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Leung AKY, Yao L, Yu H. Functional genomic assays to annotate enhancer-promoter interactions genome wide. Hum Mol Genet 2022; 31:R97-R104. [PMID: 36018818 PMCID: PMC9585677 DOI: 10.1093/hmg/ddac204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/14/2022] Open
Abstract
Enhancers are pivotal for regulating gene transcription that occurs at promoters. Identification of the interacting enhancer-promoter pairs and understanding the mechanisms behind how they interact and how enhancers modulate transcription can provide fundamental insight into gene regulatory networks. Recently, advances in high-throughput methods in three major areas-chromosome conformation capture assay, such as Hi-C to study basic chromatin architecture, ectopic reporter experiments such as self-transcribing active regulatory region sequencing (STARR-seq) to quantify promoter and enhancer activity, and endogenous perturbations such as clustered regularly interspaced short palindromic repeat interference (CRISPRi) to identify enhancer-promoter compatibility-have further our knowledge about transcription. In this review, we will discuss the major method developments and key findings from these assays.
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Affiliation(s)
- Alden King-Yung Leung
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Genomics and Proteomics Technology Development (CGPT), Cornell University, Ithaca NY 14853, USA
| | - Li Yao
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Genomics and Proteomics Technology Development (CGPT), Cornell University, Ithaca NY 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
- Center for Genomics and Proteomics Technology Development (CGPT), Cornell University, Ithaca NY 14853, USA
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52
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Kim K, Orvis J, Stolfi A. Pax3/7 regulates neural tube closure and patterning in a non-vertebrate chordate. Front Cell Dev Biol 2022; 10:999511. [PMID: 36172287 PMCID: PMC9511217 DOI: 10.3389/fcell.2022.999511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Pax3/7 factors play numerous roles in the development of the dorsal nervous system of vertebrates. From specifying neural crest at the neural plate borders, to regulating neural tube closure and patterning of the resulting neural tube. However, it is unclear which of these roles are conserved in non-vertebrate chordates. Here we investigate the expression and function of Pax3/7 in the model tunicate Ciona. Pax3/7 is expressed in neural plate border cells during neurulation, and in central nervous system progenitors shortly after neural tube closure. We find that separate cis-regulatory elements control the expression in these two distinct lineages. Using CRISPR/Cas9-mediated mutagenesis, we knocked out Pax3/7 in F0 embryos specifically in these two separate territories. Pax3/7 knockout in the neural plate borders resulted in neural tube closure defects, suggesting an ancient role for Pax3/7 in this chordate-specific process. Furthermore, knocking out Pax3/7 in the neural impaired Motor Ganglion neuron specification, confirming a conserved role for this gene in patterning the neural tube as well. Taken together, these results suggests that key functions of Pax3/7 in neural tube development are evolutionarily ancient, dating back at least to the last common ancestor of vertebrates and tunicates.
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53
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Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis. Commun Biol 2022; 5:876. [PMID: 36028576 PMCID: PMC9418141 DOI: 10.1038/s42003-022-03831-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/10/2022] [Indexed: 02/01/2023] Open
Abstract
Most human genes are co-expressed with a nearby gene. Previous studies have revealed this local gene co-expression to be widespread across chromosomes and across dozens of tissues. Yet, so far these studies used bulk RNA-seq, averaging gene expression measurements across millions of cells, thus being unclear if this co-expression stems from transcription events in single cells. Here, we leverage single cell datasets in >85 individuals to identify gene co-expression across cells, unbiased by cell-type heterogeneity and benefiting from the co-occurrence of transcription events in single cells. We discover >3800 co-expressed gene pairs in two human cell types, induced pluripotent stem cells (iPSCs) and lymphoblastoid cell lines (LCLs) and (i) compare single cell to bulk RNA-seq in identifying local gene co-expression, (ii) show that many co-expressed genes – but not the majority – are composed of functionally related genes and (iii) using proteomics data, provide evidence that their co-expression is maintained up to the protein level. Finally, using single cell RNA-sequencing (scRNA-seq) and single cell ATAC-sequencing (scATAC-seq) data for the same single cells, we identify gene-enhancer associations and reveal that >95% of co-expressed gene pairs share regulatory elements. These results elucidate the potential reasons for co-expression in single cell gene regulatory networks and warrant a deeper study of shared regulatory elements, in view of explaining disease comorbidity due to affecting several genes. Our in-depth view of local gene co-expression and regulatory element co-activity advances our understanding of the shared regulatory architecture between genes. Using single-cell data from cell lines, the co-expression of genes and co-activity of regulatory elements is analyzed, providing insight into shared architecture and regulation between genes.
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54
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Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022; 138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is an emblematic population of embryonic stem-like cells with remarkable migratory ability. These distinctive attributes have inspired the curiosity of developmental biologists for over 150 years, however only recently the regulatory mechanisms controlling the complex features of the NC have started to become elucidated at genomic scales. Regulatory control of NC development is achieved through combinatorial transcription factor binding and recruitment of associated transcriptional complexes to distal cis-regulatory elements. Together, they regulate when, where and to what extent transcriptional programmes are actively deployed, ultimately shaping ontogenetic processes. Here, we discuss how transcriptional networks control NC ontogeny, with a special emphasis on the molecular mechanisms underlying specification of the cephalic NC. We also cover emerging properties of transcriptional regulation revealed in diverse developmental systems, such as the role of three-dimensional conformation of chromatin, and how they are involved in the regulation of NC ontogeny. Finally, we highlight how advances in deciphering the NC transcriptional network have afforded new insights into the molecular basis of human diseases.
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Affiliation(s)
- Ivan L Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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55
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Espíndola-Hernández P, Mueller JC, Kempenaers B. Genomic signatures of the evolution of a diurnal lifestyle in Strigiformes. G3 GENES|GENOMES|GENETICS 2022; 12:6595023. [PMID: 35640557 PMCID: PMC9339318 DOI: 10.1093/g3journal/jkac135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
Abstract
Understanding the targets of selection associated with changes in behavioral traits represents an important challenge of current evolutionary research. Owls (Strigiformes) are a diverse group of birds, most of which are considered nocturnal raptors. However, a few owl species independently adopted a diurnal lifestyle in their recent evolutionary history. We searched for signals of accelerated rates of evolution associated with a diurnal lifestyle using a genome-wide comparative approach. We estimated substitution rates in coding and noncoding conserved regions of the genome of seven owl species, including three diurnal species. Substitution rates of the noncoding elements were more accelerated than those of protein-coding genes. We identified new, owl-specific conserved noncoding elements as candidates of parallel evolution during the emergence of diurnality in owls. Our results shed light on the molecular basis of adaptation to a new niche and highlight the importance of regulatory elements for evolutionary changes in behavior. These elements were often involved in the neuronal development of the brain.
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Affiliation(s)
- Pamela Espíndola-Hernández
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology , 82319 Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology , 82319 Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology , 82319 Seewiesen, Germany
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56
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Farfán-Pira KJ, Martínez-Cuevas TI, Reyes R, Evans TA, Nahmad M. The vestigial Quadrant Enhancer is dispensable for pattern formation and development of the Drosophila wing. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000585. [PMID: 35783575 PMCID: PMC9242444 DOI: 10.17912/micropub.biology.000585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/06/2022]
Abstract
In Drosophila , the pattern of the wing selector gene, vestigial ( vg ), is established by at least two enhancers: the Boundary Enhancer, which drives expression along the disc's Dorsal-Ventral boundary; and the Quadrant Enhancer (QE) that patterns the rest of the wing pouch. Using CRISPR/Cas9 editing, we deleted DNA fragments around the reported QE sequence and found that the full Vg pattern is formed. Furthermore, adult wings arising from these gene-edited animals are normal in shape and pattern, but slightly smaller in size, although this reduction is not wing-specific in males. We suggest that other enhancers act redundantly to establish the vg pattern and rescue wing development.
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Affiliation(s)
- Keity J Farfán-Pira
- Department of Physiology, Biophysics, and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN)
| | - Teresa I Martínez-Cuevas
- Department of Physiology, Biophysics, and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN)
| | - Rosalio Reyes
- Department of Physiology, Biophysics, and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN)
| | | | - Marcos Nahmad
- Department of Physiology, Biophysics, and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN)
,
Correspondence to: Marcos Nahmad (
)
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57
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Mulero Hernández J, Fernández-Breis JT. Analysis of the landscape of human enhancer sequences in biological databases. Comput Struct Biotechnol J 2022; 20:2728-2744. [PMID: 35685360 PMCID: PMC9168495 DOI: 10.1016/j.csbj.2022.05.045] [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: 03/28/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/01/2022] Open
Abstract
The process of gene regulation extends as a network in which both genetic sequences and proteins are involved. The levels of regulation and the mechanisms involved are multiple. Transcription is the main control mechanism for most genes, being the downstream steps responsible for refining the transcription patterns. In turn, gene transcription is mainly controlled by regulatory events that occur at promoters and enhancers. Several studies are focused on analyzing the contribution of enhancers in the development of diseases and their possible use as therapeutic targets. The study of regulatory elements has advanced rapidly in recent years with the development and use of next generation sequencing techniques. All this information has generated a large volume of information that has been transferred to a growing number of public repositories that store this information. In this article, we analyze the content of those public repositories that contain information about human enhancers with the aim of detecting whether the knowledge generated by scientific research is contained in those databases in a way that could be computationally exploited. The analysis will be based on three main aspects identified in the literature: types of enhancers, type of evidence about the enhancers, and methods for detecting enhancer-promoter interactions. Our results show that no single database facilitates the optimal exploitation of enhancer data, most types of enhancers are not represented in the databases and there is need for a standardized model for enhancers. We have identified major gaps and challenges for the computational exploitation of enhancer data.
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Affiliation(s)
- Juan Mulero Hernández
- Dept. Informática y Sistemas, Universidad de Murcia, CEIR Campus Mare Nostrum, IMIB-Arrixaca, Spain
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58
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Perkins ML, Gandara L, Crocker J. A synthetic synthesis to explore animal evolution and development. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200517. [PMID: 35634925 PMCID: PMC9149795 DOI: 10.1098/rstb.2020.0517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identifying the general principles by which genotypes are converted into phenotypes remains a challenge in the post-genomic era. We still lack a predictive understanding of how genes shape interactions among cells and tissues in response to signalling and environmental cues, and hence how regulatory networks generate the phenotypic variation required for adaptive evolution. Here, we discuss how techniques borrowed from synthetic biology may facilitate a systematic exploration of evolvability across biological scales. Synthetic approaches permit controlled manipulation of both endogenous and fully engineered systems, providing a flexible platform for investigating causal mechanisms in vivo. Combining synthetic approaches with multi-level phenotyping (phenomics) will supply a detailed, quantitative characterization of how internal and external stimuli shape the morphology and behaviour of living organisms. We advocate integrating high-throughput experimental data with mathematical and computational techniques from a variety of disciplines in order to pursue a comprehensive theory of evolution. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin Crocker
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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59
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Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish. Nat Genet 2022; 54:684-693. [PMID: 35551306 DOI: 10.1038/s41588-022-01049-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Cis-regulatory changes are key drivers of adaptative evolution. However, their contribution to the metabolic adaptation of organisms is not well understood. Here, we used a unique vertebrate model, Astyanax mexicanus-different morphotypes of which survive in nutrient-rich surface and nutrient-deprived cave waters-to uncover gene regulatory networks underlying metabolic adaptation. We performed genome-wide epigenetic profiling in the liver tissues of Astyanax and found that many of the identified cis-regulatory elements (CREs) have genetically diverged and have differential chromatin features between surface and cave morphotypes, while retaining remarkably similar regulatory signatures between independently derived cave populations. One such CRE in the hpdb gene harbors a genomic deletion in cavefish that abolishes IRF2 repressor binding and derepresses enhancer activity in reporter assays. Selection of this mutation in multiple independent cave populations supports its importance in cave adaptation, and provides novel molecular insights into the evolutionary trade-off between loss of pigmentation and adaptation to food-deprived caves.
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60
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Murray JI, Preston E, Crawford JP, Rumley JD, Amom P, Anderson BD, Sivaramakrishnan P, Patel SD, Bennett BA, Lavon TD, Hsiao E, Peng F, Zacharias AL. The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo. PLoS Genet 2022; 18:e1010187. [PMID: 35500030 PMCID: PMC9098060 DOI: 10.1371/journal.pgen.1010187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 05/12/2022] [Accepted: 04/04/2022] [Indexed: 12/18/2022] Open
Abstract
Hox transcription factors play a conserved role in specifying positional identity during animal development, with posterior Hox genes typically repressing the expression of more anterior Hox genes. Here, we dissect the regulation of the posterior Hox genes nob-1 and php-3 in the nematode C. elegans. We show that nob-1 and php-3 are co-expressed in gastrulation-stage embryos in cells that previously expressed the anterior Hox gene ceh-13. This expression is controlled by several partially redundant transcriptional enhancers. These enhancers act in a ceh-13-dependant manner, providing a striking example of an anterior Hox gene positively regulating a posterior Hox gene. Several other regulators also act positively through nob-1/php-3 enhancers, including elt-1/GATA, ceh-20/ceh-40/Pbx, unc-62/Meis, pop-1/TCF, ceh-36/Otx, and unc-30/Pitx. We identified defects in both cell position and cell division patterns in ceh-13 and nob-1;php-3 mutants, suggesting that these factors regulate lineage identity in addition to positional identity. Together, our results highlight the complexity and flexibility of Hox gene regulation and function and the ability of developmental transcription factors to regulate different targets in different stages of development.
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Affiliation(s)
- John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elicia Preston
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jeremy P. Crawford
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jonathan D. Rumley
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Prativa Amom
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Breana D. Anderson
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shaili D. Patel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barrington Alexander Bennett
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Teddy D. Lavon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erin Hsiao
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amanda L. Zacharias
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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61
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Tsaryk R, Yucel N, Leonard EV, Diaz N, Bondareva O, Odenthal-Schnittler M, Arany Z, Vaquerizas JM, Schnittler H, Siekmann AF. Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites. Sci Rep 2022; 12:4795. [PMID: 35314737 PMCID: PMC8938417 DOI: 10.1038/s41598-022-08645-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Endothelial cells (ECs) lining blood vessels are exposed to mechanical forces, such as shear stress. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation. Despite a good understanding of the genes responding to shear stress, our insight into the transcriptional regulation of these genes is much more limited. Here, we set out to study alterations in the chromatin landscape of human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress. To do so, we performed ChIP-Seq for H3K27 acetylation, indicative of active enhancer elements and ATAC-Seq to mark regions of open chromatin in addition to RNA-Seq on HUVEC exposed to 6 h of laminar shear stress. Our results show a correlation of gained and lost enhancers with up and downregulated genes, respectively. DNA motif analysis revealed an over-representation of KLF transcription factor (TF) binding sites in gained enhancers, while lost enhancers contained more ETV/ETS motifs. We validated a subset of flow responsive enhancers using luciferase-based reporter constructs and CRISPR-Cas9 mediated genome editing. Lastly, we characterized the shear stress response in ECs of zebrafish embryos using RNA-Seq. Our results lay the groundwork for the exploration of shear stress responsive elements in controlling EC biology.
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Affiliation(s)
- Roman Tsaryk
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nora Yucel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Elvin V Leonard
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Noelia Diaz
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Olga Bondareva
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, 04103, Leipzig, Germany
| | - Maria Odenthal-Schnittler
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Institute of Neuropathology, Westfälische Wilhelms-Universität Münster, Pottkamp 2, 48149, Münster, Germany
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Hans Schnittler
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
- Institute of Anatomy and Vascular Biology, Faculty of Medicine, Westfälische Wilhelms-Universität Münster, Vesaliusweg 2-4, 48149, Münster, Germany
- Institute of Neuropathology, Westfälische Wilhelms-Universität Münster, Pottkamp 2, 48149, Münster, Germany
| | - Arndt F Siekmann
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149, Münster, Germany.
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany.
- Department of Cell and Developmental Biology and Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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62
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Bourbon HMG, Benetah MH, Guillou E, Mojica-Vazquez LH, Baanannou A, Bernat-Fabre S, Loubiere V, Bantignies F, Cavalli G, Boube M. A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg. PLoS Genet 2022; 18:e1010083. [PMID: 35294439 PMCID: PMC8959175 DOI: 10.1371/journal.pgen.1010083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/28/2022] [Accepted: 02/07/2022] [Indexed: 11/18/2022] Open
Abstract
Gene duplications and transcriptional enhancer emergence/modifications are thought having greatly contributed to phenotypic innovations during animal evolution. Nevertheless, little is known about how enhancers evolve after gene duplication and how regulatory information is rewired between duplicated genes. The Drosophila melanogaster bric-a-brac (bab) complex, comprising the tandem paralogous genes bab1 and bab2, provides a paradigm to address these issues. We previously characterized an intergenic enhancer (named LAE) regulating bab2 expression in the developing legs. We show here that bab2 regulators binding directly the LAE also govern bab1 expression in tarsal cells. LAE excision by CRISPR/Cas9-mediated genome editing reveals that this enhancer appears involved but not strictly required for bab1 and bab2 co-expression in leg tissues. Instead, the LAE enhancer is critical for paralog-specific bab2 expression along the proximo-distal leg axis. Chromatin features and phenotypic rescue experiments indicate that LAE functions partly redundantly with leg-specific regulatory information overlapping the bab1 transcription unit. Phylogenomics analyses indicate that (i) the bab complex originates from duplication of an ancestral singleton gene early on within the Cyclorrhapha dipteran sublineage, and (ii) LAE sequences have been evolutionarily-fixed early on within the Brachycera suborder thus predating the gene duplication event. This work provides new insights on enhancers, particularly about their emergence, maintenance and functional diversification during evolution.
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Affiliation(s)
- Henri-Marc G. Bourbon
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Mikhail H. Benetah
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Emmanuelle Guillou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Luis Humberto Mojica-Vazquez
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Aissette Baanannou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Sandra Bernat-Fabre
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Vincent Loubiere
- Institute of Human Genetics, University of Montpellier, CNRS Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS Montpellier, France
| | - Muriel Boube
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
- * E-mail:
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63
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Akiyama N, Sato S, Tanaka KM, Sakai T, Takahashi A. The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster. G3 (BETHESDA, MD.) 2022; 12:jkac010. [PMID: 35100378 PMCID: PMC8895987 DOI: 10.1093/g3journal/jkac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/06/2022] [Indexed: 11/15/2022]
Abstract
The spatiotemporal regulation of gene expression is essential to ensure robust phenotypic outcomes. Pigmentation patterns in Drosophila are determined by pigments biosynthesized in the developing epidermis and the cis-regulatory elements of the genes involved in this process are well-characterized. Here, we report that the known primary epidermal enhancer is dispensable for the transcriptional activation of ebony (involved in light-colored pigment synthesis) in the developing epidermis of Drosophila melanogaster. The evidence was obtained by introducing an approximately 1 kbp deletion at the primary epidermal enhancer by genome editing. The effect of the primary epidermal enhancer deletion on pigmentation and on the endogenous expression pattern of a mCherry-fused ebony allele was examined in the abdomen. The expression levels of the mCherry-fused ebony in the primary epidermal enhancer-deleted strains were slightly higher than that of the control strain, indicating that the sequences outside the primary epidermal enhancer have an ability to drive an expression of this gene in the epidermis. Interestingly, the primary epidermal enhancer deletion resulted in a derepression of this gene in the dorsal midline of the abdominal tergites, where dark pigmentation is present in the wild-type individuals. This indicated that the primary epidermal enhancer fragment contains a silencer. Furthermore, the endogenous expression pattern of ebony in the 2 additional strains with partially deleted primary epidermal enhancer revealed that the silencer resides within a 351-bp fragment in the 5' portion of the primary epidermal enhancer. These results demonstrated that deletion assays combined with reporter assays are highly effective in detecting the presence of positively and negatively regulating sequences within and outside the focal cis-regulatory elements.
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Affiliation(s)
- Noriyoshi Akiyama
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Shoma Sato
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Kentaro M Tanaka
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Takaomi Sakai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji 192-0397, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji 192-0397, Japan
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64
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Luecke D, Rice G, Kopp A. Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes. Evol Dev 2022; 24:37-60. [PMID: 35239254 PMCID: PMC9179014 DOI: 10.1111/ede.12398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022]
Abstract
The evolution of gene expression via cis-regulatory changes is well established as a major driver of phenotypic evolution. However, relatively little is known about the influence of enhancer architecture and intergenic interactions on regulatory evolution. We address this question by examining chemosensory system evolution in Drosophila. Drosophila prolongata males show a massively increased number of chemosensory bristles compared to females and males of sibling species. This increase is driven by sex-specific transformation of ancestrally mechanosensory organs. Consistent with this phenotype, the Pox neuro transcription factor (Poxn), which specifies chemosensory bristle identity, shows expanded expression in D. prolongata males. Poxn expression is controlled by nonadditive interactions among widely dispersed enhancers. Although some D. prolongata Poxn enhancers show increased activity, the additive component of this increase is slight, suggesting that most changes in Poxn expression are due to epistatic interactions between Poxn enhancers and trans-regulatory factors. Indeed, the expansion of D. prolongata Poxn enhancer activity is only observed in cells that express doublesex (dsx), the gene that controls sexual differentiation in Drosophila and also shows increased expression in D. prolongata males due to cis-regulatory changes. Although expanded dsx expression may contribute to increased activity of D. prolongata Poxn enhancers, this interaction is not sufficient to explain the full expansion of Poxn expression, suggesting that cis-trans interactions between Poxn, dsx, and additional unknown genes are necessary to produce the derived D. prolongata phenotype. Overall, our results demonstrate the importance of epistatic gene interactions for evolution, particularly when pivotal genes have complex regulatory architecture.
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Affiliation(s)
- David Luecke
- Department of Evolution and Ecology, University of California – Davis,Current Address: Department of Integrative Biology, Michigan State University
| | - Gavin Rice
- Department of Evolution and Ecology, University of California – Davis,Current Address: Department of Biological Sciences, University of Pittsburgh
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California – Davis
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65
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Okada H, Saga Y. Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1. PLoS Genet 2022; 18:e1010000. [PMID: 35025872 PMCID: PMC8791502 DOI: 10.1371/journal.pgen.1010000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/26/2022] [Accepted: 12/17/2021] [Indexed: 11/25/2022] Open
Abstract
Organisms are inherently equipped with buffering systems against genetic perturbations. Genetic compensation, the compensatory response by upregulating another gene or genes, is one such buffering mechanism. Recently, a well-conserved compensatory mechanism was proposed: transcriptional adaptation of homologs under the nonsense-mediated mRNA decay pathways. However, this model cannot explain the onset of all compensatory events. We report a novel genetic compensation mechanism operating over the Mesp gene locus. Mesp1 and Mesp2 are paralogs located adjacently in the genome. Mesp2 loss is partially rescued by Mesp1 upregulation in the presomitic mesoderm (PSM). Using a cultured PSM induction system, we reproduced the compensatory response in vitro and found that the Mesp2-enhancer is required to promote Mesp1. We revealed that the Mesp2-enhancer directly interacts with the Mesp1 promoter, thereby upregulating Mesp1 expression upon the loss of Mesp2. Of note, this interaction is established by genomic arrangement upon PSM development independently of Mesp2 disruption. We propose that the repurposing of this established enhancer-promoter communication is the mechanism underlying this compensatory response for the upregulation of the adjacent gene. Genetic compensation, the compensatory response by upregulating another gene or genes, is one of the inherent mechanisms against gene disruption to confer cellular fitness. However, the regulatory mechanisms are largely unknown. Nonsense-mediated mutant mRNA degradation was recently proposed as a conserved mechanism across species to upregulate homologous genes to compensate for a disrupted gene, but this cannot explain compensation events with no mutant mRNA. This study investigated the compensation mechanism operating over adjacent paralogs, Mesp1 and Mesp2, in the genome. Mesp genes encode essential transcription factors in the presomitic mesoderm for development. In general, an enhancer is considered to activate a target gene when it physically interacts with the target. The communication of the Mesp2-enhancer with the Mesp1 promoter is established upon differentiation of the presomitic mesoderm, but this communication activates Mesp1 only when Mesp2 is disrupted, leading to compensation. We revealed a novel compensation mechanism depending on the repurposing of this enhancer-promoter communication by gene disruption. Our study also provides new insight into transcriptional regulation by providing the concept that an enhancer changes its target even among its physically interacting genes in a context-dependent manner.
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Affiliation(s)
- Hajime Okada
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Yumiko Saga
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advised Studies (SOKENDAI), Mishima, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- * E-mail:
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66
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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67
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Bakoulis S, Krautz R, Alcaraz N, Salvatore M, Andersson R. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2111-2127. [PMID: 35166831 PMCID: PMC8887488 DOI: 10.1093/nar/gkac088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/22/2022] [Accepted: 01/27/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Nicolas Alcaraz
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marco Salvatore
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robin Andersson
- To whom correspondence should be addressed. Tel: +45 35330245;
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68
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Sousa E, Flames N. Transcriptional regulation of neuronal identity. Eur J Neurosci 2021; 55:645-660. [PMID: 34862697 PMCID: PMC9306894 DOI: 10.1111/ejn.15551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Neuronal diversity is an intrinsic feature of the nervous system. Transcription factors (TFs) are key regulators in the establishment of different neuronal identities; how are the actions of different TFs coordinated to orchestrate this diversity? Are there common features shared among the different neuron types of an organism or even among different animal groups? In this review, we provide a brief overview on common traits emerging on the transcriptional regulation of neuron type diversification with a special focus on the comparison between mouse and Caenorhabditis elegans model systems. In the first part, we describe general concepts on neuronal identity and transcriptional regulation of gene expression. In the second part of the review, TFs are classified in different categories according to their key roles at specific steps along the protracted process of neuronal specification and differentiation. The same TF categories can be identified both in mammals and nematodes. Importantly, TFs are very pleiotropic: Depending on the neuron type or the time in development, the same TF can fulfil functions belonging to different categories. Finally, we describe the key role of transcriptional repression at all steps controlling neuronal diversity and propose that acquisition of neuronal identities could be considered a metastable process.
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Affiliation(s)
- Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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69
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Blobel GA, Higgs DR, Mitchell JA, Notani D, Young RA. Testing the super-enhancer concept. Nat Rev Genet 2021; 22:749-755. [PMID: 34480110 DOI: 10.1038/s41576-021-00398-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Gerd A Blobel
- The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
| | - Dimple Notani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
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70
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No Need to Stick Together to Be Connected: Multiple Types of Enhancers' Networking. Cancers (Basel) 2021; 13:cancers13205201. [PMID: 34680347 PMCID: PMC8533737 DOI: 10.3390/cancers13205201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Transcription regulation programs require the functional interaction of distal and proximal regulatory regions, interacting by specific 3D chromatin configurations. Enhancers are cis-acting regulatory elements able to promote gene expression regardless their orientation and distance from the transcription starting site. Their systematic mapping by genome-wide chromatin profiling and chromosome conformation analysis, combined with the development of gene-editing approaches to modulate their function, revealed that many enhancers work together to fine-tune the expression of their target genes. This review aim to describe the functions of different types of enhancers and the modalities of enhancers’ interaction, focusing on their role in the regulation of complex biological processes like cancer development. Abstract The control of gene expression at a transcriptional level requires a widespread landscape of regulatory elements. Central to these regulatory circuits are enhancers (ENHs), which are defined as cis-acting DNA elements able to increase the transcription of a target gene in a distance- and orientation-independent manner. ENHs are not independent functional elements but work in a complex and dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The information from each of these elements converges on the target promoter, contributing to improving the precision and sharpness of gene modulation. ENHs’ interplay varies in its nature and extent, ranging from an additive to redundant effect depending on contexts. Moving from super-enhancers that drive the high expression levels of identity genes, to shadow-enhancers, whose redundant functions contribute to buffering the variation in gene expression, this review aims to describe the different modalities of ENHs’ interaction and their role in the regulation of complex biological processes like cancer development.
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71
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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72
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Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity. Nat Commun 2021; 12:5557. [PMID: 34548488 PMCID: PMC8455560 DOI: 10.1038/s41467-021-25810-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Precise cis-regulatory control of gene expression is essential for normal embryogenesis and tissue development. The BMP antagonist Gremlin1 (Grem1) is a key node in the signalling system that coordinately controls limb bud development. Here, we use mouse reverse genetics to identify the enhancers in the Grem1 genomic landscape and the underlying cis-regulatory logics that orchestrate the spatio-temporal Grem1 expression dynamics during limb bud development. We establish that transcript levels are controlled in an additive manner while spatial regulation requires synergistic interactions among multiple enhancers. Disrupting these interactions shows that altered spatial regulation rather than reduced Grem1 transcript levels prefigures digit fusions and loss. Two of the enhancers are evolutionary ancient and highly conserved from basal fishes to mammals. Analysing these enhancers from different species reveal the substantial spatial plasticity in Grem1 regulation in tetrapods and basal fishes, which provides insights into the fin-to-limb transition and evolutionary diversification of pentadactyl limbs. The BMP antagonist Gremlin1 balances BMP and SHH signalling, endowing limb bud development with robustness. Here, the authors identify enhancers controlling Grem1 levels in an additive, and spatial regulation in a synergistic manner, providing digit patterning with cis-regulatory robustness and evolutionary plasticity.
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73
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Graham PL, Fischer MD, Giri A, Pick L. The fushi tarazu zebra element is not required for Drosophila viability or fertility. G3-GENES GENOMES GENETICS 2021; 11:6358135. [PMID: 34518886 PMCID: PMC8527495 DOI: 10.1093/g3journal/jkab300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022]
Abstract
Expression of genes in precisely controlled spatiotemporal patterns is essential for embryonic development. Much of our understanding of mechanisms regulating gene expression comes from the study of cis-regulatory elements (CREs) that direct expression of reporter genes in transgenic organisms. This reporter-transgene approach identifies genomic regions sufficient to drive expression but fails to provide information about quantitative and qualitative contributions to endogenous expression, although such conclusions are often inferred. Here we evaluated the endogenous function of a classic Drosophila CRE, the fushi tarazu (ftz) zebra element. ftz is a pair-rule segmentation gene expressed in seven stripes during embryogenesis, necessary for formation of alternate body segments. Reporter transgenes identified the promoter-proximal zebra element as a major driver of the seven ftz stripes. We generated a precise genomic deletion of the zebra element (ftzΔZ) to assess its role in the context of native chromatin and neighboring CREs, expecting large decreases in ftz seven-stripe expression. However, significant reduction in expression was found for only one stripe, ftz stripe 4, expressed at ∼25% of wild type levels in ftzΔZ homozygotes. Defects in corresponding regions of ftzΔZ mutants suggest this level of expression borders the threshold required to promote morphological segmentation. Further, we established true-breeding lines of homozygous ftzΔZ flies, demonstrating that the body segments missing in the mutants are not required for viability or fertility. These results highlight the different types of conclusions drawn from different experimental designs and emphasize the importance of examining transcriptional regulatory mechanisms in the context of the native genomic environment.
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Affiliation(s)
- Patricia L Graham
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Matthew D Fischer
- Graduate Program in Molecular & Cell Biology, University of Maryland, College Park, MD 20742, USA
| | - Abhigya Giri
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Leslie Pick
- Department of Entomology, University of Maryland, College Park, MD 20742, USA.,Graduate Program in Molecular & Cell Biology, University of Maryland, College Park, MD 20742, USA
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74
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Schember I, Halfon MS. Identification of new Anopheles gambiae transcriptional enhancers using a cross-species prediction approach. INSECT MOLECULAR BIOLOGY 2021; 30:410-419. [PMID: 33866636 PMCID: PMC8266755 DOI: 10.1111/imb.12705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/09/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
The success of transgenic mosquito vector control approaches relies on well-targeted gene expression, requiring the identification and characterization of a diverse set of mosquito promoters and transcriptional enhancers. However, few enhancers have been characterized in Anopheles gambiae to date. Here, we employ the SCRMshaw method we previously developed to predict enhancers in the A. gambiae genome, preferentially targeting vector-relevant tissues such as the salivary glands, midgut and nervous system. We demonstrate a high overall success rate, with at least 8 of 11 (73%) tested sequences validating as enhancers in an in vivo xenotransgenic assay. Four tested sequences drive expression in either the salivary gland or the midgut, making them directly useful for probing the biology of these infection-relevant tissues. The success of our study suggests that computational enhancer prediction should serve as an effective means for identifying A. gambiae enhancers with activity in tissues involved in malaria propagation and transmission.
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Affiliation(s)
- Isabella Schember
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203
- NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203
- Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263
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75
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Zheng J, Su G, Wang W, Zhao X, Liu M, Bi J, Zhao Z, Shi J, Lu W, Zhang L. Two Enhancers Regulate HoxB Genes Expression During Retinoic Acid-Induced Early Embryonic Stem Cells Differentiation Through Long-Range Chromatin Interactions. Stem Cells Dev 2021; 30:683-695. [PMID: 34030475 DOI: 10.1089/scd.2021.0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Homeobox B cluster (HoxB) genes play important roles in retinoic acid (RA)-induced early embryonic stem cells (ESCs) differentiation. Knowledge of regulation network of HoxB is important to further unveil the mechanism of ESCs differentiation. In this study, we identified two enhancers that were activated by RA treatment and 4C data showed long-range interactions between HoxB genes and the two enhancers. CRISPR/Cas9-mediated individual or compound deletion of the two enhancers significantly inhibits HoxB gene expression, and transcriptome analysis revealed that RA-induced early ESCs differentiation was blocked in the enhancer KO cells. We propose new mechanism by which two enhancers regulate HoxB gene expression by different regulation modes during RA-induced early ESCs differentiation through long-range chromatin interactions.
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Affiliation(s)
- Jian Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenbin Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xueyuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Man Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jinfang Bi
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
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76
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Tissue context determines the penetrance of regulatory DNA variation. Nat Commun 2021; 12:2850. [PMID: 33990600 PMCID: PMC8121920 DOI: 10.1038/s41467-021-23139-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
Functional assessment of disease-associated sequence variation at non-coding regulatory elements is complicated by their high degree of context sensitivity to both the local chromatin and nuclear environments. Allelic profiling of DNA accessibility across individuals has shown that only a select minority of sequence variation affects transcription factor (TF) occupancy, yet low sequence diversity in human populations means that no experimental assessment is available for the majority of disease-associated variants. Here we describe high-resolution in vivo maps of allelic DNA accessibility in liver, kidney, lung and B cells from 5 increasingly diverged strains of F1 hybrid mice. The high density of heterozygous sites in these hybrids enables precise quantification of effect size and cell-type specificity for hundreds of thousands of variants throughout the mouse genome. We show that chromatin-altering variants delineate characteristic sensitivity profiles for hundreds of TF motifs. We develop a compendium of TF-specific sensitivity profiles accounting for genomic context effects. Finally, we link maps of allelic accessibility to allelic transcript levels in the same samples. This work provides a foundation for quantitative prediction of cell-type specific effects of non-coding variation on TF activity, which will facilitate both fine-mapping and systems-level analyses of common disease-associated variation in human genomes.
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77
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Abstract
Shadow enhancers are seemingly redundant transcriptional cis-regulatory elements that regulate the same gene and drive overlapping expression patterns. Recent studies have shown that shadow enhancers are remarkably abundant and control most developmental gene expression in both invertebrates and vertebrates, including mammals. Shadow enhancers might provide an important mechanism for buffering gene expression against mutations in non-coding regulatory regions of genes implicated in human disease. Technological advances in genome editing and live imaging have shed light on how shadow enhancers establish precise gene expression patterns and confer phenotypic robustness. Shadow enhancers can interact in complex ways and may also help to drive the formation of transcriptional hubs within the nucleus. Despite their apparent redundancy, the prevalence and evolutionary conservation of shadow enhancers underscore their key role in emerging metazoan gene regulatory networks.
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78
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Recently Evolved Enhancers Emerge with High Interindividual Variability and Less Frequently Associate with Disease. Cell Rep 2021; 31:107799. [PMID: 32579926 DOI: 10.1016/j.celrep.2020.107799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/23/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023] Open
Abstract
Mutations in non-coding regulatory DNA such as enhancers underlie a wide variety of diseases including developmental disorders and cancer. As enhancers rapidly evolve, understanding their function and configuration in non-human disease models can have important clinical applications. Here, we analyze enhancer configurations in tissues isolated from the common marmoset, a widely used primate model for human disease. Integrating these data with human and mouse data, we find that enhancers containing trait-associated variants are preferentially conserved. In contrast, most human-specific enhancers are highly variable between individuals, with a subset failing to contact promoters. These are located further away from genes and more often reside in inactive B-compartments. Our data show that enhancers typically emerge as instable elements with minimal biological impact prior to their integration in a transcriptional program. Furthermore, our data provide insight into which trait variations in enhancers can be faithfully modeled using the common marmoset.
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79
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Jindal GA, Farley EK. Enhancer grammar in development, evolution, and disease: dependencies and interplay. Dev Cell 2021; 56:575-587. [PMID: 33689769 PMCID: PMC8462829 DOI: 10.1016/j.devcel.2021.02.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/19/2022]
Abstract
Each language has standard books describing that language's grammatical rules. Biologists have searched for similar, albeit more complex, principles relating enhancer sequence to gene expression. Here, we review the literature on enhancer grammar. We introduce dependency grammar, a model where enhancers encode information based on dependencies between enhancer features shaped by mechanistic, evolutionary, and biological constraints. Classifying enhancers based on the types of dependencies may identify unifying principles relating enhancer sequence to gene expression. Such rules would allow us to read the instructions for development within genomes and pinpoint causal enhancer variants underlying disease and evolutionary changes.
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Affiliation(s)
- Granton A Jindal
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA.
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80
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Floc'hlay S, Wong ES, Zhao B, Viales RR, Thomas-Chollier M, Thieffry D, Garfield DA, Furlong EEM. Cis-acting variation is common across regulatory layers but is often buffered during embryonic development. Genome Res 2021; 31:211-224. [PMID: 33310749 PMCID: PMC7849415 DOI: 10.1101/gr.266338.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Precise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequences, and chromatin. How DNA mutations affecting any one of these regulatory "layers" are buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses at three embryonic stages, yielding a comprehensive data set of 240 samples spanning multiple regulatory layers. Genetic variation (allelic imbalance) impacts gene expression more frequently than chromatin features, with metabolic and environmental response genes being most often affected. Allelic imbalance in cis-regulatory elements (enhancers) is common and highly heritable, yet its functional impact does not generally propagate to gene expression. When it does, genetic variation impacts RNA levels through two alternative mechanisms involving either H3K4me3 or chromatin accessibility and H3K27ac. Changes in RNA are more predictive of variation in H3K4me3 than vice versa, suggesting a role for H3K4me3 downstream from transcription. The impact of a substantial proportion of genetic variation is consistent across embryonic stages, with 50% of allelic imbalanced features at one stage being also imbalanced at subsequent developmental stages. Crucially, buffering, as well as the magnitude and evolutionary impact of genetic variants, is influenced by regulatory complexity (i.e., number of enhancers regulating a gene), with transcription factors being most robust to cis-acting, but most influenced by trans-acting, variation.
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Affiliation(s)
- Swann Floc'hlay
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Emily S Wong
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales 2052, Australia
| | - Bingqing Zhao
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Morgane Thomas-Chollier
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Denis Thieffry
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
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81
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Irizarry J, Stathopoulos A. Dynamic patterning by morphogens illuminated by cis-regulatory studies. Development 2021; 148:148/2/dev196113. [PMID: 33472851 DOI: 10.1242/dev.196113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Morphogen concentration changes in space as well as over time during development. However, how these dynamics are interpreted by cells to specify fate is not well understood. Here, we focus on two morphogens: the maternal transcription factors Bicoid and Dorsal, which directly regulate target genes to pattern Drosophila embryos. The actions of these factors at enhancers has been thoroughly dissected and provides a rich platform for understanding direct input by morphogens and their changing roles over time. Importantly, Bicoid and Dorsal do not work alone; we also discuss additional inputs that work with morphogens to control spatiotemporal gene expression in embryos.
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Affiliation(s)
- Jihyun Irizarry
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Blvd., Pasadena, CA 91125, USA
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82
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Azambuja AP, Simoes-Costa M. A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation. PLoS Genet 2021; 17:e1009296. [PMID: 33465092 PMCID: PMC7846109 DOI: 10.1371/journal.pgen.1009296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/29/2021] [Accepted: 12/05/2020] [Indexed: 01/15/2023] Open
Abstract
The process of cell fate commitment involves sequential changes in the gene expression profiles of embryonic progenitors. This is exemplified in the development of the neural crest, a migratory stem cell population derived from the ectoderm of vertebrate embryos. During neural crest formation, cells transition through distinct transcriptional states in a stepwise manner. The mechanisms underpinning these shifts in cell identity are still poorly understood. Here we employ enhancer analysis to identify a genetic sub-circuit that controls developmental transitions in the nascent neural crest. This sub-circuit links Wnt target genes in an incoherent feedforward loop that controls the sequential activation of genes in the neural crest lineage. By examining the cis-regulatory apparatus of Wnt effector gene AXUD1, we found that multipotency factor SP5 directly promotes neural plate border identity, while inhibiting premature expression of specification genes. Our results highlight the importance of repressive interactions in the neural crest gene regulatory network and illustrate how genes activated by the same upstream signal become temporally segregated during progressive fate restriction.
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Affiliation(s)
- Ana Paula Azambuja
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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83
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Hatleberg WL, Hinman VF. Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change. Curr Top Dev Biol 2021; 141:39-73. [DOI: 10.1016/bs.ctdb.2020.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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84
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Abstract
Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.
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Affiliation(s)
- Felix Wong
- Institute for Medical Engineering & Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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85
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Minnoye L, Taskiran II, Mauduit D, Fazio M, Van Aerschot L, Hulselmans G, Christiaens V, Makhzami S, Seltenhammer M, Karras P, Primot A, Cadieu E, van Rooijen E, Marine JC, Egidy G, Ghanem GE, Zon L, Wouters J, Aerts S. Cross-species analysis of enhancer logic using deep learning. Genome Res 2020; 30:1815-1834. [PMID: 32732264 PMCID: PMC7706731 DOI: 10.1101/gr.260844.120] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022]
Abstract
Deciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation and empower the generation of cell type-specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable enhancer models. We apply this strategy to decipher the enhancer code in melanoma, a relevant case study owing to the presence of distinct melanoma cell states. We trained and validated a deep learning model, called DeepMEL, using chromatin accessibility data of 26 melanoma samples across six different species. We show the accuracy of DeepMEL predictions on the CAGI5 challenge, where it significantly outperforms existing models on the melanoma enhancer of IRF4 Next, we exploit DeepMEL to analyze enhancer architectures and identify accurate transcription factor binding sites for the core regulatory complexes in the two different melanoma states, with distinct roles for each transcription factor, in terms of nucleosome displacement or enhancer activation. Finally, DeepMEL identifies orthologous enhancers across distantly related species, where sequence alignment fails, and the model highlights specific nucleotide substitutions that underlie enhancer turnover. DeepMEL can be used from the Kipoi database to predict and optimize candidate enhancers and to prioritize enhancer mutations. In addition, our computational strategy can be applied to other cancer or normal cell types.
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Affiliation(s)
- Liesbeth Minnoye
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - David Mauduit
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Maurizio Fazio
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Linde Van Aerschot
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
- Laboratory for Disease Mechanisms in Cancer, KU Leuven, 3000 Leuven, Belgium
| | - Gert Hulselmans
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Valerie Christiaens
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Samira Makhzami
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Monika Seltenhammer
- Center for Forensic Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Livestock Sciences (NUWI) - BOKU University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Panagiotis Karras
- VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- KU Leuven, Department of Oncology KU Leuven, 3000 Leuven, Belgium
| | - Aline Primot
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, 35000 Rennes, France
| | - Edouard Cadieu
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, 35000 Rennes, France
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jean-Christophe Marine
- VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- KU Leuven, Department of Oncology KU Leuven, 3000 Leuven, Belgium
| | - Giorgia Egidy
- Université Paris-Saclay, INRA, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Ghanem-Elias Ghanem
- Institut Jules Bordet, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Leonard Zon
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jasper Wouters
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
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86
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Abstract
Key discoveries in Drosophila have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in Drosophila has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these cis-regulatory elements operate in development and disease.
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Affiliation(s)
- Stephen Small
- Department of Biology, Developmental Systems Training Program, New York University, 10003 and
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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87
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Miesfeld JB, Ghiasvand NM, Marsh-Armstrong B, Marsh-Armstrong N, Miller EB, Zhang P, Manna SK, Zawadzki RJ, Brown NL, Glaser T. The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development. Proc Natl Acad Sci U S A 2020; 117:21690-21700. [PMID: 32817515 PMCID: PMC7474671 DOI: 10.1073/pnas.2006888117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The retinal ganglion cell (RGC) competence factor ATOH7 is dynamically expressed during retinal histogenesis. ATOH7 transcription is controlled by a promoter-adjacent primary enhancer and a remote shadow enhancer (SE). Deletion of the ATOH7 human SE causes nonsyndromic congenital retinal nonattachment (NCRNA) disease, characterized by optic nerve aplasia and total blindness. We used genome editing to model NCRNA in mice. Deletion of the murine SE reduces Atoh7 messenger RNA (mRNA) fivefold but does not recapitulate optic nerve loss; however, SEdel/knockout (KO) trans heterozygotes have thin optic nerves. By analyzing Atoh7 mRNA and protein levels, RGC development and survival, and chromatin landscape effects, we show that the SE ensures robust Atoh7 transcriptional output. Combining SE deletion and KO and wild-type alleles in a genotypic series, we determined the amount of Atoh7 needed to produce a normal complement of adult RGCs, and the secondary consequences of graded reductions in Atoh7 dosage. Together, these data reveal the workings of an evolutionary fail-safe, a duplicate enhancer mechanism that is hard-wired in the machinery of vertebrate retinal ganglion cell genesis.
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Affiliation(s)
- Joel B Miesfeld
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Noor M Ghiasvand
- Department of Biology, Grand Valley State University, Allendale, MI 49401
- Functional Neurosurgery Research Center, Shohada Tajrish Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Brennan Marsh-Armstrong
- Department of Ophthalmology and Vision Science, University of California Davis School of Medicine, Sacramento, CA 95817
| | - Nicholas Marsh-Armstrong
- Department of Ophthalmology and Vision Science, University of California Davis School of Medicine, Sacramento, CA 95817
| | - Eric B Miller
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Pengfei Zhang
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Suman K Manna
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Robert J Zawadzki
- Department of Ophthalmology and Vision Science, University of California Davis School of Medicine, Sacramento, CA 95817
| | - Nadean L Brown
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616
| | - Tom Glaser
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA 95616;
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88
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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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89
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Waymack R, Fletcher A, Enciso G, Wunderlich Z. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic. eLife 2020; 9:e59351. [PMID: 32804082 PMCID: PMC7556877 DOI: 10.7554/elife.59351] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/14/2020] [Indexed: 12/26/2022] Open
Abstract
Shadow enhancers, groups of seemingly redundant enhancers, are found in a wide range of organisms and are critical for robust developmental patterning. However, their mechanism of action is unknown. We hypothesized that shadow enhancers drive consistent expression levels by buffering upstream noise through a separation of transcription factor (TF) inputs at the individual enhancers. By measuring the transcriptional dynamics of several Kruppel shadow enhancer configurations in live Drosophila embryos, we showed that individual member enhancers act largely independently. We found that TF fluctuations are an appreciable source of noise that the shadow enhancer pair can better buffer than duplicated enhancers. The shadow enhancer pair is also uniquely able to maintain low levels of expression noise across a wide range of temperatures. A stochastic model demonstrated the separation of TF inputs is sufficient to explain these findings. Our results suggest the widespread use of shadow enhancers is partially due to their noise suppressing ability.
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Affiliation(s)
- Rachel Waymack
- Department of Developmental and Cell Biology, University of California, IrvineIrvineUnited States
| | - Alvaro Fletcher
- Mathematical, Computational, and Systems Biology Graduate Program, University of California, IrvineIrvineUnited States
| | - German Enciso
- Department of Developmental and Cell Biology, University of California, IrvineIrvineUnited States
- Department of Mathematics, University of California, IrvineIrvineUnited States
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, IrvineIrvineUnited States
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90
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Carayon A, Bataillé L, Lebreton G, Dubois L, Pelletier A, Carrier Y, Wystrach A, Vincent A, Frendo JL. Intrinsic control of muscle attachment sites matching. eLife 2020; 9:57547. [PMID: 32706334 PMCID: PMC7431191 DOI: 10.7554/elife.57547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Myogenesis is an evolutionarily conserved process. Little known, however, is how the morphology of each muscle is determined, such that movements relying upon contraction of many muscles are both precise and coordinated. Each Drosophila larval muscle is a single multinucleated fibre whose morphology reflects expression of distinctive identity Transcription Factors (iTFs). By deleting transcription cis-regulatory modules of one iTF, Collier, we generated viable muscle identity mutants, allowing live imaging and locomotion assays. We show that both selection of muscle attachment sites and muscle/muscle matching is intrinsic to muscle identity and requires transcriptional reprogramming of syncytial nuclei. Live-imaging shows that the staggered muscle pattern involves attraction to tendon cells and heterotypic muscle-muscle adhesion. Unbalance leads to formation of branched muscles, and this correlates with locomotor behavior deficit. Thus, engineering Drosophila muscle identity mutants allows to investigate, in vivo, physiological and mechanical properties of abnormal muscles.
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Affiliation(s)
- Alexandre Carayon
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laetitia Bataillé
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gaëlle Lebreton
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laurence Dubois
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Aurore Pelletier
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yannick Carrier
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Antoine Wystrach
- Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Alain Vincent
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jean-Louis Frendo
- Centre de Biologie du Développement (CBD), Toulouse, France.,Centre de Recherche sur la Cognition Animale (CRCA), Toulouse, France.,Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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91
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Koromila T, Gao F, Iwasaki Y, He P, Pachter L, Gergen JP, Stathopoulos A. Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. eLife 2020; 9:e59610. [PMID: 32701060 PMCID: PMC7417190 DOI: 10.7554/elife.59610] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/22/2020] [Indexed: 01/29/2023] Open
Abstract
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa's role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.
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Affiliation(s)
- Theodora Koromila
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Fan Gao
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Yasuno Iwasaki
- Stony Brook University, Department of Biochemistry and Cell Biology and Center for Developmental GeneticsStony BrookUnited States
| | - Peng He
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Lior Pachter
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - J Peter Gergen
- Stony Brook University, Department of Biochemistry and Cell Biology and Center for Developmental GeneticsStony BrookUnited States
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
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92
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Kuroiwa A. Enhancers, development, and evolution. Dev Growth Differ 2020; 62:265-268. [DOI: 10.1111/dgd.12683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 12/25/2022]
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93
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Anderson JA, Vilgalys TP, Tung J. Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Curr Opin Genet Dev 2020; 62:16-22. [PMID: 32569794 PMCID: PMC7483836 DOI: 10.1016/j.gde.2020.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022]
Abstract
Comparative analyses have played a key role in understanding how gene regulatory evolution contributes to primate phenotypic diversity. Recently, these studies have expanded to include a wider range of species, within-population as well as interspecific analyses, and research on wild as well as captive individuals. This expansion provides context for understanding genetic and environmental effects on gene regulation in humans, including the importance of the pathogen and social environments. Although taxonomic representation remains biased, inclusion of more species has also begun to reveal the evolutionary processes that explain whether and when gene regulation is conserved. Together, this work highlights how studies in other primates contribute to understanding evolution in our own lineage, and we conclude by identifying promising avenues for future work.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya; Duke Population Research Institute, Duke University, Durham, NC 27708, USA.
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94
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Modular Organization of Cis-regulatory Control Information of Neurotransmitter Pathway Genes in Caenorhabditis elegans. Genetics 2020; 215:665-681. [PMID: 32444379 DOI: 10.1534/genetics.120.303206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
We explore here the cis-regulatory logic that dictates gene expression in specific cell types in the nervous system. We focus on a set of eight genes involved in the synthesis, transport, and breakdown of three neurotransmitter systems: acetylcholine (unc-17 /VAChT, cha-1 /ChAT, cho-1 /ChT, and ace-2 /AChE), glutamate (eat-4 /VGluT), and γ-aminobutyric acid (unc-25 /GAD, unc-46 /LAMP, and unc-47 /VGAT). These genes are specifically expressed in defined subsets of cells in the nervous system. Through transgenic reporter gene assays, we find that the cellular specificity of expression of all of these genes is controlled in a modular manner through distinct cis-regulatory elements, corroborating the previously inferred piecemeal nature of specification of neurotransmitter identity. This modularity provides the mechanistic basis for the phenomenon of "phenotypic convergence," in which distinct regulatory pathways can generate similar phenotypic outcomes (i.e., the acquisition of a specific neurotransmitter identity) in different neuron classes. We also identify cases of enhancer pleiotropy, in which the same cis-regulatory element is utilized to control gene expression in distinct neuron types. We engineered a cis-regulatory allele of the vesicular acetylcholine transporter, unc-17 /VAChT, to assess the functional contribution of a "shadowed" enhancer. We observed a selective loss of unc-17 /VAChT expression in one cholinergic pharyngeal pacemaker motor neuron class and a behavioral phenotype that matches microsurgical removal of this neuron. Our analysis illustrates the value of understanding cis-regulatory information to manipulate gene expression and control animal behavior.
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95
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On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution? Curr Top Dev Biol 2020; 139:375-405. [PMID: 32450967 DOI: 10.1016/bs.ctdb.2020.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The process of multicellular organismal development hinges upon the specificity of developmental programs: for different parts of the organism to form unique features, processes must exist to specify each part. This specificity is thought to be hardwired into gene regulatory networks, which activate cohorts of genes in particular tissues at particular times during development. However, the evolution of gene regulatory networks sometimes occurs by mechanisms that sacrifice specificity. One such mechanism is network co-option, in which existing gene networks are redeployed in new developmental contexts. While network co-option may offer an efficient mechanism for generating novel phenotypes, losses of tissue specificity at redeployed network genes could restrict the ability of the affected traits to evolve independently. At present, there has not been a detailed discussion regarding how tissue specificity of network genes might be altered due to gene network co-option at its initiation, as well as how trait independence can be retained or restored after network co-option. A lack of clarity about network co-option makes it more difficult to speculate on the long-term evolutionary implications of this mechanism. In this review, we will discuss the possible initial outcomes of network co-option, outline the mechanisms by which networks may retain or subsequently regain specificity after network co-option, and comment on some of the possible evolutionary consequences of network co-option. We place special emphasis on the need to consider selectively-neutral outcomes of network co-option to improve our understanding of the role of this mechanism in trait evolution.
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96
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Delás MJ, Briscoe J. Repressive interactions in gene regulatory networks: When you have no other choice. Curr Top Dev Biol 2020; 139:239-266. [PMID: 32450962 DOI: 10.1016/bs.ctdb.2020.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tightly regulated gene expression programs, orchestrated by complex interactions between transcription factors, control cell type specification during development. Repressive interactions play a critical role in these networks, facilitating decision-making between two or more alternative cell fates. Here, we use the ventral neural tube as an example to illustrate how cross repressive interactions within a network drive pattern formation and specify cell types in response to a graded patterning signal. This and other systems serve to highlight how external signals are integrated through the cis regulatory elements controlling key genes and provide insight into the molecular underpinning of the process. Even the simplest networks can lead to counterintuitive results and we argue that a combination of experimental dissection and modeling approaches will be necessary to fully understand network behavior and the underlying design principles. Studying these gene regulatory networks as a whole ultimately allows us to extract fundamental properties applicable across systems that can expand our mechanistic understanding of how organisms develop.
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Affiliation(s)
| | - James Briscoe
- The Francis Crick Institute, London, United Kingdom.
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97
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Gasperini M, Tome JM, Shendure J. Towards a comprehensive catalogue of validated and target-linked human enhancers. Nat Rev Genet 2020; 21:292-310. [PMID: 31988385 PMCID: PMC7845138 DOI: 10.1038/s41576-019-0209-0] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
The human gene catalogue is essentially complete, but we lack an equivalently vetted inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers have been nominated via biochemical annotations; however, only a handful of these have been validated and confidently linked to their target genes. Here we review emerging technologies for discovering, characterizing and validating human enhancers at scale. We furthermore propose a new framework for operationally defining enhancers that accommodates the heterogeneous and complementary results that are emerging from reporter assays, biochemical measurements and CRISPR screens.
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Affiliation(s)
- Molly Gasperini
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacob M Tome
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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98
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Amândio AR, Lopez-Delisle L, Bolt CC, Mascrez B, Duboule D. A complex regulatory landscape involved in the development of mammalian external genitals. eLife 2020; 9:e52962. [PMID: 32301703 PMCID: PMC7185996 DOI: 10.7554/elife.52962] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/17/2020] [Indexed: 02/04/2023] Open
Abstract
Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. We used a TAD flanking the mouse HoxD cluster to study how these regulatory architectures are formed and deconstructed once their function achieved. We describe this TAD as a functional unit, with several regulatory sequences acting together to elicit a transcriptional response. With one exception, deletion of these sequences didn't modify the transcriptional outcome, a result at odds with a conventional view of enhancer function. The deletion and inversion of a CTCF site located near these regulatory sequences did not affect transcription of the target gene. Slight modifications were nevertheless observed, in agreement with the loop extrusion model. We discuss these unexpected results considering both conventional and alternative explanations relying on the accumulation of poorly specific factors within the TAD backbone.
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Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
- Collège de FranceParisFrance
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99
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Xu D, Gokcumen O, Khurana E. Loss-of-function tolerance of enhancers in the human genome. PLoS Genet 2020; 16:e1008663. [PMID: 32243438 PMCID: PMC7159235 DOI: 10.1371/journal.pgen.1008663] [Citation(s) in RCA: 6] [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: 08/29/2019] [Revised: 04/15/2020] [Accepted: 02/12/2020] [Indexed: 12/21/2022] Open
Abstract
Previous studies have surveyed the potential impact of loss-of-function (LoF) variants and identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to losing enhancers has not yet been evaluated. Here we present the catalog of LoF-tolerant enhancers using structural variants from whole-genome sequences. Using a conservative approach, we estimate that individual human genomes possess at least 28 LoF-tolerant enhancers on average. We assessed the properties of LoF-tolerant enhancers in a unified regulatory network constructed by integrating tissue-specific enhancers and gene-gene interactions. We find that LoF-tolerant enhancers tend to be more tissue-specific and regulate fewer and more dispensable genes relative to other enhancers. They are enriched in immune-related cells while enhancers with low LoF-tolerance are enriched in kidney and brain/neuronal stem cells. We developed a supervised learning approach to predict the LoF-tolerance of all enhancers, which achieved an area under the receiver operating characteristics curve (AUROC) of 98%. We predict 3,519 more enhancers would be likely tolerant to LoF and 129 enhancers that would have low LoF-tolerance. Our predictions are supported by a known set of disease enhancers and novel deletions from PacBio sequencing. The LoF-tolerance scores provided here will serve as an important reference for disease studies. Enhancers are elements where transcription factors bind and regulate the expression of protein-coding genes. Although multiple previous studies have focused on which genes can tolerate loss-of-function (LoF), none has systematically evaluated the tolerance of all enhancers in the human genome to LoF. Individual studies have shown a broad range of phenotypic effects of enhancer LoF. The phenotypic effects of enhancer LoF likely fall into a spectrum where deletion of LoF-tolerant enhancers would not elicit substantial phenotypic impact, while some enhancers are likely to cause fitness defects when deleted. Here we report a systematic computational approach that uses machine learning and properties of enhancers in a unified human regulatory network with tissue-specific annotations to predict the LoF-tolerance of all enhancers identified in the human genome. The LoF-tolerance scores of enhancers provided in this study can significantly facilitate the interpretation and prioritization of non-coding sequence variants for disease and functional studies.
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Affiliation(s)
- Duo Xu
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States of America
- Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, United States of America
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States of America
- Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, United States of America
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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100
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Li Y, Tao T, Du L, Zhu X. Three-dimensional genome: developmental technologies and applications in precision medicine. J Hum Genet 2020; 65:497-511. [PMID: 32152365 DOI: 10.1038/s10038-020-0737-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 12/17/2022]
Abstract
In the 20th century, our familiar structure of DNA was the double helix. Due to technical limitations, we do not have a good way to understand the finer structure of the genome, let alone its transcriptional regulation. Until the advent of 3C technologies, we were no longer blind to this one. Three-dimensional (3D) genomics is a new subject, which mainly studies the 3D structure and transcriptional regulation of eukaryotic genomes. Now, this field mainly has Hi-C series and CHIA-PET series technologies. Through 3D genomics, we can understand the basic structure of DNA, understand the growth and development of organisms and the occurrence of diseases, so as to promote human medical and health undertakings. The review introduces the main research techniques of 3D genomics and their characteristics, the latest development of 3D genome structure, the relationship between diseases and 3D genome structure, the applications of 3D genome in precision medicine, and the development of the 4D nucleome project.
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Affiliation(s)
- Yingqi Li
- Marine Medical Research Institute of Guangdong Zhanjiang (GDZJMMRI), Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, 255000, China
| | - Likun Du
- First Affiliated Hospital, Heilongjiang University of Traditional Chinese Medicine, Harbin, 150040, China.
| | - Xiao Zhu
- Marine Medical Research Institute of Guangdong Zhanjiang (GDZJMMRI), Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.
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