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Oriol F, Alberto M, Joachim AP, Patrick G, M BP, Ruben MF, Jaume B, Altair CH, Ferran P, Oriol G, Narcis FF, Baldo O. Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements. NAR Genom Bioinform 2024; 6:lqae068. [PMID: 38867914 PMCID: PMC11167492 DOI: 10.1093/nargab/lqae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/18/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Transcription factor (TF) binding is a key component of genomic regulation. There are numerous high-throughput experimental methods to characterize TF-DNA binding specificities. Their application, however, is both laborious and expensive, which makes profiling all TFs challenging. For instance, the binding preferences of ∼25% human TFs remain unknown; they neither have been determined experimentally nor inferred computationally. We introduce a structure-based learning approach to predict the binding preferences of TFs and the automated modelling of TF regulatory complexes. We show the advantage of using our approach over the classical nearest-neighbor prediction in the limits of remote homology. Starting from a TF sequence or structure, we predict binding preferences in the form of motifs that are then used to scan a DNA sequence for occurrences. The best matches are either profiled with a binding score or collected for their subsequent modeling into a higher-order regulatory complex with DNA. Co-operativity is modelled by: (i) the co-localization of TFs and (ii) the structural modeling of protein-protein interactions between TFs and with co-factors. We have applied our approach to automatically model the interferon-β enhanceosome and the pioneering complexes of OCT4, SOX2 (or SOX11) and KLF4 with a nucleosome, which are compared with the experimentally known structures.
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Affiliation(s)
- Fornes Oriol
- Centre for Molecular Medicine and Therapeutics. BC Children's Hospital Research Institute. Department of Medical Genetics. University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Meseguer Alberto
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | | | - Gohl Patrick
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Bota Patricia M
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Molina-Fernández Ruben
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Bonet Jaume
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
- Laboratory of Protein Design & Immunoengineering. School of Engineering. Ecole Polytechnique Federale de Lausanne. Lausanne 1015, Vaud, Switzerland
| | - Chinchilla-Hernandez Altair
- Live-Cell Structural Biology. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Pegenaute Ferran
- Live-Cell Structural Biology. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Gallego Oriol
- Live-Cell Structural Biology. Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
| | - Fernandez-Fuentes Narcis
- Institute of Biological, Environmental and Rural Science. Aberystwyth University, SY23 3DA Aberystwyth, UK
| | - Oliva Baldo
- Structural Bioinformatics Lab (GRIB-IMIM). Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005 Catalonia, Spain
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Kiontke K, Herrera RA, Mason DA, Woronik A, Vernooy S, Patel Y, Fitch DHA. Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575210. [PMID: 38260477 PMCID: PMC10802606 DOI: 10.1101/2024.01.12.575210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs. dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the UPR (unfolded protein response) pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.
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Affiliation(s)
- Karin Kiontke
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
| | | | - D Adam Mason
- Biology Department, Siena College, 515 Loudon Road, Loudonville, NY 12211
| | - Alyssa Woronik
- Sacred Heart University, 5151 Park Avenue, Fairfield, CT 06825
| | - Stephanie Vernooy
- Biology Department, Siena College, 515 Loudon Road, Loudonville, NY 12211
| | - Yash Patel
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
| | - David H A Fitch
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
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Li Y, Chen S, Liu W, Zhao D, Gao Y, Hu S, Liu H, Li Y, Qu L, Liu X. A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans. Nat Commun 2024; 15:358. [PMID: 38195740 PMCID: PMC10776613 DOI: 10.1038/s41467-023-42677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/18/2023] [Indexed: 01/11/2024] Open
Abstract
Invariant cell lineage in C. elegans enables spatiotemporal resolution of transcriptional regulatory mechanisms controlling the fate of each cell. Here, we develop RAPCAT (Robust-point-matching- And Piecewise-affine-based Cell Annotation Tool) to automate cell identity assignment in three-dimensional image stacks of L1 larvae and profile reporter expression of 620 transcription factors in every cell. Transcription factor profile-based clustering analysis defines 80 cell types distinct from conventional phenotypic cell types and identifies three general phenotypic modalities related to these classifications. First, transcription factors are broadly downregulated in quiescent stage Hermaphrodite Specific Neurons, suggesting stage- and cell type-specific variation in transcriptome size. Second, transcription factor expression is more closely associated with morphology than other phenotypic modalities in different pre- and post-differentiation developmental stages. Finally, embryonic cell lineages can be associated with specific transcription factor expression patterns and functions that persist throughout postembryonic life. This study presents a comprehensive transcription factor atlas for investigation of intra-cell type heterogeneity.
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Affiliation(s)
- Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Siyu Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Weihong Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Intelligent Perception Lab, Hanwang Technology Co., Ltd, Beijing, 100193, China
| | - Di Zhao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Institute of Sport, Exercise & Health, Tianjin University of Sport, Tianjin, 300381, China
| | - Yimeng Gao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Shipeng Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Hanyu Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuanyuan Li
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, 230039, China
| | - Lei Qu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, 230039, China
| | - Xiao Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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Birgersson M, Indukuri R, Lindquist L, Stepanauskaite L, Luo Q, Deng Q, Archer A, Williams C. Ovarian ERβ cistrome and transcriptome reveal chromatin interaction with LRH-1. BMC Biol 2023; 21:277. [PMID: 38031019 PMCID: PMC10688478 DOI: 10.1186/s12915-023-01773-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Estrogen receptor beta (ERβ, Esr2) plays a pivotal role in folliculogenesis and ovulation, yet its exact mechanism of action is mainly uncharacterized. RESULTS We here performed ERβ ChIP-sequencing of mouse ovaries followed by complementary RNA-sequencing of wild-type and ERβ knockout ovaries. By integrating the ERβ cistrome and transcriptome, we identified its direct target genes and enriched biological functions in the ovary. This demonstrated its strong impact on genes regulating organism development, cell migration, lipid metabolism, response to hypoxia, and response to estrogen. Cell-type deconvolution analysis of the bulk RNA-seq data revealed a decrease in luteal cells and an increased proportion of theca cells and a specific type of cumulus cells upon ERβ loss. Moreover, we identified a significant overlap with the gene regulatory network of liver receptor homolog 1 (LRH-1, Nr5a2) and showed that ERβ and LRH-1 extensively bound to the same chromatin locations in granulosa cells. Using ChIP-reChIP, we corroborated simultaneous ERβ and LRH-1 co-binding at the ERβ-repressed gene Greb1 but not at the ERβ-upregulated genes Cyp11a1 and Fkbp5. Transactivation assay experimentation further showed that ERβ and LRH-1 can inhibit their respective transcriptional activity at classical response elements. CONCLUSIONS By characterizing the genome-wide endogenous ERβ chromatin binding, gene regulations, and extensive crosstalk between ERβ and LRH-1, along with experimental corroborations, our data offer genome-wide mechanistic underpinnings of ovarian physiology and fertility.
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Affiliation(s)
- Madeleine Birgersson
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Rajitha Indukuri
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
| | - Linnéa Lindquist
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Lina Stepanauskaite
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Qing Luo
- Department of Physiology and Pharmacology, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Amena Archer
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Cecilia Williams
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
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Yuan M, Liu X, Wang M, Li Z, Li H, Leng L, Wang S. A Functional Variant Alters the Binding of Bone morphogenetic protein 2 to the Transcription Factor NF-κB to Regulate Bone morphogenetic protein 2 Gene Expression and Chicken Abdominal Fat Deposition. Animals (Basel) 2023; 13:3401. [PMID: 37958155 PMCID: PMC10650395 DOI: 10.3390/ani13213401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
In this study, we employed a dual-luciferase reporter assay and electrophoretic mobility shift analysis (EMSA) in vitro to explore whether a 12-base pair (bp) insertion/deletion (InDel) variant (namely g.14798187_14798188insTCCCTGCCCCCT) within intron 2 of the chicken BMP2 gene, which was significantly associated with chicken abdominal fat weight and abdominal fat percentage, is a functional marker and its potential regulatory mechanism. The reporter analysis demonstrated that the luciferase activity of the deletion allele was extremely significantly higher than that of the insertion allele (p < 0.01). A bioinformatics analysis revealed that compared to the deletion allele, the insertion allele created a transcription factor binding site of nuclear factor-kappa B (NF-κB), which exhibited an inhibitory effect on fat deposition. A dual-luciferase reporter assay demonstrated that the inhibitory effect of NF-κB on the deletion allele was stronger than that on the insertion allele. EMSA indicated that the binding affinity of NF-κB for the insertion allele was stronger than that for the deletion allele. In conclusion, the 12-bp InDel chicken BMP2 gene variant is a functional variant affecting fat deposition in chickens, which may partially regulate BMP2 gene expression by affecting the binding of transcription factor NF-κB to the BMP2 gene.
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Affiliation(s)
- Meng Yuan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xin Liu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Mengdie Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Ziwei Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, China; (M.Y.); (X.L.); (M.W.); (Z.L.); (H.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
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6
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Reilly DK, Schwarz EM, Muirhead CS, Robidoux AN, Narayan A, Doma MK, Sternberg PW, Srinivasan J. Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans. Genetics 2023; 223:iyad026. [PMID: 36801937 PMCID: PMC10319972 DOI: 10.1093/genetics/iyad026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 02/20/2023] Open
Abstract
The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside #8 (ascr#8) mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males. Males sense ascr#8 via the ciliated male-specific cephalic sensory (CEM) neurons, which exhibit radial symmetry along dorsal-ventral and left-right axes. Calcium imaging studies suggest a complex neural coding mechanism that translates stochastic physiological responses in these neurons to reliable behavioral outputs. To test the hypothesis that neurophysiological complexity arises from differential expression of genes, we performed cell-specific transcriptomic profiling; this revealed between 18 and 62 genes with at least twofold higher expression in a specific CEM neuron subtype vs both other CEM neurons and adult males. These included two G protein-coupled receptor (GPCR) genes, srw-97 and dmsr-12, that were specifically expressed in nonoverlapping subsets of CEM neurons and whose expression was confirmed by GFP reporter analysis. Single CRISPR-Cas9 knockouts of either srw-97 or dmsr-12 resulted in partial defects, while a double knockout of both srw-97 and dmsr-12 completely abolished the attractive response to ascr#8. Together, our results suggest that the evolutionarily distinct GPCRs SRW-97 and DMSR-12 act nonredundantly in discrete olfactory neurons to facilitate male-specific sensation of ascr#8.
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Affiliation(s)
- Douglas K Reilly
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Caroline S Muirhead
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Annalise N Robidoux
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Anusha Narayan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Meenakshi K Doma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01605, USA
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Katsanos D, Barkoulas M. Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. SCIENCE ADVANCES 2022; 8:eabk3141. [PMID: 35119932 PMCID: PMC8816332 DOI: 10.1126/sciadv.abk3141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they display complex patterns of expression and binding to their targets, hence, tissue specificity is required in the characterization of transcription factor-target interactions. We introduce here targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact Caenorhabditis elegans animals. We use TaDa to recover targets in the epidermis for two factors, the HES1 homolog LIN-22, and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signaling pathway through repression of the Frizzled receptor lin-17. We report a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.
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Patel N, Bush WS. Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources. BMC Bioinformatics 2021; 22:200. [PMID: 33874910 PMCID: PMC8056605 DOI: 10.1186/s12859-021-04126-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/09/2021] [Indexed: 11/17/2022] Open
Abstract
Background Transcriptional regulation is complex, requiring multiple cis (local) and trans acting mechanisms working in concert to drive gene expression, with disruption of these processes linked to multiple diseases. Previous computational attempts to understand the influence of regulatory mechanisms on gene expression have used prediction models containing input features derived from cis regulatory factors. However, local chromatin looping and trans-acting mechanisms are known to also influence transcriptional regulation, and their inclusion may improve model accuracy and interpretation. In this study, we create a general model of transcription factor influence on gene expression by incorporating both cis and trans gene regulatory features. Results We describe a computational framework to model gene expression for GM12878 and K562 cell lines. This framework weights the impact of transcription factor-based regulatory data using multi-omics gene regulatory networks to account for both cis and trans acting mechanisms, and measures of the local chromatin context. These prediction models perform significantly better compared to models containing cis-regulatory features alone. Models that additionally integrate long distance chromatin interactions (or chromatin looping) between distal transcription factor binding regions and gene promoters also show improved accuracy. As a demonstration of their utility, effect estimates from these models were used to weight cis-regulatory rare variants for sequence kernel association test analyses of gene expression. Conclusions Our models generate refined effect estimates for the influence of individual transcription factors on gene expression, allowing characterization of their roles across the genome. This work also provides a framework for integrating multiple data types into a single model of transcriptional regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04126-3.
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Affiliation(s)
- Neel Patel
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
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Ahier A, Suman SK, Jarriault S. Gene bashing of ceh-6 locus identifies genomic regions important for ceh-6 rectal cell expression and rescue of its mutant lethality. MICROPUBLICATION BIOLOGY 2020; 2020. [PMID: 33364555 PMCID: PMC7753896 DOI: 10.17912/micropub.biology.000339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Strong loss-of-function or null mutants can sometimes lead to a penetrant early lethality, impairing the study of these genes’ function. This is the case for the ceh-6 null mutant, which exhibits 100% penetrant lethality. Here, we describe how we used gene bashing to identify distinct regulatory regions in the ceh-6 locus. This allowed us to generate a ceh-6 null strain that is viable and still displays ceh-6 mutant Y-to-PDA transdifferentiation phenotype. Such strategy can be applied to many other mutants impacting viability.
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Affiliation(s)
- Arnaud Ahier
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch CU Strasbourg, 67404 France.,current address: Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Shashi Kumar Suman
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch CU Strasbourg, 67404 France
| | - Sophie Jarriault
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch CU Strasbourg, 67404 France
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10
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Abstract
Comprehensive mapping of protein-DNA interactions is essential to uncover the mechanisms involved in gene regulation. However, the data generated has been sparse given the number of regulatory elements and transcription factors (TFs) encoded in the genomes of metazoan organisms. Yeast one-hybrid (Y1H) assays provide a powerful "DNA-centered" method, complementary to "TF-centered" methods such as chromatin immunoprecipitation, to identify the TFs that can bind a DNA sequence of interest. Here, we present different technical variations that should be considered when using a Y1H system, including the type of DNA sequence to test, source of TF clones, as well as types of vectors and screening format. Finally, we discuss limitations of the assay and future challenges.
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Shrestha S, Liu X, Santoso CS, Fuxman Bass JI. Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences. J Vis Exp 2019. [PMID: 30799854 DOI: 10.3791/59192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Identifying the sets of transcription factors (TFs) that regulate each human gene is a daunting task that requires integrating numerous experimental and computational approaches. One such method is the yeast one-hybrid (Y1H) assay, in which interactions between TFs and DNA regions are tested in the milieu of the yeast nucleus using reporter genes. Y1H assays involve two components: a 'DNA-bait' (e.g., promoters, enhancers, silencers, etc.) and a 'TF-prey,' which can be screened for reporter gene activation. Most published protocols for performing Y1H screens are based on transforming TF-prey libraries or arrays into DNA-bait yeast strains. Here, we describe a pipeline, called enhanced Y1H (eY1H) assays, where TF-DNA interactions are interrogated by mating DNA-bait strains with an arrayed collection of TF-prey strains using a high density array (HDA) robotic platform that allows screening in a 1,536 colony format. This allows for a dramatic increase in throughput (60 DNA-bait sequences against >1,000 TFs takes two weeks per researcher) and reproducibility. We illustrate the different types of expected results by testing human promoter sequences against an array of 1,086 human TFs, as well as examples of issues that can arise during screens and how to troubleshoot them.
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Affiliation(s)
| | - Xing Liu
- Department of Biology, Boston University
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12
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Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Gene-Centered Yeast One-Hybrid Assays. Cold Spring Harb Protoc 2016; 2016:2016/12/pdb.top077669. [PMID: 27934693 PMCID: PMC5443116 DOI: 10.1101/pdb.top077669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful "gene-centered" method to identify the TFs that can bind a DNA sequence of interest. In this introduction, we describe the basic principles of the Y1H assay and its advantages and disadvantages and briefly discuss how it is complementary to "TF-centered" methods that identify protein-DNA interactions for a known protein of interest.
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Affiliation(s)
- Juan I. Fuxman Bass
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - John S. Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Albertha J.M. Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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13
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Ma JE, Lang QQ, Qiu FF, Zhang L, Li XG, Luo W, Wang J, Wang X, Lin XR, Liu WS, Nie QH, Zhang XQ. Negative Glucocorticoid Response-Like Element from the First Intron of the Chicken Growth Hormone Gene Represses Gene Expression in the Rat Pituitary Tumor Cell Line. Int J Mol Sci 2016; 17:ijms17111863. [PMID: 27834851 PMCID: PMC5133863 DOI: 10.3390/ijms17111863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/19/2016] [Accepted: 10/25/2016] [Indexed: 12/29/2022] Open
Abstract
The effects of introns, especially the first intron, on the regulation of gene expression remains unclear. Therefore, the objective of the present study was to investigate the transcriptional regulatory function of intron 1 on the chicken growth hormone (cGH) gene in the rat pituitary tumor cell line (GH4-C1). Transient transfection using first-intron-inserted cGH complete coding sequences (CDSs) and non-intron-inserted cGH CDS plasmids, quantitative RT-PCR (qRT-PCR) and western blot assays were used to detect the expression of cGH. The reporter gene assay was also used to investigate the effect of a series of fragments in the first intron of cGH on gene expression in GH4-C1. All of the results revealed that a 200-bp fragment located in the +485/+684 region of intron 1 was essential for repressing the expression of cGH. Further informatics analysis showed that there was a cluster of 13 transcriptional factor binding sites (TFBSs) in the +485/+684 region of the cGH intron 1. Disruption of a glucocorticoid response-like element (the 19-nucleotide sequence 5'-AGGCTTGACAGTGACCTCC-3') containing a T-box motif (TGACCT) located within this DNA fragment increased the expression of the reporter gene in GH4-C1. In addition, an electrophoretic mobility shift assay (EMSA) revealed a glucocorticoid receptor (GR) protein of rat binding to the glucocorticoid response-like element. Together, these results indicate that there is a negative glucocorticoid response-like element (nGRE) located in the +591/+609 region within the first intron of cGH, which is essential for the down-regulation of cGH expression.
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Affiliation(s)
- Jing-E Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qian-Qian Lang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Feng-Fang Qiu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Li Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Xiang-Guang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Juan Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Xing Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Xi-Ran Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Wen-Sheng Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qing-Hua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Xi-Quan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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14
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Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. Mol Syst Biol 2016; 12:884. [PMID: 27777270 PMCID: PMC5081483 DOI: 10.15252/msb.20167131] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein–DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene‐centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two‐thirds of which are novel, as well as integrate gene expression, protein–protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Lucie Kozlowski
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - John S Reece-Hoyes
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amy D Holdorf
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Akihiro Mori
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Albertha Jm Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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15
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Mora-Lorca JA, Sáenz-Narciso B, Gaffney CJ, Naranjo-Galindo FJ, Pedrajas JR, Guerrero-Gómez D, Dobrzynska A, Askjaer P, Szewczyk NJ, Cabello J, Miranda-Vizuete A. Glutathione reductase gsr-1 is an essential gene required for Caenorhabditis elegans early embryonic development. Free Radic Biol Med 2016; 96:446-61. [PMID: 27117030 PMCID: PMC8386055 DOI: 10.1016/j.freeradbiomed.2016.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/18/2016] [Indexed: 12/22/2022]
Abstract
Glutathione is the most abundant thiol in the vast majority of organisms and is maintained in its reduced form by the flavoenzyme glutathione reductase. In this work, we describe the genetic and functional analysis of the Caenorhabditis elegans gsr-1 gene that encodes the only glutathione reductase protein in this model organism. By using green fluorescent protein reporters we demonstrate that gsr-1 produces two GSR-1 isoforms, one located in the cytoplasm and one in the mitochondria. gsr-1 loss of function mutants display a fully penetrant embryonic lethal phenotype characterized by a progressive and robust cell division delay accompanied by an aberrant distribution of interphasic chromatin in the periphery of the cell nucleus. Maternally expressed GSR-1 is sufficient to support embryonic development but these animals are short-lived, sensitized to chemical stress, have increased mitochondrial fragmentation and lower mitochondrial DNA content. Furthermore, the embryonic lethality of gsr-1 worms is prevented by restoring GSR-1 activity in the cytoplasm but not in mitochondria. Given the fact that the thioredoxin redox systems are dispensable in C. elegans, our data support a prominent role of the glutathione reductase/glutathione pathway in maintaining redox homeostasis in the nematode.
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Affiliation(s)
- José Antonio Mora-Lorca
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain; Departamento de Farmacología, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain
| | | | - Christopher J Gaffney
- MRC/ARUK Centre for Musculoskeletal Ageing Research, University of Nottingham and Medical School Royal Derby Hospital, DE22 3DT Derby, United Kingdom
| | - Francisco José Naranjo-Galindo
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - José Rafael Pedrajas
- Grupo de Bioquímica y Señalización Celular, Departamento de Biología Experimental, Universidad de Jaén, 23071 Jaén, Spain
| | - David Guerrero-Gómez
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain
| | - Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Nathaniel J Szewczyk
- MRC/ARUK Centre for Musculoskeletal Ageing Research, University of Nottingham and Medical School Royal Derby Hospital, DE22 3DT Derby, United Kingdom
| | - Juan Cabello
- Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain.
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Sevilla, Spain.
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16
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Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJM. Human gene-centered transcription factor networks for enhancers and disease variants. Cell 2015; 161:661-673. [PMID: 25910213 PMCID: PMC4409666 DOI: 10.1016/j.cell.2015.03.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/26/2014] [Accepted: 01/30/2015] [Indexed: 01/16/2023]
Abstract
Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild-type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations. We detect both loss and gain of TF interactions with mutant loci that are concordant with target gene expression changes. This work establishes eY1H assays as a powerful addition to the toolkit of mapping human GRNs and for the high-throughput characterization of genomic variants that are rapidly being identified by genome-wide association studies.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nidhi Sahni
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Aurian Garcia-Gonzalez
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Akihiro Mori
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Numana Bhat
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Song Yi
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David E Hill
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Marc Vidal
- Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Albertha J M Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Cancer Biology, Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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17
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Lee MH, Cha DS, Mamillapalli SS, Kwon YC, Koo HS. Transgene-mediated co-suppression of DNA topoisomerase-1 gene in Caenorhabditis elegans. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 5:11-20. [PMID: 24955284 PMCID: PMC4058960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 04/12/2014] [Indexed: 06/03/2023]
Abstract
Ectopic expression of multi-transgenic copies can result in reduced expression of the transgene and can induce silence of endogenous gene; this process is called as co-suppression. Using a transgene-mediated co-suppression technique, we demonstrated the biological function of DNA topoisomerase-1 (top-1) in C. elegans development. Introduction of full-length top-1 transgene sufficiently induced the co-suppression of endogenous top-1 gene, causing embryonic lethality and abnormal germline development. We also found that the co-suppression of top-1 gene affected morphogenesis, lifespan and larval growth that were not observed in top-1 (RNAi) animals. Strikingly, co-suppression effects were significantly reduced by the elimination of top-1 introns, suggesting that efficient co-suppression may require intron(s) in C. elegans. Sequence analysis revealed that the introns 1 and 2 of top-1 gene possess consensus binding sites for several transcription factors, including MAB-3, LIN-14, TTX-3/CEH-10, CEH-1, and CEH-22. Among them, we examined a genetic link between ceh-22 and top-1. The ceh-22 is partially required for the specification of distal tip cells (DTC), which functions as a stem cell niche in the C. elegans gonad. Intriguingly, top-1 (RNAi) significantly enhanced DTC loss in ceh-22 mutant gonads, indicating that top-1 may play an important role in CEH-22-mediated DTC fate specification. Therefore, our findings suggest that transgene-mediated co-suppression facilitates the silencing of the specific genes and the study of gene function in vivo.
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Affiliation(s)
- Myon-Hee Lee
- Department of Oncology, Brody School of Medicine, East Carolina UniversityGreenville, NC 27834, USA
- Leo W. Jenkins Cancer Center, Brody School of Medicine, East Carolina UniversityGreenville, NC 27834, USA
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel Hill, NC 27599, USA
| | - Dong Seok Cha
- Department of Oncology, Brody School of Medicine, East Carolina UniversityGreenville, NC 27834, USA
- Department of Oriental Pharmacy, College of Pharmacy, Woosuk UniversityJeonbuk 565-701, Republic of Korea
| | | | - Young Chul Kwon
- Department of Oncology, Brody School of Medicine, East Carolina UniversityGreenville, NC 27834, USA
| | - Hyeon-Sook Koo
- Department of Biochemistry, Yonsei UniversitySeoul 120-749, Republic of Korea
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18
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Glauser DA. The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites. BMC Genomics 2014; 15:364. [PMID: 24884695 PMCID: PMC4039745 DOI: 10.1186/1471-2164-15-364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/15/2014] [Indexed: 11/28/2022] Open
Abstract
Background Alternative splicing diversifies the pool of messenger RNA molecules encoded by individual genes. This diversity is particularly high when multiple splicing decisions cause a combinatorial arrangement of several alternate exons. We know very little on how the multiple decisions occurring during the maturation of single transcripts are coordinated and whether specific sequence elements might be involved. Results Here, the Caenorhabditis elegans genome was surveyed in order to identify sequence elements that might play a specific role in the regulation of multiple splicing decisions. The introns flanking alternate exons in transcripts whose maturation involves multiple alternative splicing decisions were compared to those whose maturation involves a single decision. Fifty-eight penta-, hexa-, and hepta-meric elements, clustered in 17 groups, were significantly over-represented in genes subject to multiple alternative splicing decisions. Most of these motifs relate to known splicing regulatory elements and appear to be well conserved in the related species Caenorhabditis briggsae. The usage of specific motifs is not linked to the gene product function, but rather depends on the gene structure, since it is influenced by the distance separating the multiple splicing decision sites. Two of these motifs are part of the CeRep25B minisatellite, which is also over-represented at the vicinity of alternative splicing regions. Most of the remaining motifs are not part of repeated sequence elements, but tend to occur in specific heterologous pairs in genes subject to multiple alternative splicing decisions. Conclusions The existence of specific intronic sequence elements linked to multiple alternative splicing decisions is intriguing and suggests that these elements might have some specialized regulatory role during splicing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-364) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dominique A Glauser
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
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