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Akiyama T, Raftery LA, Wharton KA. Bone morphogenetic protein signaling: the pathway and its regulation. Genetics 2024; 226:iyad200. [PMID: 38124338 PMCID: PMC10847725 DOI: 10.1093/genetics/iyad200] [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: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023] Open
Abstract
In the mid-1960s, bone morphogenetic proteins (BMPs) were first identified in the extracts of bone to have the remarkable ability to induce heterotopic bone. When the Drosophila gene decapentaplegic (dpp) was first identified to share sequence similarity with mammalian BMP2/BMP4 in the late-1980s, it became clear that secreted BMP ligands can mediate processes other than bone formation. Following this discovery, collaborative efforts between Drosophila geneticists and mammalian biochemists made use of the strengths of their respective model systems to identify BMP signaling components and delineate the pathway. The ability to conduct genetic modifier screens in Drosophila with relative ease was critical in identifying the intracellular signal transducers for BMP signaling and the related transforming growth factor-beta/activin signaling pathway. Such screens also revealed a host of genes that encode other core signaling components and regulators of the pathway. In this review, we provide a historical account of this exciting time of gene discovery and discuss how the field has advanced over the past 30 years. We have learned that while the core BMP pathway is quite simple, composed of 3 components (ligand, receptor, and signal transducer), behind the versatility of this pathway lies multiple layers of regulation that ensures precise tissue-specific signaling output. We provide a sampling of these discoveries and highlight many questions that remain to be answered to fully understand the complexity of BMP signaling.
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Affiliation(s)
- Takuya Akiyama
- Department of Biology, Rich and Robin Porter Cancer Research Center, The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA
| | - Laurel A Raftery
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Kristi A Wharton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
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2
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Rosales-Vega M, Reséndez-Pérez D, Vázquez M. Antennapedia: The complexity of a master developmental transcription factor. Genesis 2024; 62:e23561. [PMID: 37830148 DOI: 10.1002/dvg.23561] [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: 06/23/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023]
Abstract
Hox genes encode transcription factors that play an important role in establishing the basic body plan of animals. In Drosophila, Antennapedia is one of the five genes that make up the Antennapedia complex (ANT-C). Antennapedia determines the identity of the second thoracic segment, known as the mesothorax. Misexpression of Antennapedia at different developmental stages changes the identity of the mesothorax, including the muscles, nervous system, and cuticle. In Drosophila, Antennapedia has two distinct promoters highly regulated throughout development by several transcription factors. Antennapedia proteins are found with other transcription factors in different ANTENNAPEDIA transcriptional complexes to regulate multiple subsets of target genes. In this review, we describe the different mechanisms that regulate the expression and function of Antennapedia and the role of this Hox gene in the development of Drosophila.
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Affiliation(s)
- Marco Rosales-Vega
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Diana Reséndez-Pérez
- Facultad de Ciencias Biológicas, Departamento de Inmunología y Virología, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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3
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Masuda LHP, Sabino AU, Reinitz J, Ramos AF, Machado-Lima A, Andrioli LP. Global repression by tailless during segmentation. Dev Biol 2024; 505:11-23. [PMID: 37879494 PMCID: PMC10949167 DOI: 10.1016/j.ydbio.2023.09.014] [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: 12/30/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The orphan nuclear receptor Tailless (Tll) exhibits conserved roles in brain formation and maintenance that are shared, for example, with vertebrate orthologous forms (Tlx). However, the early expression of tll in two gap domains in the segmentation cascade of Drosophila is unusual even for most other insects. Here we investigate tll regulation on pair-rule stripes. With ectopic misexpression of tll we detected unexpected repression of almost all pair-rule stripes of hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz). Examining Tll embryonic ChIP-chip data with regions mapped as Cis-Regulatory Modules (CRMs) of pair-rule stripes we verified Tll interactions to these regions. With the ChIP-chip data we also verified Tll interactions to the CRMs of gap domains and in the misexpression assay, Tll-mediated repression on Kruppel (Kr), kni (kni) and giant (gt) according to their differential sensitivity to Tll. These results with gap genes confirmed previous data from the literature and argue against indirect repression roles of Tll in the striped pattern. Moreover, the prediction of Tll binding sites in the CRMs of eve stripes and the mathematical modeling of their removal using an experimentally validated theoretical framework shows effects on eve stripes compatible with the absence of a repressor binding to the CRMs. In addition, modeling increased tll levels in the embryo results in the differential repression of eve stripes, agreeing well with the results of the misexpression assay. In genetic assays we investigated eve 5, that is strongly repressed by the ectopic domain and representative of more central stripes not previously implied to be under direct regulation of tll. While this stripe is little affected in tll-, its posterior border is expanded in gt- but detected with even greater expansion in gt-;tll-. We end up by discussing tll with key roles in combinatorial repression mechanisms to contain the expression of medial patterns of the segmentation cascade in the extremities of the embryo.
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Affiliation(s)
| | - Alan Utsuni Sabino
- Departamento de Radiologia e Oncologia, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - John Reinitz
- Departments of Statistics, Ecology and Evolution, Molecular Genetics & Cell Biology, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | | | - Ariane Machado-Lima
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Paulo Andrioli
- Escola de Artes, Ciências e Humanidades da Universidade de São Paulo, São Paulo, Brazil.
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4
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Bordet G, Bamgbose G, Tulin AV. Poly(ADP-ribosyl)ating enzymes coordinate changes in the expression of metabolic genes with developmental progression. Sci Rep 2023; 13:20320. [PMID: 37985852 PMCID: PMC10661653 DOI: 10.1038/s41598-023-47691-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Metabolism, known to be temporally regulated to meet evolving energy demands, plays a crucial role in shaping developmental pace. Recent studies have demonstrated that two key proteins PARP1 and PARG play a regulatory role in the transcription of both morphogenic and metabolic genes. Intriguingly, in Drosophila, the depletion of PARP1 or PARG proteins causes a developmental arrest before pupation, resulting in individuals unable to complete their development. This phenotype highlights the critical involvement of poly(ADP-ribosyl)ating enzymes in regulating the metamorphic process. In this study, we provide compelling evidence that these enzymes intricately coordinate transcriptional changes in both developmental and metabolic pathways during metamorphosis. Specifically, they promote the expression of genes crucial for pupation, while simultaneously negatively regulating the expression of metabolic genes before the transition to the pupal stage. Additionally, these enzymes suppress the expression of genes that are no longer required during this transformative period. Our findings shed light on the intricate interplay between poly(ADP-ribosyl)ating enzymes, developmental processes, and metabolic regulation before metamorphosis and highlight a new role of poly(ADP-ribosyl)ating enzymes in the global regulation of transcription.
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Affiliation(s)
- Guillaume Bordet
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA
| | - Gbolahan Bamgbose
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA
| | - Alexei V Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA.
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5
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Bazzi W, Monticelli S, Delaporte C, Riet C, Giangrande A, Cattenoz PB. Gcm counteracts Toll-induced inflammation and impacts hemocyte number through cholinergic signaling. Front Immunol 2023; 14:1293766. [PMID: 38035083 PMCID: PMC10684909 DOI: 10.3389/fimmu.2023.1293766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
Hemocytes, the myeloid-like immune cells of Drosophila, fulfill a variety of functions that are not completely understood, ranging from phagocytosis to transduction of inflammatory signals. We here show that downregulating the hemocyte-specific Glial cell deficient/Glial cell missing (Glide/Gcm) transcription factor enhances the inflammatory response to the constitutive activation of the Toll pathway. This correlates with lower levels of glutathione S-transferase, suggesting an implication of Glide/Gcm in reactive oxygen species (ROS) signaling and calling for a widespread anti-inflammatory potential of Glide/Gcm. In addition, our data reveal the expression of acetylcholine receptors in hemocytes and that Toll activation affects their expressions, disclosing a novel aspect of the inflammatory response mediated by neurotransmitters. Finally, we provide evidence for acetylcholine receptor nicotinic acetylcholine receptor alpha 6 (nAchRalpha6) regulating hemocyte proliferation in a cell autonomous fashion and for non-cell autonomous cholinergic signaling regulating the number of hemocytes. Altogether, this study provides new insights on the molecular pathways involved in the inflammatory response.
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Affiliation(s)
- Wael Bazzi
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Sara Monticelli
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Claude Delaporte
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Céline Riet
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Angela Giangrande
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Pierre B. Cattenoz
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
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6
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Cascianelli S, Ceddia G, Marchesi A, Masseroli M. Identification of transcription factor high accumulation DNA zones. BMC Bioinformatics 2023; 24:395. [PMID: 37864168 PMCID: PMC10590011 DOI: 10.1186/s12859-023-05528-1] [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: 04/03/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Transcription factors (TF) play a crucial role in the regulation of gene transcription; alterations of their activity and binding to DNA areas are strongly involved in cancer and other disease onset and development. For proper biomedical investigation, it is hence essential to correctly trace TF dense DNA areas, having multiple bindings of distinct factors, and select DNA high occupancy target (HOT) zones, showing the highest accumulation of such bindings. Indeed, systematic and replicable analysis of HOT zones in a large variety of cells and tissues would allow further understanding of their characteristics and could clarify their functional role. RESULTS Here, we propose, thoroughly explain and discuss a full computational procedure to study in-depth DNA dense areas of transcription factor accumulation and identify HOT zones. This methodology, developed as a computationally efficient parametric algorithm implemented in an R/Bioconductor package, uses a systematic approach with two alternative methods to examine transcription factor bindings and provide comparative and fully-reproducible assessments. It offers different resolutions by introducing three distinct types of accumulation, which can analyze DNA from single-base to region-oriented levels, and a moving window, which can estimate the influence of the neighborhood for each DNA base under exam. CONCLUSIONS We quantitatively assessed the full procedure by using our implemented software package, named TFHAZ, in two example applications of biological interest, proving its full reliability and relevance.
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Affiliation(s)
- Silvia Cascianelli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio 34/5, 20133 Milan, Italy
| | - Gaia Ceddia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Alberto Marchesi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio 34/5, 20133 Milan, Italy
| | - Marco Masseroli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio 34/5, 20133 Milan, Italy
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7
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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8
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Traniello IM, Bukhari SA, Dibaeinia P, Serrano G, Avalos A, Ahmed AC, Sankey AL, Hernaez M, Sinha S, Zhao SD, Catchen J, Robinson GE. Single-cell dissection of aggression in honeybee colonies. Nat Ecol Evol 2023; 7:1232-1244. [PMID: 37264201 DOI: 10.1038/s41559-023-02090-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Understanding how genotypic variation results in phenotypic variation is especially difficult for collective behaviour because group phenotypes arise from complex interactions among group members. A genome-wide association study identified hundreds of genes associated with colony-level variation in honeybee aggression, many of which also showed strong signals of positive selection, but the influence of these 'colony aggression genes' on brain function was unknown. Here we use single-cell (sc) transcriptomics and gene regulatory network (GRN) analyses to test the hypothesis that genetic variation for colony aggression influences individual differences in brain gene expression and/or gene regulation. We compared soldiers, which respond to territorial intrusion with stinging attacks, and foragers, which do not. Colony environment showed stronger influences on soldier-forager differences in brain gene regulation compared with brain gene expression. GRN plasticity was strongly associated with colony aggression, with larger differences in GRN dynamics detected between soldiers and foragers from more aggressive relative to less aggressive colonies. The regulatory dynamics of subnetworks composed of genes associated with colony aggression genes were more strongly correlated with each other across different cell types and brain regions relative to other genes, especially in brain regions involved with olfaction and vision and multimodal sensory integration, which are known to mediate bee aggression. These results show how group genetics can shape a collective phenotype by modulating individual brain gene regulatory network architecture.
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Affiliation(s)
- Ian M Traniello
- Neuroscience Program, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, USA.
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | | | | | - Guillermo Serrano
- Computational Biology Program, CIMA University of Navarra, Pamplona, Spain
| | - Arian Avalos
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, Agricultural Research Services, United States Department of Agriculture, Baton Rouge, LA, USA
| | - Amy Cash Ahmed
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
| | - Alison L Sankey
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
| | - Mikel Hernaez
- Computational Biology Program, CIMA University of Navarra, Pamplona, Spain
| | - Saurabh Sinha
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
- Department of Computer Science, UIUC, Urbana, IL, USA
| | - Sihai Dave Zhao
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
- Department of Statistics, UIUC, Urbana, IL, USA
| | - Julian Catchen
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
- Department of Evolution, Ecology and Behavior, UIUC, Urbana, IL, USA
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, USA.
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA.
- Department of Entomology, UIUC, Urbana, IL, USA.
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9
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Weiner L, Brissette JL. Finding meaning in chaos: a selection signature for functional interactions and its use in molecular biology. FEBS J 2023; 290:3914-3927. [PMID: 35653424 DOI: 10.1111/febs.16542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
A primary goal of biomedical research is to elucidate molecular mechanisms, particularly those responsible for human traits, either normal or pathological. Yet achieving this goal is difficult if not impossible when the traits of interest lack tractable models and so cannot be dissected through time-honoured approaches like forward genetics or reconstitution. Arguably, no biological problem has hindered scientific progress more than this: the inability to dissect a trait's mechanism without a tractable likeness of the trait. At root, forward genetics and reconstitution are powerful approaches because they assay for specific molecular functions. Here, we discuss an alternative way to uncover important mechanistic interactions, namely, to assay for positive natural selection. If an interaction has been selected for, then it must perform an important function, a function that significantly promotes reproductive success. Accordingly, selection is a consequence and indicator of function, and uncovering multimolecular selection will reveal important functional interactions. We propose a selection signature for interactions and review recent selection-based approaches through which to dissect traits that are not inherently tractable. The review includes proof-of-principle studies in which important interactions were uncovered by screening for selection. In sum, screens for selection appear feasible when screens for specific functions are not. Selection screens thus constitute a novel tool through which to reveal the mechanisms that shape the fates of organisms.
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Affiliation(s)
- Lorin Weiner
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Janice L Brissette
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
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10
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Zhao J, Perkins ML, Norstad M, Garcia HG. A bistable autoregulatory module in the developing embryo commits cells to binary expression fates. Curr Biol 2023; 33:2851-2864.e11. [PMID: 37453424 PMCID: PMC10428078 DOI: 10.1016/j.cub.2023.06.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/13/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Bistable autoactivation has been proposed as a mechanism for cells to adopt binary fates during embryonic development. However, it is unclear whether the autoactivating modules found within developmental gene regulatory networks are bistable, unless their parameters are quantitatively determined. Here, we combine in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of the fruit fly pair-rule gene fushi tarazu (ftz), which is regulated by two known enhancers: the early (non-autoregulating) element and the autoregulatory element. Live imaging of transcription and protein concentration in the blastoderm revealed that binary Ftz fates are achieved as Ftz expression rapidly transitions from being dictated by the early element to the autoregulatory element. Moreover, we discovered that Ftz concentration alone is insufficient to activate the autoregulatory element, and that this element only becomes responsive to Ftz at a prescribed developmental time. Based on these observations, we developed a dynamical systems model and quantitated its kinetic parameters directly from experimental measurements. Our model demonstrated that the ftz autoregulatory module is indeed bistable and that the early element transiently establishes the content of the binary cell fate decision to which the autoregulatory module then commits. Further in silico analysis revealed that the autoregulatory element locks the Ftz fate quickly, within 35 min of exposure to the transient signal of the early element. Overall, our work confirms the widely held hypothesis that autoregulation can establish developmental fates through bistability and, most importantly, provides a framework for the quantitative dissection of cellular decision-making.
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Affiliation(s)
- Jiaxi Zhao
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Matthew Norstad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hernan G Garcia
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA.
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11
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Birnie A, Plat A, Korkmaz C, Bothma JP. Precisely timed regulation of enhancer activity defines the binary expression pattern of Fushi tarazu in the Drosophila embryo. Curr Biol 2023:S0960-9822(23)00453-0. [PMID: 37116484 PMCID: PMC10373528 DOI: 10.1016/j.cub.2023.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/13/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
The genes that drive development each typically have many different enhancers. Properly coordinating the action of these different enhancers is crucial to correctly specifying cell-fate decisions, yet it remains poorly understood how their activity is choregraphed in time. To shed light on this question, we used recently developed single-cell live imaging tools to dissect the regulation of Fushi tarazu (Ftz) in Drosophila melanogaster embryos. Ftz is a transcription factor that is expressed in asymmetric stripes by two distinct enhancers: autoregulatory and zebra. The anterior edge of each stripe needs to be sharply defined to specify essential lineage boundaries. Here, we tracked how boundary cells commit to either a high-Ftz or low-Ftz fate by measuring Ftz protein traces in real time and simultaneously quantifying transcription from the endogenous locus and individual enhancers. This revealed that the autoregulatory enhancer does not establish this fate choice. Instead, it perpetuates the decision defined by zebra. This is contrary to the prevailing view that autoregulation drives the fate decision by causing bi-stable Ftz expression. Furthermore, we showed that the autoregulatory enhancer is not activated based on a Ftz-concentration threshold but through a timing-based mechanism. We hypothesize that this is regulated by several ubiquitously expressed pioneer-like transcription factors, which have recently been shown to act as timers in the embryo. Our work provides new insight into how precisely timed enhancer activity can directly regulate the dynamics of gene regulatory networks, which may be a general mechanism for ensuring that embryogenesis runs like clockwork.
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Affiliation(s)
- Anthony Birnie
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Audrey Plat
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Cemil Korkmaz
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jacques P Bothma
- Hubrecht Institute-KNAW, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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12
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Harden TT, Vincent BJ, DePace AH. Transcriptional activators in the early Drosophila embryo perform different kinetic roles. Cell Syst 2023; 14:258-272.e4. [PMID: 37080162 PMCID: PMC10473017 DOI: 10.1016/j.cels.2023.03.006] [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: 03/08/2021] [Revised: 06/26/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Combinatorial regulation of gene expression by transcription factors (TFs) may in part arise from kinetic synergy-wherein TFs regulate different steps in the transcription cycle. Kinetic synergy requires that TFs play distinguishable kinetic roles. Here, we used live imaging to determine the kinetic roles of three TFs that activate transcription in the Drosophila embryo-Zelda, Bicoid, and Stat92E-by introducing their binding sites into the even-skipped stripe 2 enhancer. These TFs influence different sets of kinetic parameters, and their influence can change over time. All three TFs increased the fraction of transcriptionally active nuclei; Zelda also shortened the first-passage time into transcription and regulated the interval between transcription events. Stat92E also increased the lifetimes of active transcription. Different TFs can therefore play distinct kinetic roles in activating the transcription. This has consequences for understanding the composition and flexibility of regulatory DNA sequences and the biochemical function of TFs. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ben J Vincent
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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13
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Clark E, Battistara M, Benton MA. A timer gene network is spatially regulated by the terminal system in the Drosophila embryo. eLife 2022; 11:e78902. [PMID: 36524728 PMCID: PMC10065802 DOI: 10.7554/elife.78902] [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: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
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Affiliation(s)
- Erik Clark
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Margherita Battistara
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Matthew A Benton
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Developmental Biology Unit, EMBLHeidelbergGermany
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14
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Baltruk LJ, Lavezzo GM, Machado-Lima A, Digiampietri LA, Andrioli LP. An additive repression mechanism sets the anterior limits of anterior pair-rule stripes 1. Cells Dev 2022; 171:203802. [PMID: 35934285 DOI: 10.1016/j.cdev.2022.203802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/25/2023]
Abstract
Segments are repeated anatomical units forming the body of insects. In Drosophila, the specification of the body takes place during the blastoderm through the segmentation cascade. Pair-rule genes such as hairy (h), even-skipped (eve), runt (run), and fushi-tarazu (ftz) are of the intermediate level of the cascade and each pair-rule gene is expressed in seven transversal stripes along the antero-posterior axis of the embryo. Stripes are formed by independent cis-regulatory modules (CRMs) under the regulation of transcription factors of maternal source and of gap proteins of the first level of the cascade. The initial blastoderm of Drosophila is a syncytium and it also coincides with the mid-blastula transition when thousands of zygotic genes are transcribed and their products are able to diffuse in the cytoplasm. Thus, we anticipated a complex regulation of the CRMs of the pair-rule stripes. The CRMs of h 1, eve 1, run 1, ftz 1 are able to be activated by bicoid (bcd) throughout the anterior blastoderm and several lines of evidence indicate that they are repressed by the anterior gap genes slp1 (sloppy-paired 1), tll (tailless) and hkb (huckebein). The modest activity of these repressors led to the premise of a combinatorial mechanism regulating the expression of the CRMs of h 1, eve 1, run 1, ftz 1 in more anterior regions of the embryo. We tested this possibility by progressively removing the repression activities of slp1, tll and hkb. In doing so, we were able to expose a mechanism of additive repression limiting the anterior borders of stripes 1. Stripes 1 respond depending on their distance from the anterior end and repressors operating at different levels.
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Affiliation(s)
| | - Guilherme Miura Lavezzo
- Program on Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | - Ariane Machado-Lima
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil; Program on Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | - Luiz Paulo Andrioli
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil.
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15
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ASC proneural factors are necessary for chromatin remodeling during neuroectodermal to neuroblast fate transition to ensure the timely initiation of the neural stem cell program. BMC Biol 2022; 20:107. [PMID: 35549704 PMCID: PMC9102361 DOI: 10.1186/s12915-022-01300-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 04/20/2022] [Indexed: 11/11/2022] Open
Abstract
Background In both Drosophila and mammals, the achaete-scute (ASC/ASCL) proneural bHLH transcription factors are expressed in the developing central and peripheral nervous systems, where they function during specification and maintenance of the neural stem cells in opposition to Notch signaling. In addition to their role in nervous system development, ASC transcription factors are oncogenic and exhibit chromatin reprogramming activity; however, the impact of ASC on chromatin dynamics during neural stem cell generation remains elusive. Here, we investigate the chromatin changes accompanying neural commitment using an integrative genetics and genomics methodology. Results We found that ASC factors bind equally strongly to two distinct classes of cis-regulatory elements: open regions remodeled earlier during maternal to zygotic transition by Zelda and less accessible, Zelda-independent regions. Both classes of cis-elements exhibit enhanced chromatin accessibility during neural specification and correlate with transcriptional regulation of genes involved in a variety of biological processes necessary for neuroblast function/homeostasis. We identified an ASC-Notch regulated TF network that includes likely prime regulators of neuroblast function. Using a cohort of ASC target genes, we report that ASC null neuroblasts are defectively specified, remaining initially stalled, unable to divide, and lacking expression of many proneural targets. When mutant neuroblasts eventually start proliferating, they produce compromised progeny. Reporter lines driven by proneural-bound enhancers display ASC dependency, suggesting that the partial neuroblast identity seen in the absence of ASC genes is likely driven by other, proneural-independent, cis-elements. Neuroblast impairment and the late differentiation defects of ASC mutants are corrected by ectodermal induction of individual ASC genes but not by individual members of the TF network downstream of ASC. However, in wild-type embryos, the induction of individual members of this network induces CNS hyperplasia, suggesting that they synergize with the activating function of ASC to consolidate the chromatin dynamics that promote neural specification. Conclusions We demonstrate that ASC proneural transcription factors are indispensable for the timely initiation of the neural stem cell program at the chromatin level by regulating a large number of enhancers in the vicinity of neural genes. This early chromatin remodeling is crucial for both neuroblast homeostasis as well as future progeny fidelity. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01300-8.
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16
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Batut PJ, Bing XY, Sisco Z, Raimundo J, Levo M, Levine MS. Genome organization controls transcriptional dynamics during development. Science 2022; 375:566-570. [PMID: 35113722 PMCID: PMC10368186 DOI: 10.1126/science.abi7178] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Past studies offer contradictory claims for the role of genome organization in the regulation of gene activity. Here, we show through high-resolution chromosome conformation analysis that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. Quantitative live imaging and targeted genome editing demonstrate that this two-tiered organization is critical for the precise temporal dynamics of Hox gene transcription during development. Tethering elements mediate long-range enhancer-promoter interactions and foster fast activation kinetics. Conversely, the boundaries of topologically associating domains (TADs) prevent spurious interactions with enhancers and silencers located in neighboring TADs. These two levels of genome organization operate independently of one another to ensure precision of transcriptional dynamics and the reliability of complex patterning processes.
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Affiliation(s)
- Philippe J Batut
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xin Yang Bing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zachary Sisco
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - João Raimundo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michal Levo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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17
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Prazak L, Iwasaki Y, Kim AR, Kozlov K, King K, Gergen JP. A dual role for DNA binding by Runt in activation and repression of sloppy paired transcription. Mol Biol Cell 2021; 32:ar26. [PMID: 34432496 PMCID: PMC8693977 DOI: 10.1091/mbc.e20-08-0509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This work investigates the role of DNA binding by Runt in regulating the sloppy paired 1 (slp1) gene and in particular two distinct cis-regulatory elements that mediate regulation by Runt and other pair-rule transcription factors during Drosophila segmentation. We find that a DNA-binding-defective form of Runt is ineffective at repressing both the distal (DESE) and proximal (PESE) early stripe elements of slp1 and is also compromised for DESE-dependent activation. The function of Runt-binding sites in DESE is further investigated using site-specific transgenesis and quantitative imaging techniques. When DESE is tested as an autonomous enhancer, mutagenesis of the Runt sites results in a clear loss of Runt-dependent repression but has little to no effect on Runt-dependent activation. Notably, mutagenesis of these same sites in the context of a reporter gene construct that also contains the PESE enhancer results in a significant reduction of DESE-dependent activation as well as the loss of repression observed for the autonomous mutant DESE enhancer. These results provide strong evidence that DNA binding by Runt directly contributes to the regulatory interplay of interactions between these two enhancers in the early embryo.
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Affiliation(s)
- Lisa Prazak
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021.,Department of Biochemistry and Cell Biology and Center for Developmental Genetics.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794-5215
| | - Yasuno Iwasaki
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics
| | - Ah-Ram Kim
- Graduate Program in Biochemistry and Structural Biology, and
| | - Konstantin Kozlov
- Department of Applied Mathematics, St. Petersburg State Polytechnical University, St. Petersburg, Russia 195251
| | - Kevin King
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics.,Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794-5215
| | - J Peter Gergen
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics
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18
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Gaiewski MJ, Drewell RA, Dresch JM. Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm. Math Biosci 2021; 342:108716. [PMID: 34687735 DOI: 10.1016/j.mbs.2021.108716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
A detailed comprehension of transcriptional regulation is critical to understanding the genetic control of development and disease across many different organisms. To more fully investigate the complex molecular interactions controlling the precise expression of genes, many groups have constructed mathematical models to complement their experimental approaches. A critical step in such studies is choosing the most appropriate parameter estimation algorithm to enable detailed analysis of the parameters that contribute to the models. In this study, we develop a novel set of evolutionary algorithms that use a pseudo-random Sobol Set to construct the initial population and incorporate parameter sensitivities into the adaptation of mutation rates, using local, global, and hybrid strategies. Comparison of the performance of these new algorithms to a number of current state-of-the-art global parameter estimation algorithms on a range of continuous test functions, as well as synthetic biological data representing models of gene regulatory systems, reveals improved performance of the new algorithms in terms of runtime, error and reproducibility. In addition, by analyzing the ability of these algorithms to fit datasets of varying quality, we provide the experimentalist with a guide to how the algorithms perform across a range of noisy data. These results demonstrate the improved performance of the new set of parameter estimation algorithms and facilitate meaningful integration of model parameters and predictions in our understanding of the molecular mechanisms of gene regulation.
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Affiliation(s)
- Michael J Gaiewski
- Department of Mathematics and Computer Science, Clark University, Worcester, MA, USA; Department of Mathematics, University of Connecticut, Storrs, CT, USA.
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19
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Mortimer NT, Fischer ML, Waring AL, Kr P, Kacsoh BZ, Brantley SE, Keebaugh ES, Hill J, Lark C, Martin J, Bains P, Lee J, Vrailas-Mortimer AD, Schlenke TA. Extracellular matrix protein N-glycosylation mediates immune self-tolerance in Drosophila melanogaster. Proc Natl Acad Sci U S A 2021; 118:e2017460118. [PMID: 34544850 PMCID: PMC8488588 DOI: 10.1073/pnas.2017460118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
In order to respond to infection, hosts must distinguish pathogens from their own tissues. This allows for the precise targeting of immune responses against pathogens and also ensures self-tolerance, the ability of the host to protect self tissues from immune damage. One way to maintain self-tolerance is to evolve a self signal and suppress any immune response directed at tissues that carry this signal. Here, we characterize the Drosophila tuSz1 mutant strain, which mounts an aberrant immune response against its own fat body. We demonstrate that this autoimmunity is the result of two mutations: 1) a mutation in the GCS1 gene that disrupts N-glycosylation of extracellular matrix proteins covering the fat body, and 2) a mutation in the Drosophila Janus Kinase ortholog that causes precocious activation of hemocytes. Our data indicate that N-glycans attached to extracellular matrix proteins serve as a self signal and that activated hemocytes attack tissues lacking this signal. The simplicity of this invertebrate self-recognition system and the ubiquity of its constituent parts suggests it may have functional homologs across animals.
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Affiliation(s)
- Nathan T Mortimer
- School of Biological Sciences, Illinois State University, Normal, IL 61790;
| | - Mary L Fischer
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Ashley L Waring
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Pooja Kr
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Balint Z Kacsoh
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Susanna E Brantley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Joshua Hill
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Chris Lark
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Julia Martin
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Pravleen Bains
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Jonathan Lee
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | | | - Todd A Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ 85719
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20
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Asma H, Halfon MS. Annotating the Insect Regulatory Genome. INSECTS 2021; 12:591. [PMID: 34209769 PMCID: PMC8305585 DOI: 10.3390/insects12070591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
Abstract
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods.
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Affiliation(s)
- Hasiba Asma
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
| | - Marc S. Halfon
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203, USA
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21
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Zhu I, Song W, Ovcharenko I, Landsman D. A model of active transcription hubs that unifies the roles of active promoters and enhancers. Nucleic Acids Res 2021; 49:4493-4505. [PMID: 33872375 DOI: 10.1093/nar/gkab235] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
An essential questions of gene regulation is how large number of enhancers and promoters organize into gene regulatory loops. Using transcription-factor binding enrichment as an indicator of enhancer strength, we identified a portion of H3K27ac peaks as potentially strong enhancers and found a universal pattern of promoter and enhancer distribution: At actively transcribed regions of length of ∼200-300 kb, the numbers of active promoters and enhancers are inversely related. Enhancer clusters are associated with isolated active promoters, regardless of the gene's cell-type specificity. As the number of nearby active promoters increases, the number of enhancers decreases. At regions where multiple active genes are closely located, there are few distant enhancers. With Hi-C analysis, we demonstrate that the interactions among the regulatory elements (active promoters and enhancers) occur predominantly in clusters and multiway among linearly close elements and the distance between adjacent elements shows a preference of ∼30 kb. We propose a simple rule of spatial organization of active promoters and enhancers: Gene transcriptions and regulations mainly occur at local active transcription hubs contributed dynamically by multiple elements from linearly close enhancers and/or active promoters. The hub model can be represented with a flower-shaped structure and implies an enhancer-like role of active promoters.
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Affiliation(s)
- Iris Zhu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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22
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Grosveld F, van Staalduinen J, Stadhouders R. Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms. Annu Rev Genomics Hum Genet 2021; 22:127-146. [PMID: 33951408 DOI: 10.1146/annurev-genom-122220-093818] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate control of gene expression in the right cell at the right moment is of fundamental importance to animal development and homeostasis. At the heart of gene regulation lie the enhancers, a class of gene regulatory elements that ensures precise spatiotemporal activation of gene transcription. Mammalian genomes are littered with enhancers, which are frequently organized in cooperative clusters such as locus control regions and superenhancers. Here, we discuss our current knowledge of enhancer biology, including an overview of the discovery of the various enhancer subsets and the mechanistic models used to explain their gene regulatory function.
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Affiliation(s)
- Frank Grosveld
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands; ,
| | | | - Ralph Stadhouders
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands; , .,Department of Pulmonary Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands
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23
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Mousavi R, Konuru SH, Lobo D. Inference of dynamic spatial GRN models with multi-GPU evolutionary computation. Brief Bioinform 2021; 22:6217729. [PMID: 33834216 DOI: 10.1093/bib/bbab104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/15/2021] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
Reverse engineering mechanistic gene regulatory network (GRN) models with a specific dynamic spatial behavior is an inverse problem without analytical solutions in general. Instead, heuristic machine learning algorithms have been proposed to infer the structure and parameters of a system of equations able to recapitulate a given gene expression pattern. However, these algorithms are computationally intensive as they need to simulate millions of candidate models, which limits their applicability and requires high computational resources. Graphics processing unit (GPU) computing is an affordable alternative for accelerating large-scale scientific computation, yet no method is currently available to exploit GPU technology for the reverse engineering of mechanistic GRNs from spatial phenotypes. Here we present an efficient methodology to parallelize evolutionary algorithms using GPU computing for the inference of mechanistic GRNs that can develop a given gene expression pattern in a multicellular tissue area or cell culture. The proposed approach is based on multi-CPU threads running the lightweight crossover, mutation and selection operators and launching GPU kernels asynchronously. Kernels can run in parallel in a single or multiple GPUs and each kernel simulates and scores the error of a model using the thread parallelism of the GPU. We tested this methodology for the inference of spatiotemporal mechanistic gene regulatory networks (GRNs)-including topology and parameters-that can develop a given 2D gene expression pattern. The results show a 700-fold speedup with respect to a single CPU implementation. This approach can streamline the extraction of knowledge from biological and medical datasets and accelerate the automatic design of GRNs for synthetic biology applications.
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Affiliation(s)
- Reza Mousavi
- Department of Biological Sciences at the University of Maryland, Baltimore, MD 21250, USA
| | - Sri Harsha Konuru
- Department of Biological Sciences at the University of Maryland, Baltimore, MD 21250, USA
| | - Daniel Lobo
- Department of Biological Sciences at the University of Maryland, Baltimore, MD 21250, USA
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24
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Spierer AN, Mossman JA, Smith SP, Crawford L, Ramachandran S, Rand DM. Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PLoS Genet 2021; 17:e1008887. [PMID: 33735180 PMCID: PMC7971549 DOI: 10.1371/journal.pgen.1008887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
The winged insects of the order Diptera are colloquially named for their most recognizable phenotype: flight. These insects rely on flight for a number of important life history traits, such as dispersal, foraging, and courtship. Despite the importance of flight, relatively little is known about the genetic architecture of flight performance. Accordingly, we sought to uncover the genetic modifiers of flight using a measure of flies’ reaction and response to an abrupt drop in a vertical flight column. We conducted a genome wide association study (GWAS) using 197 of the Drosophila Genetic Reference Panel (DGRP) lines, and identified a combination of additive and marginal variants, epistatic interactions, whole genes, and enrichment across interaction networks. Egfr, a highly pleiotropic developmental gene, was among the most significant additive variants identified. We functionally validated 13 of the additive candidate genes’ (Adgf-A/Adgf-A2/CG32181, bru1, CadN, flapper (CG11073), CG15236, flippy (CG9766), CREG, Dscam4, form3, fry, Lasp/CG9692, Pde6, Snoo), and introduce a novel approach to whole gene significance screens: PEGASUS_flies. Additionally, we identified ppk23, an Acid Sensing Ion Channel (ASIC) homolog, as an important hub for epistatic interactions. We propose a model that suggests genetic modifiers of wing and muscle morphology, nervous system development and function, BMP signaling, sexually dimorphic neural wiring, and gene regulation are all important for the observed differences flight performance in a natural population. Additionally, these results represent a snapshot of the genetic modifiers affecting drop-response flight performance in Drosophila, with implications for other insects. Insect flight is a widely recognizable phenotype of many winged insects, hence the name: flies. While fruit flies, or Drosophila melanogaster, are a genetically tractable model, flight performance is a highly integrative phenotype, and therefore challenging to identify comprehensively which genetic modifiers contribute to its genetic architecture. Accordingly, we screened 197 Drosophila Genetic Reference Panel lines for their ability to react and respond to an abrupt drop. Using several computational approaches, we identified additive, marginal, and epistatic variants, as well as whole genes and altered sub-networks of gene-gene and protein-protein interaction networks that contribute to variation in flight performance. More generally, we demonstrate the benefits of employing multiple methodologies to elucidate the genetic architecture of complex traits. Many variants and genes mapped to regions of the genome that affect neurodevelopment, wing and muscle development, and regulation of gene expression. We also introduce PEGASUS_flies, a Drosophila-adapted version of the PEGASUS platform first used in human studies, to infer gene-level significance of association based on the gene’s distribution of individual variant P-values. Our results contribute to the debate over the relative importance of individual, additive factors and epistatic, or higher order, interactions, in the mapping of genotype to phenotype.
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Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Samuel Pattillo Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Microsoft Research New England, Cambridge, Massachusetts, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
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25
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Seo J, Koçak DD, Bartelt LC, Williams CA, Barrera A, Gersbach CA, Reddy TE. AP-1 subunits converge promiscuously at enhancers to potentiate transcription. Genome Res 2021; 31:538-550. [PMID: 33674350 PMCID: PMC8015846 DOI: 10.1101/gr.267898.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022]
Abstract
The AP-1 transcription factor (TF) dimer contributes to many biological processes and environmental responses. AP-1 can be composed of many interchangeable subunits. Unambiguously determining the binding locations of these subunits in the human genome is challenging because of variable antibody specificity and affinity. Here, we definitively establish the genome-wide binding patterns of five AP-1 subunits by using CRISPR to introduce a common antibody tag on each subunit. We find limited evidence for strong dimerization preferences between subunits at steady state and find that, under a stimulus, dimerization patterns reflect changes in the transcriptome. Further, our analysis suggests that canonical AP-1 motifs indiscriminately recruit all AP-1 subunits to genomic sites, which we term AP-1 hotspots. We find that AP-1 hotspots are predictive of cell type–specific gene expression and of genomic responses to glucocorticoid signaling (more so than super-enhancers) and are significantly enriched in disease-associated genetic variants. Together, these results support a model where promiscuous binding of many AP-1 subunits to the same genomic location play a key role in regulating cell type–specific gene expression and environmental responses.
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Affiliation(s)
- Jungkyun Seo
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - D Dewran Koçak
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Luke C Bartelt
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Courtney A Williams
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - Alejandro Barrera
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Surgery, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Division of Integrative Genomics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Center for Advanced Genomic Technologies, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
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26
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Ludl AA, Michoel T. Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast. Mol Omics 2021; 17:241-251. [PMID: 33438713 DOI: 10.1039/d0mo00140f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a segregating population are combined, genomic variants can be used to orient the direction of causality between gene expression traits. Instrumental variable methods use a local expression quantitative trait locus (eQTL) as a randomized instrument for a gene's expression level, and assign target genes based on distal eQTL associations. Mediation-based methods additionally require that distal eQTL associations are mediated by the source gene. A detailed comparison between these methods has not yet been conducted, due to the lack of a standardized implementation of different methods, the limited sample size of most multi-omics datasets, and the absence of ground-truth networks for most organisms. Here we used Findr, a software package providing uniform implementations of instrumental variable, mediation, and coexpression-based methods, a recent dataset of 1012 segregants from a cross between two budding yeast strains, and the Yeastract database of known transcriptional interactions to compare causal gene network inference methods. We found that causal inference methods result in a significant overlap with the ground-truth, whereas coexpression did not perform better than random. A subsampling analysis revealed that the performance of mediation saturates at large sample sizes, due to a loss of sensitivity when residual correlations become significant. Instrumental variable methods on the other hand contain false positive predictions, due to genomic linkage between eQTL instruments. Instrumental variable and mediation-based methods also have complementary roles for identifying causal genes underlying transcriptional hotspots. Instrumental variable methods correctly predicted STB5 targets for a hotspot centred on the transcription factor STB5, whereas mediation failed due to Stb5p auto-regulating its own expression. Mediation suggests a new candidate gene, DNM1, for a hotspot on Chr XII, whereas instrumental variable methods could not distinguish between multiple genes located within the hotspot. In conclusion, causal inference from genomics and transcriptomics data is a powerful approach for reconstructing causal gene networks, which could be further improved by the development of methods to control for residual correlations in mediation analyses, and for genomic linkage and pleiotropic effects from transcriptional hotspots in instrumental variable analyses.
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Affiliation(s)
- Adriaan-Alexander Ludl
- Computational Biology Unit, Department of Informatics, University of Bergen, PO Box 7803, 5020 Bergen, Norway.
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27
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Tanevski J, Nguyen T, Truong B, Karaiskos N, Ahsen ME, Zhang X, Shu C, Xu K, Liang X, Hu Y, Pham HV, Xiaomei L, Le TD, Tarca AL, Bhatti G, Romero R, Karathanasis N, Loher P, Chen Y, Ouyang Z, Mao D, Zhang Y, Zand M, Ruan J, Hafemeister C, Qiu P, Tran D, Nguyen T, Gabor A, Yu T, Guinney J, Glaab E, Krause R, Banda P, Stolovitzky G, Rajewsky N, Saez-Rodriguez J, Meyer P. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Sci Alliance 2020; 3:e202000867. [PMID: 32972997 PMCID: PMC7536825 DOI: 10.26508/lsa.202000867] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 11/24/2022] Open
Abstract
Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize clusters of cells. Selection of predictor genes was essential for this task. Predictor genes showed a relatively high expression entropy, high spatial clustering and included prominent developmental genes such as gap and pair-rule genes and tissue markers. Application of the top 10 methods to a zebra fish embryo dataset yielded similar performance and statistical properties of the selected genes than in the Drosophila data. This suggests that methods developed in this challenge are able to extract generalizable properties of genes that are useful to accurately reconstruct the spatial arrangement of cells in tissues.
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Affiliation(s)
- Jovan Tanevski
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | | | - Buu Truong
- University of South Australia, Mawson Lakes, Australia
| | - Nikos Karaiskos
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mehmet Eren Ahsen
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- University of Illinois, Urbana-Champaign, Champaign, IL, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Liang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Hoang Vv Pham
- University of South Australia, Mawson Lakes, Australia
| | - Li Xiaomei
- University of South Australia, Mawson Lakes, Australia
| | - Thuc D Le
- University of South Australia, Mawson Lakes, Australia
| | - Adi L Tarca
- Department of Obstetrics and Gynecology and Department of Computer Science, Wayne State University, Detroit, MI, USA
| | - Gaurav Bhatti
- Perinatology Research Branch, National Institute of Child Health and Human Development (NICHD)/National Insitutes of Health (NIH)/ Department of Health & Human Services (DHHS), Bethesda, MD, USA
- Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, National Institute of Child Health and Human Development (NICHD)/National Insitutes of Health (NIH)/ Department of Health & Human Services (DHHS), Bethesda, MD, USA
- Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, MI, USA
| | | | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yang Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Maryam Zand
- University of Texas at San Antonio, San Antonio, TX, USA
| | - Jianhua Ruan
- University of Texas at San Antonio, San Antonio, TX, USA
| | | | - Peng Qiu
- Georgia Institute of Technology, Atlanta, GA, USA
- Emory University, Atlanta, GA, USA
| | - Duc Tran
- University of Nevada, Reno, NV, USA
| | | | - Attila Gabor
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
| | | | | | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
| | - Roland Krause
- Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
| | - Peter Banda
- Bioinformatics Core Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur Alzette, Luxembourg
| | - Gustavo Stolovitzky
- International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
- Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Pablo Meyer
- International Buisness Machines (IBM) T.J. Watson Research Center, Yorktown Heights, NY, USA
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28
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Overton IM, Sims AH, Owen JA, Heale BSE, Ford MJ, Lubbock ALR, Pairo-Castineira E, Essafi A. Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling. Cancers (Basel) 2020; 12:cancers12102823. [PMID: 33007944 PMCID: PMC7652213 DOI: 10.3390/cancers12102823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/16/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted "neutral" (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington's epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.
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Affiliation(s)
- Ian M. Overton
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
- Department of Systems Biology, Harvard University, Boston, MA 02115, USA;
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH9 3BF, UK
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
- Correspondence:
| | - Andrew H. Sims
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Jeremy A. Owen
- Department of Systems Biology, Harvard University, Boston, MA 02115, USA;
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bret S. E. Heale
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Matthew J. Ford
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Alexander L. R. Lubbock
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Erola Pairo-Castineira
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
| | - Abdelkader Essafi
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; (A.H.S.); (B.S.E.H.); (M.J.F.); (A.L.R.L.); (E.P.-C.); (A.E.)
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29
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Koromila T, Stathopoulos A. Distinct Roles of Broadly Expressed Repressors Support Dynamic Enhancer Action and Change in Time. Cell Rep 2020; 28:855-863.e5. [PMID: 31340149 PMCID: PMC6927530 DOI: 10.1016/j.celrep.2019.06.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/02/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022] Open
Abstract
How broadly expressed repressors regulate gene expression is incompletely understood. To gain insight, we investigated how Suppressor of Hairless-Su(H)-and Runt regulate expression of bone morphogenetic protein (BMP) antagonist short-gastrulation via the sog_Distal enhancer. A live imaging protocol was optimized to capture this enhancer's spatiotemporal output throughout the early Drosophila embryo, finding in this context that Runt regulates transcription initiation, Su(H) regulates transcription rate, and both factors control spatial expression. Furthermore, whereas Su(H) functions as a dedicated repressor, Runt temporally switches from repressor to activator. Our results demonstrate that broad repressors play temporally distinct roles and contribute to dynamic gene expression. Both Run and Su(H)'s ability to influence the spatiotemporal domains of gene expression may serve to counterbalance activators and function in this manner as important regulators of the maternal-to-zygotic transition in early embryos.
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Affiliation(s)
- Theodora Koromila
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA.
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30
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Tamberg L, Jaago M, Säälik K, Sirp A, Tuvikene J, Shubina A, Kiir CS, Nurm K, Sepp M, Timmusk T, Palgi M. Daughterless, the Drosophila orthologue of TCF4, is required for associative learning and maintenance of the synaptic proteome. Dis Model Mech 2020; 13:dmm042747. [PMID: 32641419 PMCID: PMC7406316 DOI: 10.1242/dmm.042747] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/24/2020] [Indexed: 12/11/2022] Open
Abstract
Mammalian transcription factor 4 (TCF4) has been linked to schizophrenia and intellectual disabilities, such as Pitt-Hopkins syndrome (PTHS). Here, we show that similarly to mammalian TCF4, fruit fly orthologue Daughterless (Da) is expressed widely in the Drosophila brain. Furthermore, silencing of da, using several central nervous system-specific Gal4 driver lines, impairs appetitive associative learning of the larvae and leads to decreased levels of the synaptic proteins Synapsin (Syn) and Discs large 1 (Dlg1), suggesting the involvement of Da in memory formation. Here, we demonstrate that Syn and dlg1 are direct target genes of Da in adult Drosophila heads, as Da binds to the regulatory regions of these genes and the modulation of Da levels alter the levels of Syn and dlg1 mRNA. Silencing of da also affects negative geotaxis of the adult flies, suggesting the impairment of locomotor function. Overall, our findings suggest that Da regulates Drosophila larval memory and adult negative geotaxis, possibly via its synaptic target genes Syn and dlg1 These behavioural phenotypes can be further used as a PTHS model to screen for therapeutics.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Laura Tamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Mariliis Jaago
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
- Protobios LLC, Mäealuse 4, Tallinn 12618, Estonia
| | - Kristi Säälik
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Alex Sirp
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
- Protobios LLC, Mäealuse 4, Tallinn 12618, Estonia
| | - Anastassia Shubina
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Carl Sander Kiir
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Kaja Nurm
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Mari Sepp
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
- Protobios LLC, Mäealuse 4, Tallinn 12618, Estonia
| | - Mari Palgi
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
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31
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Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML. A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Rep 2020; 27:955-970.e7. [PMID: 30995488 PMCID: PMC6485956 DOI: 10.1016/j.celrep.2019.03.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/04/2019] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation. Combinatorial regulation by transcription factors (TFs) is one mechanism for achieving condition and tissue-specific gene regulation. Shokri et al. mapped TF-TF interactions between most Drosophila TFs, reporting a comprehensive TF-TF network integrated with previously known interactions. They used this network to discern distinct TF-DNA binding modes.
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Affiliation(s)
- Leila Shokri
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sachi Inukai
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Antonina Hafner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Kathryn Weinand
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA
| | - Korneel Hens
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Anastasia Vedenko
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen S Gisselbrecht
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Johannes Bischof
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Edy Furger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Jean-Daniel Feuz
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martha L Bulyk
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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32
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Rivera J, Keränen SVE, Gallo SM, Halfon MS. REDfly: the transcriptional regulatory element database for Drosophila. Nucleic Acids Res 2020; 47:D828-D834. [PMID: 30329093 PMCID: PMC6323911 DOI: 10.1093/nar/gky957] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022] Open
Abstract
The REDfly database provides a comprehensive curation of experimentally-validated Drosophila transcriptional cis-regulatory elements and includes information on DNA sequence, experimental evidence, patterns of regulated gene expression, and more. Now in its thirteenth year, REDfly has grown to over 23 000 records of tested reporter gene constructs and 2200 tested transcription factor binding sites. Recent developments include the start of curation of predicted cis-regulatory modules in addition to experimentally-verified ones, improved search and filtering, and increased interaction with the authors of curated papers. An expanded data model that will capture information on temporal aspects of gene regulation, regulation in response to environmental and other non-developmental cues, sexually dimorphic gene regulation, and non-endogenous (ectopic) aspects of reporter gene expression is under development and expected to be in place within the coming year. REDfly is freely accessible at http://redfly.ccr.buffalo.edu, and news about database updates and new features can be followed on Twitter at @REDfly_database.
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Affiliation(s)
- John Rivera
- Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14203, USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | | | - Steven M Gallo
- Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14203, USA.,New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Marc S Halfon
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA.,Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203, USA.,Department of Biomedical Informatics, State University of New York at Buffalo, Buffalo, NY 14203, USA.,Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA.,Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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33
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Soluri IV, Zumerling LM, Payan Parra OA, Clark EG, Blythe SA. Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. eLife 2020; 9:e53916. [PMID: 32347792 PMCID: PMC7190358 DOI: 10.7554/elife.53916] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/20/2022] Open
Abstract
Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC-seq on Drosophila embryos during the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of late segmentation network CRMs. opa-driven changes in accessibility are accompanied by equivalent changes in gene expression. Interfering with the timing of opa activity impacts the proper patterning of expression. These results indicate that dynamic systems for chromatin regulation directly impact the reading of embryonic patterning information.
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Affiliation(s)
- Isabella V Soluri
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Lauren M Zumerling
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Omar A Payan Parra
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | - Eleanor G Clark
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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34
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Castellanos M, Mothi N, Muñoz V. Eukaryotic transcription factors can track and control their target genes using DNA antennas. Nat Commun 2020; 11:540. [PMID: 31992709 PMCID: PMC6987225 DOI: 10.1038/s41467-019-14217-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/12/2019] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic transcription factors (TF) function by binding to short 6-10 bp DNA recognition sites located near their target genes, which are scattered through vast genomes. Such process surmounts enormous specificity, efficiency and celerity challenges using a molecular mechanism that remains poorly understood. Combining biophysical experiments, theory and bioinformatics, we dissect the interplay between the DNA-binding domain of Engrailed, a Drosophila TF, and the regulatory regions of its target genes. We find that Engrailed binding affinity is strongly amplified by the DNA regions flanking the recognition site, which contain long tracts of degenerate recognition-site repeats. Such DNA organization operates as an antenna that attracts TF molecules in a promiscuous exchange among myriads of intermediate affinity binding sites. The antenna ensures a local TF supply, enables gene tracking and fine control of the target site's basal occupancy. This mechanism illuminates puzzling gene expression data and suggests novel engineering strategies to control gene expression.
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Affiliation(s)
- Milagros Castellanos
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain.,Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Nivin Mothi
- Department of Bioengineering, School of Engineering, University of California, 95343, Merced, CA, USA
| | - Victor Muñoz
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain. .,Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain. .,Department of Bioengineering, School of Engineering, University of California, 95343, Merced, CA, USA.
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35
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Bell K, Skier K, Chen KH, Gergen JP. Two pair-rule responsive enhancers regulate wingless transcription in the Drosophila blastoderm embryo. Dev Dyn 2019; 249:556-572. [PMID: 31837063 DOI: 10.1002/dvdy.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND While many developmentally relevant enhancers act in a modular fashion, there is growing evidence for nonadditive interactions between distinct cis-regulatory enhancers. We investigated if nonautonomous enhancer interactions underlie transcription regulation of the Drosophila segment polarity gene, wingless. RESULTS We identified two wg enhancers active at the blastoderm stage: wg 3613u, located from -3.6 to -1.3 kb upstream of the wg transcription start site (TSS) and 3046d, located in intron two of the wg gene, from 3.0 to 4.6 kb downstream of the TSS. Genetic experiments confirm that Even Skipped (Eve), Fushi-tarazu (Ftz), Runt, Odd-paired (Opa), Odd-skipped (Odd), and Paired (Prd) contribute to spatially regulated wg expression. Interestingly, there are enhancer specific differences in response to the gain or loss of function of pair-rule gene activity. Although each element recapitulates aspects of wg expression, a composite reporter containing both enhancers more faithfully recapitulates wg regulation than would be predicted from the sum of their individual responses. CONCLUSION These results suggest that the regulation of wg by pair-rule genes involves nonadditive interactions between distinct cis-regulatory enhancers.
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Affiliation(s)
- Kimberly Bell
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
- Center for Excellence in Learning & Teaching, Stony Brook University, Stony Brook, New York
| | - Kevin Skier
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kevin H Chen
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
- Boston University School of Medicine, Boston, Massachusetts
| | - John Peter Gergen
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
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36
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Mahmud AKMF, Yang D, Stenberg P, Ioshikhes I, Nandi S. Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules. J Comput Biol 2019; 27:1313-1328. [PMID: 31855461 DOI: 10.1089/cmb.2018.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple transcription factors (TFs) bind to specific sites in the genome and interact among themselves to form the cis-regulatory modules (CRMs). They are essential in modulating the expression of genes, and it is important to study this interplay to understand gene regulation. In the present study, we integrated experimentally identified TF binding sites collected from published studies with computationally predicted TF binding sites to identify Drosophila CRMs. Along with the detection of the previously known CRMs, this approach identified novel protein combinations. We determined high-occupancy target sites, where a large number of TFs bind. Investigating these sites revealed that Giant, Dichaete, and Knirp are highly enriched in these locations. A common TAG team motif was observed at these sites, which might play a role in recruiting other TFs. While comparing the binding sites at distal and proximal promoters, we found that certain regulatory TFs, such as Zelda, were highly enriched in enhancers. Our study has shown that, from the information available concerning the TF binding sites, the real CRMs could be predicted accurately and efficiently. Although we only may claim co-occurrence of these proteins in this study, it may actually point to their interaction (as known interaction proteins typically co-occur together). Such an integrative approach can, therefore, help us to provide a better understanding of the interplay among the factors, even though further experimental verification is required.
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Affiliation(s)
| | - Doo Yang
- Ottawa Institute of Computational Biology and Bioinformatics (OICBB) and Ottawa Institute of Systems Biology (OISB) and Department of Biochemistry, Microbiology and Immunology (BMI), Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Ilya Ioshikhes
- Ottawa Institute of Computational Biology and Bioinformatics (OICBB) and Ottawa Institute of Systems Biology (OISB) and Department of Biochemistry, Microbiology and Immunology (BMI), Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Soumyadeep Nandi
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Guwahati, India; Amity University Haryana, Gurugram, India
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37
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Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun 2019; 10:4486. [PMID: 31582744 PMCID: PMC6776651 DOI: 10.1038/s41467-019-12211-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.
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Affiliation(s)
- Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anton Goloborodko
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Bryan R Lajoie
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
- Illumina, San Diego, CA, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Maxim Imakaev
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - T Niroshini Senaratne
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mohammed A Hannan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Job Dekker
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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38
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Shir-Shapira H, Sloutskin A, Adato O, Ovadia-Shochat A, Ideses D, Zehavi Y, Kassavetis G, Kadonaga JT, Unger R, Juven-Gershon T. Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PLoS One 2019; 14:e0215695. [PMID: 30998799 PMCID: PMC6472829 DOI: 10.1371/journal.pone.0215695] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/07/2019] [Indexed: 12/21/2022] Open
Abstract
The regulation of transcription initiation is critical for developmental and cellular processes. RNA polymerase II (Pol II) is recruited by the basal transcription machinery to the core promoter where Pol II initiates transcription. The core promoter encompasses the region from -40 to +40 bp relative to the +1 transcription start site (TSS). Core promoters may contain one or more core promoter motifs that confer specific properties to the core promoter, such as the TATA box, initiator (Inr) and motifs that are located downstream of the TSS, namely, motif 10 element (MTE), the downstream core promoter element (DPE) and the Bridge, a bipartite core promoter element. We had previously shown that Caudal, an enhancer-binding homeodomain transcription factor and a key regulator of the Hox gene network, is a DPE-specific activator. Interestingly, pair-rule proteins have been implicated in enhancer-promoter communication at the engrailed locus. Fushi tarazu (Ftz) is an enhancer-binding homeodomain transcription factor encoded by the ftz pair-rule gene. Ftz works in concert with its co-factor, Ftz-F1, to activate transcription. Here, we examined whether Ftz and Ftz-F1 activate transcription with a preference for a specific core promoter motif. Our analysis revealed that similarly to Caudal, Ftz and Ftz-F1 activate the promoter containing a TATA box mutation to significantly higher levels than the promoter containing a DPE mutation, thus demonstrating a preference for the DPE motif. We further discovered that Ftz target genes are enriched for a combination of functional downstream core promoter elements that are conserved among Drosophila species. Thus, the unique combination (Inr, Bridge and DPE) of functional downstream core promoter elements within Ftz target genes highlights the complexity of transcriptional regulation via the core promoter in the transcription of different developmental gene regulatory networks.
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Affiliation(s)
- Hila Shir-Shapira
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Anna Sloutskin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orit Adato
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avital Ovadia-Shochat
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yonathan Zehavi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - George Kassavetis
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - James T. Kadonaga
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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39
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Bozek M, Cortini R, Storti AE, Unnerstall U, Gaul U, Gompel N. ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Res 2019; 29:771-783. [PMID: 30962180 PMCID: PMC6499308 DOI: 10.1101/gr.242362.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization is not well understood. We profiled chromatin accessibility with ATAC-seq in narrow, genetically tagged domains along the antero-posterior axis in the Drosophila blastoderm. We demonstrate that one-quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable intervals, and their accessibility changes correlate with their regulatory activity. In an embryonic domain where an enhancer receives a net activating TF input and promotes transcription, it displays elevated accessibility in comparison to a domain where it receives a net repressive input. We propose that differential accessibility is a signature of patterning cis-regulatory elements in the Drosophila blastoderm and discuss potential mechanisms by which accessibility of enhancers may be modulated by activator and repressor TFs.
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Affiliation(s)
- Marta Bozek
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Roberto Cortini
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Andrea Ennio Storti
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Ulrich Unnerstall
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Ulrike Gaul
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Nicolas Gompel
- Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, 82152 Planegg-Martinsried, Germany
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40
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Li K, Baker NE. Transcriptional and post-transcriptional regulation of extra macrochaetae during Drosophila adult peripheral neurogenesis. Dev Biol 2019; 449:41-51. [PMID: 30771303 DOI: 10.1016/j.ydbio.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 11/18/2022]
Abstract
Regulation of the Drosophila ID protein Extra macrochaetae (Emc) is important because reduced Emc levels have been proposed to favor proneural gene activity and thereby define a prepattern for neurogenesis. Recent studies suggest a major role for post-translational control of Emc levels. To further define the mechanisms of Emc regulation, we identified two redundant cis-regulatory regions by germline transformation-rescue experiments that make use of new molecularly-defined emc mutants. We distinguished the mechanisms by which Daughterless (Da) regulated Emc expression, finding post-translational regulation in most tissues, and additional transcriptional regulation in the eye imaginal disc posterior to the morphogenetic furrow. Dpp and Hh signaling pathways repressed Emc transcriptionally and post-translationally within the morphogenetic furrow of the eye disc, whereas Wg signaling repressed Emc expression at the anterior margin of the wing imaginal disc. Although the emc 3' UTR is potentially regulatory, no effect of miRNA pathways on Emc protein levels was discernible. Our work supports recent evidence that post-transcriptional mechanisms contribute more to regulation of Emc protein levels than transcriptional mechanisms do.
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Affiliation(s)
- Ke Li
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx NY 10461, USA
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx NY 10461, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx NY 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx NY 10461, USA.
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41
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Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Nagoya-shi) 2019; 63:43-51. [PMID: 30739944 DOI: 10.1134/s0006350918010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene regulatory networks control the complex programs that drive development. Deciphering the connections between transcription factors (TFs) and target genes is challenging, in part because TFs bind to thousands of places in the genome but control expression through a subset of these binding events. We hypothesize that we can combine natural variation of expression levels and predictions of TF binding sites to identify TF targets. We gather RNA-seq data from 71 genetically distinct F1 Drosophila melanogaster embryos and calculate the correlations between TF and potential target genes' expression levels, which we call "regulatory strength." To separate direct and indirect TF targets, we hypothesize that direct TF targets will have a preponderance of binding sites in their upstream regions. Using 14 TFs active during embryogenesis, we find that 12 TFs showed a significant correlation between their binding strength and regulatory strength on downstream targets, and 10 TFs showed a significant correlation between the number of binding sites and the regulatory effect on target genes. The general roles, e.g. bicoid's role as an activator, and the particular interactions we observed between our TFs, e.g. twist's role as a repressor of sloppy paired and odd paired, generally coincide with the literature.
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Affiliation(s)
- Noha M Osman
- University of Southern California, Los Angeles, CA.,National Research Centre, Dokki, Giza, Egypt
| | | | - Srna Vlaho
- University of Southern California, Los Angeles, CA
| | | | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA.,Saint Petersburg Polytechnical University, St Petersburg, Russia
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42
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Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. Proc Natl Acad Sci U S A 2018; 116:900-908. [PMID: 30598455 PMCID: PMC6338827 DOI: 10.1073/pnas.1808833115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Identifying functional enhancer elements in metazoan systems is a major challenge. Large-scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least 70%. We used the pregrastrula-patterning network of Drosophila melanogaster to demonstrate that loss in accuracy in held-out data results from heterogeneity of functional signatures in enhancer elements. We show that at least two classes of enhancers are active during early Drosophila embryogenesis and that by focusing on a single, relatively homogeneous class of elements, greater than 98% prediction accuracy can be achieved in a balanced, completely held-out test set. The class of well-predicted elements is composed predominantly of enhancers driving multistage segmentation patterns, which we designate segmentation driving enhancers (SDE). Prediction is driven by the DNA occupancy of early developmental transcription factors, with almost no additional power derived from histone modifications. We further show that improved accuracy is not a property of a particular prediction method: after conditioning on the SDE set, naïve Bayes and logistic regression perform as well as more sophisticated tools. Applying this method to a genome-wide scan, we predict 1,640 SDEs that cover 1.6% of the genome. An analysis of 32 SDEs using whole-mount embryonic imaging of stably integrated reporter constructs chosen throughout our prediction rank-list showed >90% drove expression patterns. We achieved 86.7% precision on a genome-wide scan, with an estimated recall of at least 98%, indicating high accuracy and completeness in annotating this class of functional elements.
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43
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Luo X, Wei Y. Nonparametric Bayesian learning of heterogeneous dynamic transcription factor networks. Ann Appl Stat 2018. [DOI: 10.1214/17-aoas1129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Res 2018; 28:1272-1284. [PMID: 30097539 PMCID: PMC6120625 DOI: 10.1101/gr.233346.117] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/05/2018] [Indexed: 12/22/2022]
Abstract
Glucocorticoids are potent steroid hormones that regulate immunity and metabolism by activating the transcription factor (TF) activity of glucocorticoid receptor (GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibility predetermine GR binding and activity. However, there are vast excesses of both features relative to the number of GR binding sites. Thus, these features alone are unlikely to account for the specificity of GR binding and activity. To identify genomic and epigenetic contributions to GR binding specificity and the downstream changes resultant from GR binding, we performed hundreds of genome-wide measurements of TF binding, epigenetic state, and gene expression across a 12-h time course of glucocorticoid exposure. We found that glucocorticoid treatment induces GR to bind to nearly all pre-established enhancers within minutes. However, GR binds to only a small fraction of the set of accessible sites that lack enhancer marks. Once GR is bound to enhancers, a combination of enhancer motif composition and interactions between enhancers then determines the strength and persistence of GR binding, which consequently correlates with dramatic shifts in enhancer activation. Over the course of several hours, highly coordinated changes in TF binding and histone modification occupancy occur specifically within enhancers, and these changes correlate with changes in the expression of nearby genes. Following GR binding, changes in the binding of other TFs precede changes in chromatin accessibility, suggesting that other TFs are also sensitive to genomic features beyond that of accessibility.
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Affiliation(s)
- Ian C McDowell
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Alejandro Barrera
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Anthony M D'Ippolito
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Christopher M Vockley
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Linda K Hong
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Sarah M Leichter
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Luke C Bartelt
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - William H Majoros
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - D Dewran Koçak
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Alexander J Hartemink
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Computer Science, Duke University, Durham, North Carolina 27708, USA.,Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Gregory E Crawford
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
| | - Barbara E Engelhardt
- Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.,Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey 08540, USA
| | - Timothy E Reddy
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
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45
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Clark E, Peel AD. Evidence for the temporal regulation of insect segmentation by a conserved sequence of transcription factors. Development 2018; 145:dev.155580. [PMID: 29724758 PMCID: PMC6001374 DOI: 10.1242/dev.155580] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 04/25/2018] [Indexed: 01/20/2023]
Abstract
Long-germ insects, such as the fruit fly Drosophila melanogaster, pattern their segments simultaneously, whereas short-germ insects, such as the beetle Tribolium castaneum, pattern their segments sequentially, from anterior to posterior. While the two modes of segmentation at first appear quite distinct, much of this difference might simply reflect developmental heterochrony. We now show here that, in both Drosophila and Tribolium, segment patterning occurs within a common framework of sequential Caudal, Dichaete, and Odd-paired expression. In Drosophila these transcription factors are expressed like simple timers within the blastoderm, while in Tribolium they form wavefronts that sweep from anterior to posterior across the germband. In Drosophila, all three are known to regulate pair-rule gene expression and influence the temporal progression of segmentation. We propose that these regulatory roles are conserved in short-germ embryos, and that therefore the changing expression profiles of these genes across insects provide a mechanistic explanation for observed differences in the timing of segmentation. In support of this hypothesis we demonstrate that Odd-paired is essential for segmentation in Tribolium, contrary to previous reports.
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Affiliation(s)
- Erik Clark
- Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, UK
| | - Andrew D Peel
- Faculty of Biological Sciences, University of Leeds, UK
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Haines JE, Eisen MB. Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo. PLoS Genet 2018; 14:e1007367. [PMID: 29727464 PMCID: PMC5955596 DOI: 10.1371/journal.pgen.1007367] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 05/16/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of open chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear how regions of activity are established during early embryogenesis, and if they are the product of spatially restricted or ubiquitous processes. To shed light on this question, we probed chromatin accessibility across the anterior-posterior axis (A-P) of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is highly similar between the two halves, with regions that manifest significant accessibility in one half of the embryo almost always accessible in the other half, even for promoters that are active in exclusively one half of the embryo. These data support previous studies that show that chromatin accessibility is not a direct result of activity, and point to a role for ubiquitous factors or processes in establishing chromatin accessibility at promoters in the early embryo. However, in concordance with similar works, we find that at enhancers active exclusively in one half of the embryo, we observe a significant skew towards greater accessibility in the region of their activity, highlighting the role of patterning factors such as Bicoid in this process.
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Affiliation(s)
- Jenna E. Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States of America
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47
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Cornwell M, Vangala M, Taing L, Herbert Z, Köster J, Li B, Sun H, Li T, Zhang J, Qiu X, Pun M, Jeselsohn R, Brown M, Liu XS, Long HW. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics 2018; 19:135. [PMID: 29649993 PMCID: PMC5897949 DOI: 10.1186/s12859-018-2139-9] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/26/2018] [Indexed: 02/05/2023] Open
Abstract
Background RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Results Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. Conclusions VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion. Electronic supplementary material The online version of this article (10.1186/s12859-018-2139-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- MacIntosh Cornwell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Mahesh Vangala
- University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Zachary Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Johannes Köster
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Institute of Human Genetics, University of Duisburg-Essen, Essen, Germany
| | - Bo Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA
| | - Hanfei Sun
- Department of Bioinformatics, School of Life Sciences, Tongji University, Shanghai, 200092, China
| | - Taiwen Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jian Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Matthew Pun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - X Shirley Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, 02215, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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Torres-Oliva M, Schneider J, Wiegleb G, Kaufholz F, Posnien N. Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PLoS Genet 2018; 14:e1007180. [PMID: 29360820 PMCID: PMC5796731 DOI: 10.1371/journal.pgen.1007180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 02/02/2018] [Accepted: 01/01/2018] [Indexed: 01/01/2023] Open
Abstract
Drosophila melanogaster head development represents a valuable process to study the developmental control of various organs, such as the antennae, the dorsal ocelli and the compound eyes from a common precursor, the eye-antennal imaginal disc. While the gene regulatory network underlying compound eye development has been extensively studied, the key transcription factors regulating the formation of other head structures from the same imaginal disc are largely unknown. We obtained the developmental transcriptome of the eye-antennal discs covering late patterning processes at the late 2nd larval instar stage to the onset and progression of differentiation at the end of larval development. We revealed the expression profiles of all genes expressed during eye-antennal disc development and we determined temporally co-expressed genes by hierarchical clustering. Since co-expressed genes may be regulated by common transcriptional regulators, we combined our transcriptome dataset with publicly available ChIP-seq data to identify central transcription factors that co-regulate genes during head development. Besides the identification of already known and well-described transcription factors, we show that the transcription factor Hunchback (Hb) regulates a significant number of genes that are expressed during late differentiation stages. We confirm that hb is expressed in two polyploid subperineurial glia cells (carpet cells) and a thorough functional analysis shows that loss of Hb function results in a loss of carpet cells in the eye-antennal disc. Additionally, we provide for the first time functional data indicating that carpet cells are an integral part of the blood-brain barrier. Eventually, we combined our expression data with a de novo Hb motif search to reveal stage specific putative target genes of which we find a significant number indeed expressed in carpet cells. The development of different cell types must be tightly coordinated, and the eye-antennal imaginal discs of Drosophila melanogaster represent an excellent model to study the molecular mechanisms underlying this coordination. These imaginal discs contain the anlagen of nearly all adult head structures, such as the antennae, the head cuticle, the ocelli and the compound eyes. While large scale screens have been performed to unravel the gene regulatory network underlying compound eye development, a comprehensive understanding of genome wide expression dynamics throughout head development is still missing to date. We studied the genome wide gene expression dynamics during eye-antennal disc development in D. melanogaster to identify new central regulators of the underlying gene regulatory network. Expression based gene clustering and transcription factor motif enrichment analyses revealed a central regulatory role of the transcription factor Hunchback (Hb). We confirmed that hb is expressed in two polyploid retinal subperineurial glia cells (carpet cells). Our functional analysis shows that Hb is necessary for carpet cell development and we show for the first time that the carpet cells are an integral part of the blood-brain barrier.
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Affiliation(s)
- Montserrat Torres-Oliva
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Julia Schneider
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Gordon Wiegleb
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Felix Kaufholz
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Nico Posnien
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
- * E-mail:
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49
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Abstract
We developed a predictive, stable, and interpretable tool: the iterative random forest algorithm (iRF). iRF discovers high-order interactions among biomolecules with the same order of computational cost as random forests. We demonstrate the efficacy of iRF by finding known and promising interactions among biomolecules, of up to fifth and sixth order, in two data examples in transcriptional regulation and alternative splicing. Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building on random forests (RFs) and random intersection trees (RITs) and through extensive, biologically inspired simulations, we developed the iterative random forest algorithm (iRF). iRF trains a feature-weighted ensemble of decision trees to detect stable, high-order interactions with the same order of computational cost as the RF. We demonstrate the utility of iRF for high-order interaction discovery in two prediction problems: enhancer activity in the early Drosophila embryo and alternative splicing of primary transcripts in human-derived cell lines. In Drosophila, among the 20 pairwise transcription factor interactions iRF identifies as stable (returned in more than half of bootstrap replicates), 80% have been previously reported as physical interactions. Moreover, third-order interactions, e.g., between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order relationships that are candidates for follow-up experiments. In human-derived cells, iRF rediscovered a central role of H3K36me3 in chromatin-mediated splicing regulation and identified interesting fifth- and sixth-order interactions, indicative of multivalent nucleosomes with specific roles in splicing regulation. By decoupling the order of interactions from the computational cost of identification, iRF opens additional avenues of inquiry into the molecular mechanisms underlying genome biology.
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50
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Wang X, Lin P, Ho JWK. Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest. BMC Genomics 2018; 19:929. [PMID: 29363433 PMCID: PMC5780765 DOI: 10.1186/s12864-017-4340-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background It has been observed that many transcription factors (TFs) can bind to different genomic loci depending on the cell type in which a TF is expressed in, even though the individual TF usually binds to the same core motif in different cell types. How a TF can bind to the genome in such a highly cell-type specific manner, is a critical research question. One hypothesis is that a TF requires co-binding of different TFs in different cell types. If this is the case, it may be possible to observe different combinations of TF motifs – a motif grammar – located at the TF binding sites in different cell types. In this study, we develop a bioinformatics method to systematically identify DNA motifs in TF binding sites across multiple cell types based on published ChIP-seq data, and address two questions: (1) can we build a machine learning classifier to predict cell-type specificity based on motif combinations alone, and (2) can we extract meaningful cell-type specific motif grammars from this classifier model. Results We present a Random Forest (RF) based approach to build a multi-class classifier to predict the cell-type specificity of a TF binding site given its motif content. We applied this RF classifier to two published ChIP-seq datasets of TF (TCF7L2 and MAX) across multiple cell types. Using cross-validation, we show that motif combinations alone are indeed predictive of cell types. Furthermore, we present a rule mining approach to extract the most discriminatory rules in the RF classifier, thus allowing us to discover the underlying cell-type specific motif grammar. Conclusions Our bioinformatics analysis supports the hypothesis that combinatorial TF motif patterns are cell-type specific. Electronic supplementary material The online version of this article (10.1186/s12864-017-4340-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Wang
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Peijie Lin
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia. .,St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia.
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