these elements, we found that the RhoA Exd/Hth/Hox site configuration that mediates Abd-A specific activation can convey transcriptional repression by both Ubx and Abd-A when placed into the DCRE. We further show that the orientation and spacing of Hox sites relative to additional binding sites within the RhoA and DCRE is critical to mediate cell- and segment-specific output. These results indicate that the configuration of Exd, Hth, and Hox site within RhoA is neither Abd-A specific nor activation specific. Instead Hox specific output is largely dependent upon the presence of appropriately spaced and oriented binding sites for additional TF inputs. Taken together, these studies provide insight into the cis-regulatory logic used to generate cell-specific outputs via recruiting Hox transcription factor complexes.
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Affiliation(s)
- Arya Zandvakili
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Juli D Uhl
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Ian Campbell
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph Salomone
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA; Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Yuntao Charlie Song
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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