1
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Wang H, Bollepogu Raja KK, Yeung K, Morrison CA, Terrizzano A, Khodadadi-Jamayran A, Chen P, Jordan A, Fritsch C, Sprecher SG, Mardon G, Treisman JE. Synergistic activation by Glass and Pointed promotes neuronal identity in the Drosophila eye disc. Nat Commun 2024; 15:7091. [PMID: 39154080 PMCID: PMC11330500 DOI: 10.1038/s41467-024-51429-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
The integration of extrinsic signaling with cell-intrinsic transcription factors can direct progenitor cells to differentiate into distinct cell fates. In the developing Drosophila eye, differentiation of photoreceptors R1-R7 requires EGFR signaling mediated by the transcription factor Pointed, and our single-cell RNA-Seq analysis shows that the same photoreceptors require the eye-specific transcription factor Glass. We find that ectopic expression of Glass and activation of EGFR signaling synergistically induce neuronal gene expression in the wing disc in a Pointed-dependent manner. Targeted DamID reveals that Glass and Pointed share many binding sites in the genome of developing photoreceptors. Comparison with transcriptomic data shows that Pointed and Glass induce photoreceptor differentiation through intermediate transcription factors, including the redundant homologs Scratch and Scrape, as well as directly activating neuronal effector genes. Our data reveal synergistic activation of a multi-layered transcriptional network as the mechanism by which EGFR signaling induces neuronal identity in Glass-expressing cells.
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Affiliation(s)
- Hongsu Wang
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Carolyn A Morrison
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA
- 10x Genomics, Pleasanton, CA, 94588, USA
| | - Antonia Terrizzano
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA
- Biology of Centrosomes and Genetic Instability Team, Curie Institute, PSL Research University, CNRS, UMR144, 12 rue Lhomond, Paris, 75005, France
| | | | - Phoenix Chen
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Ashley Jordan
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA
| | - Cornelia Fritsch
- Department of Biology, Université de Fribourg, Fribourg, Switzerland
| | - Simon G Sprecher
- Department of Biology, Université de Fribourg, Fribourg, Switzerland
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jessica E Treisman
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA.
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2
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Alnasir JJ, Shanahan HP. Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq. J Comput Biol 2023; 30:131-148. [PMID: 36689201 DOI: 10.1089/cmb.2021.0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Given the wide variability in the quality of next-generation sequencing data submitted to public repositories, it is essential to identify methods that can perform quality control on these data sets when additional quality control data, such as mean tile data, are missing from public repositories. In this study, we present evidence that correlating counts of reads corresponding to pairs of motifs separated over specific distances on individual exons can be used as a proxy mean tile data in the data sets we analyzed and hence could be used when mean tile data are not available. As test data sets we use the Homo sapiens in vitro transcribed (IVT) data set, and a Drosophila melanogaster data set comprising wild and mutant types. We find that a FastQC analysis of the available parts of these data sets demonstrates that the per-tile sequencing quality is good for all the data sets apart from the mutant-type data where the mutant-r3 data are worse than the mutant-r2 data. Correspondingly, intra-exon motif correlations are reasonably large for all data sets except this latter case where the mutant-r2 correlations are low and the mutant-r3 correlations close to zero. We propose that these extremely low correlations are indicative of bias of technical origin, such as flowcell errors. In addition to this, the intra-exon motif correlations as a function of both guanosine-cytosine (GC) content parameters are somewhat higher and less dependent on the GC content parameters in the IVT-Plasmids messenger RNA (mRNA) selection free RNA-Seq sample (control) than in the other RNA-Seq samples that did undergo mRNA selection: both ribosomal depletion (IVT-Only) and PolyA selection (IVT-PolyA, wild type, and mutant).
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Affiliation(s)
- Jamie J Alnasir
- Department of Computing, Imperial College, London, United Kingdom
| | - Hugh P Shanahan
- Department of Computer Science, Royal Holloway, University of London, Egham, United Kingdom
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3
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Rylee J, Mahato S, Aldrich J, Bergh E, Sizemore B, Feder LE, Grega S, Helms K, Maar M, Britt SG, Zelhof AC. A TRiP RNAi screen to identify molecules necessary for Drosophila photoreceptor differentiation. G3 GENES|GENOMES|GENETICS 2022; 12:6758253. [DOI: 10.1093/g3journal/jkac257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022]
Abstract
Abstract
Drosophila rhabdomeric terminal photoreceptor differentiation is an extended process taking several days to complete. Following ommatidial patterning by the morphogenetic furrow, photoreceptors are sequentially recruited and specified, and terminal differentiation begins. Key events of terminal differentiation include the establishment of apical and basolateral domains, rhabdomere and stalk formation, inter-rhabdomeral space formation, and expression of phototransduction machinery. While many key regulators of these processes have been identified, the complete network of transcription factors to downstream effector molecules necessary for regulating each of these major events remains incomplete. Here, we report an RNAi screen to identify additional molecules and cellular pathways required for photoreceptor terminal differentiation. First, we tested several eye-specific GAL4 drivers for correct spatial and temporal specificity and identified Pph13-GAL4 as the most appropriate GAL4 line for our screen. We screened lines available through the Transgenic RNAi Project and isolated lines that when combined with Pph13-GAL4 resulted in the loss of the deep pseudopupil, as a readout for abnormal differentiation. In the end, we screened 6,189 lines, representing 3,971 genes, and have identified 64 genes, illuminating potential new regulatory molecules and cellular pathways for the differentiation and organization of Drosophila rhabdomeric photoreceptors.
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Affiliation(s)
- Johnathan Rylee
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Simpla Mahato
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - John Aldrich
- Department of Neurology and Ophthalmology, Dell Medical School, University of Texas , Austin, TX 78712, USA
| | - Emma Bergh
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Brandon Sizemore
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Lauren E Feder
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Shaun Grega
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Kennedy Helms
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Megan Maar
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
| | - Steven G Britt
- Department of Neurology and Ophthalmology, Dell Medical School, University of Texas , Austin, TX 78712, USA
| | - Andrew C Zelhof
- Department of Biology, Indiana University , Bloomington, IN 47405, USA
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4
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Douthit J, Hairston A, Lee G, Morrison CA, Holguera I, Treisman JE. R7 photoreceptor axon targeting depends on the relative levels of lost and found expression in R7 and its synaptic partners. eLife 2021; 10:65895. [PMID: 34003117 PMCID: PMC8205486 DOI: 10.7554/elife.65895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/17/2021] [Indexed: 01/17/2023] Open
Abstract
As neural circuits form, growing processes select the correct synaptic partners through interactions between cell surface proteins. The presence of such proteins on two neuronal processes may lead to either adhesion or repulsion; however, the consequences of mismatched expression have rarely been explored. Here, we show that the Drosophila CUB-LDL protein Lost and found (Loaf) is required in the UV-sensitive R7 photoreceptor for normal axon targeting only when Loaf is also present in its synaptic partners. Although targeting occurs normally in loaf mutant animals, removing loaf from photoreceptors or expressing it in their postsynaptic neurons Tm5a/b or Dm9 in a loaf mutant causes mistargeting of R7 axons. Loaf localizes primarily to intracellular vesicles including endosomes. We propose that Loaf regulates the trafficking or function of one or more cell surface proteins, and an excess of these proteins on the synaptic partners of R7 prevents the formation of stable connections.
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Affiliation(s)
- Jessica Douthit
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Ariel Hairston
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Gina Lee
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Carolyn A Morrison
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
| | - Isabel Holguera
- Department of Biology, New York University, New York, United States
| | - Jessica E Treisman
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, NYU School of Medicine, New York, United States
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5
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Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE. New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics 2021; 217:6117222. [PMID: 33681970 DOI: 10.1093/genetics/iyab007] [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] [Received: 03/15/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
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Affiliation(s)
- Manon Quiquand
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nan Qiao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chunyu Zhao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Matthew Slattery
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jackie J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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6
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Yeung K, Wang F, Li Y, Wang K, Mardon G, Chen R. Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development. Nucleic Acids Res 2019; 46:11743-11758. [PMID: 30295802 PMCID: PMC6294497 DOI: 10.1093/nar/gky892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/02/2018] [Indexed: 01/22/2023] Open
Abstract
Eyeless (ey) is one of the most critical transcription factors for initiating the entire eye development in Drosophila. However, the molecular mechanisms through which Ey regulates target genes and pathways have not been characterized at the genomic level. Using ChIP-Seq, we generated an endogenous Ey-binding profile in Drosophila developing eyes. We found that Ey binding occurred more frequently at promoter compared to non-promoter regions. Ey promoter binding was correlated with the active transcription of genes involved in development and transcription regulation. An integrative analysis revealed that Ey directly regulated a broad and highly connected genetic network, including many essential patterning pathways, and known and novel eye genes. Interestingly, we observed that Ey could target multiple components of the same pathway, which might enhance its control of these pathways during eye development. In addition to protein-coding genes, we discovered Ey also targeted non-coding RNAs, which represents a new regulatory mechanism employed by Ey. These findings suggest that Ey could use multiple molecular mechanisms to regulate target gene expression and pathway function, which might enable Ey to exhibit a greater flexibility in controlling different processes during eye development.
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Affiliation(s)
- Kelvin Yeung
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Feng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rui Chen
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.,Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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7
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Fritsch C, Bernardo-Garcia FJ, Humberg TH, Mishra AK, Miellet S, Almeida S, Frochaux MV, Deplancke B, Huber A, Sprecher SG. Multilevel regulation of the glass locus during Drosophila eye development. PLoS Genet 2019; 15:e1008269. [PMID: 31299050 PMCID: PMC6655844 DOI: 10.1371/journal.pgen.1008269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/24/2019] [Accepted: 06/23/2019] [Indexed: 12/28/2022] Open
Abstract
Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control identity of photoreceptor as well as non-photoreceptor cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintenance of differentiated tissues. The molecular mechanisms that control expression of glass, however, remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alternative small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible Glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but is able to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is largely unaffected by targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.
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Affiliation(s)
- Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - F. Javier Bernardo-Garcia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | | | | | - Sara Miellet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - Silvia Almeida
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Bart Deplancke
- Laboratory of Systems Biology, IBI, SV, EPFL, Lausanne, Switzerland
| | - Armin Huber
- Institute of Physiology, University of Hohenheim, Hohenheim, Germany
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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8
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Sánchez-Aragón M, Cantisán-Gómez J, Luque CM, Brás-Pereira C, Lopes CS, Lemos MC, Casares F. A Toggle-Switch and a Feed-Forward Loop Engage in the Control of the Drosophila Retinal Determination Gene Network. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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9
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Masuko K, Fuse N, Komaba K, Katsuyama T, Nakajima R, Furuhashi H, Kurata S. winged eye Induces Transdetermination of Drosophila Imaginal Disc by Acting in Concert with a Histone Methyltransferase, Su(var)3-9. Cell Rep 2019; 22:206-217. [PMID: 29298422 DOI: 10.1016/j.celrep.2017.11.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 07/12/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022] Open
Abstract
Drosophila imaginal disc cells exhibit a remarkable ability to convert cell fates in response to various perturbations, a phenomenon called transdetermination (TD). We previously identified winged eye (wge) as a factor that induces eye-to-wing TD upon overexpression in eye imaginal discs, but the molecular mechanisms underlying TD have remained largely unclear. Here, we found that wge induces various histone modifications and enhances the methylation of Lys9 on histone H3 (H3K9), a feature of heterochromatin. A histone methyltransferase, Su(var)3-9, is required for wge-mediated H3K9 methylation and eye-to-wing TD. Su(var)3-9 is also required for classical wound-induced TD but not for normal development, suggesting its involvement in several types of imaginal disc TDs. Transcriptome analysis revealed that wge represses eye identity genes independently of Su(var)3-9 and activates TD-related genes by acting together with Su(var)3-9. These findings provide new insights into diverse types of chromatin regulation at progressive steps of cell-fate conversions.
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Affiliation(s)
- Keita Masuko
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Naoyuki Fuse
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kanae Komaba
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Tomonori Katsuyama
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Rumi Nakajima
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Hirofumi Furuhashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Shoichiro Kurata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
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10
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Alexandre PA, Naval-Sanchez M, Porto-Neto LR, Ferraz JBS, Reverter A, Fukumasu H. Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle. Front Genet 2019; 10:230. [PMID: 30967894 PMCID: PMC6439317 DOI: 10.3389/fgene.2019.00230] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/04/2019] [Indexed: 11/20/2022] Open
Abstract
Systems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (Illumina HiSeq 2500, 100 bp, pared-end). From the 17,354 expressed genes considering all tissues, 1,335 were prioritized by five selection categories (differentially expressed, harboring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB1 were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated with FE. Moreover, we indicated potential biomarkers of FE, which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed the main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.
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Affiliation(s)
- Pâmela A. Alexandre
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Marina Naval-Sanchez
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Laercio R. Porto-Neto
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - José Bento S. Ferraz
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
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11
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Bernardo-Garcia FJ, Syed M, Jékely G, Sprecher SG. Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans. EvoDevo 2019; 10:4. [PMID: 30873275 PMCID: PMC6399963 DOI: 10.1186/s13227-019-0117-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/15/2019] [Indexed: 12/14/2022] Open
Abstract
Across metazoans, visual systems employ different types of photoreceptor neurons (PRs) to detect light. These include rhabdomeric PRs, which exist in distantly related phyla and possess an evolutionarily conserved phototransduction cascade. While the development of rhabdomeric PRs has been thoroughly studied in the fruit fly Drosophila melanogaster, we still know very little about how they form in other species. To investigate this question, we tested whether the transcription factor Glass, which is crucial for instructing rhabdomeric PR formation in Drosophila, may play a similar role in other metazoans. Glass homologues exist throughout the animal kingdom, indicating that this protein evolved prior to the metazoan radiation. Interestingly, our work indicates that glass is not expressed in rhabdomeric photoreceptors in the planarian Schmidtea mediterranea nor in the annelid Platynereis dumerilii. Combined with a comparative analysis of the Glass DNA-binding domain, our data suggest that the fate of rhabdomeric PRs is controlled by Glass-dependent and Glass-independent mechanisms in different animal clades.
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Affiliation(s)
- F Javier Bernardo-Garcia
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.,2Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158 USA
| | - Maryam Syed
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gáspár Jékely
- 3Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Simon G Sprecher
- 1Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
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12
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Torres J, Monti R, Moore AL, Seimiya M, Jiang Y, Beerenwinkel N, Beisel C, Beira JV, Paro R. A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila. eLife 2018; 7:32697. [PMID: 29560857 PMCID: PMC5862528 DOI: 10.7554/elife.32697] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/04/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor initiation is often linked to a loss of cellular identity. Transcriptional programs determining cellular identity are preserved by epigenetically-acting chromatin factors. Although such regulators are among the most frequently mutated genes in cancer, it is not well understood how an abnormal epigenetic condition contributes to tumor onset. In this work, we investigated the gene signature of tumors caused by disruption of the Drosophila epigenetic regulator, polyhomeotic (ph). In larval tissue ph mutant cells show a shift towards an embryonic-like signature. Using loss- and gain-of-function experiments we uncovered the embryonic transcription factor knirps (kni) as a new oncogene. The oncogenic potential of kni lies in its ability to activate JAK/STAT signaling and block differentiation. Conversely, tumor growth in ph mutant cells can be substantially reduced by overexpressing a differentiation factor. This demonstrates that epigenetically derailed tumor conditions can be reversed when targeting key players in the transcriptional network. When an animal is developing as an embryo, different cells start to specialize into the specific cell types needed to form the tissues and organs of the body. How an individual cell commits to become a certain type of cell is mostly determined by which of the genes in its DNA are active. In animal cells, DNA is wrapped around proteins called histones, and one way that cells can maintain their distinct pattern of gene activity is via chemical tags on the histones. These tags can switch nearby genes on or off, and are added or removed by other proteins called epigenetic regulators. The epigenetic tags are also stably inherited when the cell divides, meaning that a cell’s identity can be maintained over many cell generations. If epigenetic regulators fail to work properly or get disrupted, the pattern of gene activity in a cell becomes altered. As a consequence, that cell can lose its identity and will often turn into a cancer cell. In fact, mutations in epigenetic regulators are found in several human cancers. It is not yet understood how these changes in gene expression lead cells to become cancerous. Torres et al. have now analyzed an epigenetic regulator called Polyhomeotic in developing larvae of the fruit fly, Drosophila melanogaster. The results show that when Polyhomeotic is not produced the fly larvae develop tumors. Moreover, the mutant cells without Polyhomeotic had different gene expression profiles compared to normal cells. This in turn caused the mutant cells, which had previously committed to a certain fate, to become more like the unspecialized cells found in early embryos. Torres et al. next showed that, among the genes that were incorrectly regulated when Polyhomeotic’s activity was compromised, one gene called knirps was switched on by mistake, which led the mutant cells to become tumor cells. When the activity of knirps was reduced instead, almost no tumors grew. Additionally, Torres et al. found that the protein encoded by knirps activates a signaling pathway that keeps tumor cells unspecialized by blocking their normal progress to a more mature and specialized state – a process known as differentiation. Experimentally raising the levels of a different molecule that ultimately promotes differentiation caused the tumor cells to grow less. These findings suggest that tumors caused when epigenetic regulation goes awry may be reversed by targeting key genes such as knirps. Further work is now needed to test whether these findings will also extend to humans. Forcing cancer cells from a highly dividing, non-specialized state into a dead-end, mature state may lead to new ways to treat cancer.
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Affiliation(s)
- Joana Torres
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Remo Monti
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ariane L Moore
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Yanrui Jiang
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Jorge V Beira
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
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Torres-Oliva M, Schneider J, Wiegleb G, Kaufholz F, Posnien N. Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PLoS Genet 2018; 14:e1007180. [PMID: 29360820 PMCID: PMC5796731 DOI: 10.1371/journal.pgen.1007180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 02/02/2018] [Accepted: 01/01/2018] [Indexed: 01/01/2023] Open
Abstract
Drosophila melanogaster head development represents a valuable process to study the developmental control of various organs, such as the antennae, the dorsal ocelli and the compound eyes from a common precursor, the eye-antennal imaginal disc. While the gene regulatory network underlying compound eye development has been extensively studied, the key transcription factors regulating the formation of other head structures from the same imaginal disc are largely unknown. We obtained the developmental transcriptome of the eye-antennal discs covering late patterning processes at the late 2nd larval instar stage to the onset and progression of differentiation at the end of larval development. We revealed the expression profiles of all genes expressed during eye-antennal disc development and we determined temporally co-expressed genes by hierarchical clustering. Since co-expressed genes may be regulated by common transcriptional regulators, we combined our transcriptome dataset with publicly available ChIP-seq data to identify central transcription factors that co-regulate genes during head development. Besides the identification of already known and well-described transcription factors, we show that the transcription factor Hunchback (Hb) regulates a significant number of genes that are expressed during late differentiation stages. We confirm that hb is expressed in two polyploid subperineurial glia cells (carpet cells) and a thorough functional analysis shows that loss of Hb function results in a loss of carpet cells in the eye-antennal disc. Additionally, we provide for the first time functional data indicating that carpet cells are an integral part of the blood-brain barrier. Eventually, we combined our expression data with a de novo Hb motif search to reveal stage specific putative target genes of which we find a significant number indeed expressed in carpet cells. The development of different cell types must be tightly coordinated, and the eye-antennal imaginal discs of Drosophila melanogaster represent an excellent model to study the molecular mechanisms underlying this coordination. These imaginal discs contain the anlagen of nearly all adult head structures, such as the antennae, the head cuticle, the ocelli and the compound eyes. While large scale screens have been performed to unravel the gene regulatory network underlying compound eye development, a comprehensive understanding of genome wide expression dynamics throughout head development is still missing to date. We studied the genome wide gene expression dynamics during eye-antennal disc development in D. melanogaster to identify new central regulators of the underlying gene regulatory network. Expression based gene clustering and transcription factor motif enrichment analyses revealed a central regulatory role of the transcription factor Hunchback (Hb). We confirmed that hb is expressed in two polyploid retinal subperineurial glia cells (carpet cells). Our functional analysis shows that Hb is necessary for carpet cell development and we show for the first time that the carpet cells are an integral part of the blood-brain barrier.
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Affiliation(s)
- Montserrat Torres-Oliva
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Julia Schneider
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Gordon Wiegleb
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Felix Kaufholz
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
| | - Nico Posnien
- Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, GZMB Ernst-Caspari-Haus, Göttingen, Germany
- * E-mail:
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14
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Morrison CA, Chen H, Cook T, Brown S, Treisman JE. Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye. PLoS Genet 2018; 14:e1007173. [PMID: 29324767 PMCID: PMC5783423 DOI: 10.1371/journal.pgen.1007173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/24/2018] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye.
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Affiliation(s)
- Carolyn A. Morrison
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Hao Chen
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Tiffany Cook
- Center of Molecular Medicine and Genomics and Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI, United States of America
| | - Stuart Brown
- Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
| | - Jessica E. Treisman
- Skirball Institute for Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY, United States of America
- * E-mail:
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15
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Alnasir J, Shanahan HP. A Novel Method to Detect Bias in Short Read NGS Data. J Integr Bioinform 2017; 14:/j/jib.2017.14.issue-3/jib-2017-0025/jib-2017-0025.xml. [PMID: 28941355 PMCID: PMC6042817 DOI: 10.1515/jib-2017-0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/10/2017] [Indexed: 11/15/2022] Open
Abstract
Detecting sources of bias in transcriptomic data is essential to determine signals of Biological significance. We outline a novel method to detect sequence specific bias in short read Next Generation Sequencing data. This is based on determining intra-exon correlations between specific motifs. This requires a mild assumption that short reads sampled from specific regions from the same exon will be correlated with each other. This has been implemented on Apache Spark and used to analyse two D. melanogaster eye-antennal disc data sets generated at the same laboratory. The wild type data set in drosophila indicates a variation due to motif GC content that is more significant than that found due to exon GC content. The software is available online and could be applied for cross-experiment transcriptome data analysis in eukaryotes.
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Bernardo-Garcia FJ, Humberg TH, Fritsch C, Sprecher SG. Successive requirement of Glass and Hazy for photoreceptor specification and maintenance in Drosophila. Fly (Austin) 2016; 11:112-120. [PMID: 27723419 PMCID: PMC5406162 DOI: 10.1080/19336934.2016.1244591] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Development of the insect compound eye requires a highly controlled interplay between transcription factors. However, the genetic mechanisms that link early eye field specification to photoreceptor terminal differentiation and fate maintenance remain largely unknown. Here, we decipher the function of 2 transcription factors, Glass and Hazy, which play a central role during photoreceptor development. The regulatory interactions between Glass and Hazy suggest that they function together in a coherent feed-forward loop in all types of Drosophila photoreceptors. While the glass mutant eye lacks the expression of virtually all photoreceptor genes, young hazy mutants correctly express most phototransduction genes. Interestingly, the expression of these genes is drastically reduced in old hazy mutants. This age-dependent loss of the phototransduction cascade correlates with a loss of phototaxis in old hazy mutant flies. We conclude that Glass can either directly or indirectly initiate the expression of most phototransduction proteins in a Hazy-independent manner, and that Hazy is mainly required for the maintenance of functional photoreceptors in adult flies.
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Affiliation(s)
| | | | - Cornelia Fritsch
- a Department of Biology , University of Fribourg , Fribourg , Switzerland
| | - Simon G Sprecher
- a Department of Biology , University of Fribourg , Fribourg , Switzerland
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17
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Two temporal functions of Glass: Ommatidium patterning and photoreceptor differentiation. Dev Biol 2016; 414:4-20. [PMID: 27105580 DOI: 10.1016/j.ydbio.2016.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/04/2016] [Accepted: 04/13/2016] [Indexed: 12/28/2022]
Abstract
Much progress has been made in elucidating the molecular networks required for specifying retinal cells, including photoreceptors, but the downstream mechanisms that maintain identity and regulate differentiation remain poorly understood. Here, we report that the transcription factor Glass has a dual role in establishing a functional Drosophila eye. Utilizing conditional rescue approaches, we confirm that persistent defects in ommatidium patterning combined with cell death correlate with the overall disruption of eye morphology in glass mutants. In addition, we reveal that Glass exhibits a separable role in regulating photoreceptor differentiation. In particular, we demonstrate the apparent loss of glass mutant photoreceptors is not only due to cell death but also a failure of the surviving photoreceptors to complete differentiation. Moreover, the late reintroduction of Glass in these developmentally stalled photoreceptors is capable of restoring differentiation in the absence of correct ommatidium patterning. Mechanistically, transcription profiling at the time of differentiation reveals that Glass is necessary for the expression of many genes implicated in differentiation, i.e. rhabdomere morphogenesis, phototransduction, and synaptogenesis. Specifically, we show Glass directly regulates the expression of Pph13, which encodes a transcription factor necessary for opsin expression and rhabdomere morphogenesis. Finally, we demonstrate the ability of Glass to choreograph photoreceptor differentiation is conserved between Drosophila and Tribolium, two holometabolous insects. Altogether, our work identifies a fundamental regulatory mechanism to generate the full complement of cells required for a functional rhabdomeric visual system and provides a critical framework to investigate the basis of differentiation and maintenance of photoreceptor identity.
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18
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Bernardo-Garcia FJ, Fritsch C, Sprecher SG. The transcription factor Glass links eye field specification with photoreceptor differentiation in Drosophila. Development 2016; 143:1413-23. [PMID: 26952983 DOI: 10.1242/dev.128801] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/22/2016] [Indexed: 12/12/2022]
Abstract
Eye development requires an evolutionarily conserved group of transcription factors, termed the retinal determination network (RDN). However, little is known about the molecular mechanism by which the RDN instructs cells to differentiate into photoreceptors. We show that photoreceptor cell identity in Drosophila is critically regulated by the transcription factor Glass, which is primarily expressed in photoreceptors and whose role in this process was previously unknown. Glass is both required and sufficient for the expression of phototransduction proteins. Our results demonstrate that the RDN member Sine oculis directly activates glass expression, and that Glass activates the expression of the transcription factors Hazy and Otd. We identified hazy as a direct target of Glass. Induced expression of Hazy in the retina partially rescues the glass mutant phenotype. Together, our results provide a transcriptional link between eye field specification and photoreceptor differentiation in Drosophila, placing Glass at a central position in this developmental process.
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Affiliation(s)
| | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
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19
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Friedrich M, Cook T, Zelhof AC. Ancient default activators of terminal photoreceptor differentiation in the pancrustacean compound eye: the homeodomain transcription factors Otd and Pph13. CURRENT OPINION IN INSECT SCIENCE 2016; 13:33-42. [PMID: 27436551 PMCID: PMC5221501 DOI: 10.1016/j.cois.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 06/06/2023]
Abstract
The origin of the Drosophila compound eye predates the ancestor of Pancrustacea, the arthropod clade that includes insects and Crustaceans. Recent studies in emerging model systems for pancrustacean development-the red flour beetle Tribolium castaneum and water flea Daphnia pulex-have begun to shed light on the evolutionary conservation of transcriptional mechanisms found for the Drosophila compound eye. Here, we discuss the conserved roles of the transcription factors Otd and Pph13, which complement each other in two terminal events of photoreceptor differentiation: rhabdomere morphogenesis and transcriptional default activation of opsin gene expression. The synthesis of these data allows us to frame an evolutionary developmental model of the earliest events that generated the wavelength-specific photoreceptor subtypes of pancrustacean compound eyes.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Tiffany Cook
- Center of Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Ophthalmology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Andrew C Zelhof
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Gracida X, Norris AD, Calarco JA. Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:229-61. [DOI: 10.1007/978-3-319-29073-7_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers. BMC Genomics 2015; 16:700. [PMID: 26377945 PMCID: PMC4574355 DOI: 10.1186/s12864-015-1897-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/02/2015] [Indexed: 11/15/2022] Open
Abstract
Background One of the major challenges in developmental biology is to understand the regulatory events that generate neuronal diversity. During Drosophila embryonic neural lineage development, cellular temporal identity is established in part by a transcription factor (TF) regulatory network that mediates a cascade of cellular identity decisions. Two of the regulators essential to this network are the POU-domain TFs Nubbin and Pdm-2, encoded by adjacent genes collectively known as pdm. The focus of this study is the discovery and characterization of cis-regulatory DNA that governs their expression. Results Phylogenetic footprinting analysis of a 125 kb genomic region that spans the pdm locus identified 116 conserved sequence clusters. To determine which of these regions function as cis-regulatory enhancers that regulate the dynamics of pdm gene expression, we tested each for in vivo enhancer activity during embryonic development and postembryonic neurogenesis. Our screen revealed 77 unique enhancers positioned throughout the noncoding region of the pdm locus. Many of these activated neural-specific gene expression during different developmental stages and many drove expression in overlapping patterns. Sequence comparisons of functionally related enhancers that activate overlapping expression patterns revealed that they share conserved elements that can be predictive of enhancer behavior. To facilitate data accessibility, the results of our analysis are catalogued in cisPatterns, an online database of the structure and function of these and other Drosophila enhancers. Conclusions These studies reveal a diversity of modular enhancers that most likely regulate pdm gene expression during embryonic and adult development, highlighting a high level of temporal and spatial expression specificity. In addition, we discovered clusters of functionally related enhancers throughout the pdm locus. A subset of these enhancers share conserved elements including sequences that correspond to known TF DNA binding sites. Although comparative analysis of the nubbin and pdm-2 encoding sequences indicate that these two genes most likely arose from a duplication event, we found only partial evidence of sequence duplication between their enhancers, suggesting that after the putative duplication their cis-regulatory DNA diverged at a higher rate than their coding sequences. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1897-2) contains supplementary material, which is available to authorized users.
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Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol 2015; 32:2441-55. [PMID: 25944915 PMCID: PMC4540964 DOI: 10.1093/molbev/msv107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Scoring the impact of noncoding variation on the function of cis-regulatory regions, on their chromatin state, and on the qualitative and quantitative expression levels of target genes is a fundamental problem in evolutionary genomics. A particular challenge is how to model the divergence of quantitative traits and to identify relationships between the changes across the different levels of the genome, the chromatin activity landscape, and the transcriptome. Here, we examine the use of the Ornstein-Uhlenbeck (OU) model to infer selection at the level of predicted cis-regulatory modules (CRMs), and link these with changes in transcription factor binding and chromatin activity. Using publicly available cross-species ChIP-Seq and STARR-Seq data we show how OU can be applied genome-wide to identify candidate transcription factors for which binding site and CRM turnover is correlated with changes in regulatory activity. Next, we profile open chromatin in the developing eye across three Drosophila species. We identify the recognition motifs of the chromatin remodelers, Trithorax-like and Grainyhead as mostly correlating with species-specific changes in open chromatin. In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence.
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Affiliation(s)
- Marina Naval-Sánchez
- Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Delphine Potier
- Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Gert Hulselmans
- Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Valerie Christiaens
- Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium
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Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference. Cell Rep 2014; 9:2290-303. [DOI: 10.1016/j.celrep.2014.11.038] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/24/2014] [Accepted: 11/22/2014] [Indexed: 11/20/2022] Open
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iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput Biol 2014; 10:e1003731. [PMID: 25058159 PMCID: PMC4109854 DOI: 10.1371/journal.pcbi.1003731] [Citation(s) in RCA: 608] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/27/2014] [Indexed: 01/17/2023] Open
Abstract
Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. We developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying a co-expressed gene set using cis-regulatory sequence analysis. iRegulon implements a genome-wide ranking-and-recovery approach to detect enriched transcription factor motifs and their optimal sets of direct targets. We increase the accuracy of network inference by using very large motif collections of up to ten thousand position weight matrices collected from various species, and linking these to candidate human TFs via a motif2TF procedure. We validate iRegulon on gene sets derived from ENCODE ChIP-seq data with increasing levels of noise, and we compare iRegulon with existing motif discovery methods. Next, we use iRegulon on more challenging types of gene lists, including microRNA target sets, protein-protein interaction networks, and genetic perturbation data. In particular, we over-activate p53 in breast cancer cells, followed by RNA-seq and ChIP-seq, and could identify an extensive up-regulated network controlled directly by p53. Similarly we map a repressive network with no indication of direct p53 regulation but rather an indirect effect via E2F and NFY. Finally, we generalize our computational framework to include regulatory tracks such as ChIP-seq data and show how motif and track discovery can be combined to map functional regulatory interactions among co-expressed genes. iRegulon is available as a Cytoscape plugin from http://iregulon.aertslab.org. Gene regulatory networks control developmental, homeostatic, and disease processes by governing precise levels and spatio-temporal patterns of gene expression. Determining their topology can provide mechanistic insight into these processes. Gene regulatory networks consist of interactions between transcription factors and their direct target genes. Each regulatory interaction represents the binding of the transcription factor to a specific DNA binding site near its target gene. Here we present a computational method, called iRegulon, to identify master regulators and direct target genes in a human gene signature, i.e. a set of co-expressed genes. iRegulon relies on the analysis of the regulatory sequences around each gene in the gene set to detect enriched TF motifs or ChIP-seq peaks, using databases of nearly 10.000 TF motifs and 1000 ChIP-seq data sets or “tracks”. Next, it associates enriched motifs and tracks with candidate transcription factors and determines the optimal subset of direct target genes. We validate iRegulon on ENCODE data, and use it in combination with RNA-seq and ChIP-seq data to map a p53 downstream network with new predicted co-factors and targets. iRegulon is available as a Cytoscape plugin, supporting human, mouse, and Drosophila genes, and provides access to hundreds of cancer-related TF-target subnetworks or “regulons”.
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Abstract
The construction and prediction of cell fate maps at the whole embryo level require the establishment of an accurate atlas of gene expression patterns throughout development and the identification of the corresponding cis-regulatory sequences. However, while the expression and regulation of genes encoding upstream developmental regulators such as transcription factors or signaling pathway components have been analyzed in detail, up to date the number of cis-regulatory sequences identified for downstream effector genes, like ion channels, pumps and exchangers, is very low. The control and regulation of ion homeostasis in each cell, including at blastoderm stages, are essential for normal embryonic development. In this study, we analyzed in detail the embryonic expression pattern and cis-regulatory modules of the Drosophila Na+-driven anion exchanger 1 (Ndae1) gene, involved in the regulation of pH homeostasis. We show that Ndae1 is expressed in a tight and complex spatial-temporal pattern. In particular, we report that this downstream effector gene is under the control of the canonical dorsal-ventral patterning cascade through dorsal, Toll, twist and snail at early embryogenesis. Moreover, we identify several cis-regulatory modules, some of which control discrete and non-overlapping aspects of endogenous gene expression throughout development.
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