1
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Chen PT, Levo M, Zoller B, Gregor T. Gene activity fully predicts transcriptional bursting dynamics. ARXIV 2024:arXiv:2304.08770v3. [PMID: 37131882 PMCID: PMC10153294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Transcription commonly occurs in bursts, with alternating productive (ON) and quiescent (OFF) periods, governing mRNA production rates. Yet, how transcription is regulated through bursting dynamics remains unresolved. Here, we conduct real-time measurements of endogenous transcriptional bursting with single-mRNA sensitivity. Leveraging the diverse transcriptional activities in early fly embryos, we uncover stringent relationships between bursting parameters. Specifically, we find that the durations of ON and OFF periods are linked. Regardless of the developmental stage or body-axis position, gene activity levels predict individual alleles' average ON and OFF periods. Lowly transcribing alleles predominantly modulate OFF periods (burst frequency), while highly transcribing alleles primarily tune ON periods (burst size). These relationships persist even under perturbations of cis-regulatory elements or trans-factors and account for bursting dynamics measured in other species. Our results suggest a novel mechanistic constraint governing bursting dynamics rather than a modular control of distinct parameters by distinct regulatory processes.
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Affiliation(s)
- Po-Ta Chen
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michal Levo
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Benjamin Zoller
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Stem Cell and Developmental Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Thomas Gregor
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Stem Cell and Developmental Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
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2
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Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023; 18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
The C2H2 zinc finger gene cucoid establishes anterior-posterior (AP) polarity in the early embryo of culicine mosquitoes. This gene is unrelated to genes that establish embryo polarity in other fly species (Diptera), such as the homeobox gene bicoid, which serves this function in the traditional model organism Drosophila melanogaster. The cucoid gene is a conserved single copy gene across lower dipterans but nothing is known about its function in other species, and its evolution in higher dipterans, including Drosophila, is unresolved. We found that cucoid is a member of the ZAD-containing C2H2 zinc finger (ZAD-ZNF) gene family and is orthologous to 27 of the 91 members of this family in D. melanogaster, including M1BP, ranshi, ouib, nom, zaf1, odj, Nnk, trem, Zif, and eighteen uncharacterized genes. Available knowledge of the functions of cucoid orthologs in Drosophila melanogaster suggest that the progenitor of this lineage specific expansion may have played a role in regulating chromatin. We also describe many aspects of the gene duplication history of cucoid in the brachyceran lineage of D. melanogaster, thereby providing a framework for predicting potential redundancies among these genes in D. melanogaster.
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Affiliation(s)
- Muzi Li
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Koray Kasan
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Zinnia Saha
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Yoseop Yoon
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Urs Schmidt-Ott
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
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3
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Colonnetta MM, Schedl P, Deshpande G. Germline/soma distinction in Drosophila embryos requires regulators of zygotic genome activation. eLife 2023; 12:78188. [PMID: 36598809 PMCID: PMC9812407 DOI: 10.7554/elife.78188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
In Drosophila melanogaster embryos, somatic versus germline identity is the first cell fate decision. Zygotic genome activation (ZGA) orchestrates regionalized gene expression, imparting specific identity on somatic cells. ZGA begins with a minor wave that commences at nuclear cycle (NC)8 under the guidance of chromatin accessibility factors (Zelda, CLAMP, GAF), followed by the major wave during NC14. By contrast, primordial germ cell (PGC) specification requires maternally deposited and posteriorly anchored germline determinants. This is accomplished by a centrosome coordinated release and sequestration of germ plasm during the precocious cellularization of PGCs in NC10. Here, we report a novel requirement for Zelda and CLAMP during the establishment of the germline/soma distinction. When their activity is compromised, PGC determinants are not properly sequestered, and specification is disrupted. Conversely, the spreading of PGC determinants from the posterior pole adversely influences transcription in the neighboring somatic nuclei. These reciprocal aberrations can be correlated with defects in centrosome duplication/separation that are known to induce inappropriate transmission of the germ plasm. Interestingly, consistent with the ability of bone morphogenetic protein (BMP) signaling to influence specification of embryonic PGCs, reduction in the transcript levels of a BMP family ligand, decapentaplegic (dpp), is exacerbated at the posterior pole.
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Affiliation(s)
- Megan M Colonnetta
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Girish Deshpande
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
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4
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Levo M, Raimundo J, Bing XY, Sisco Z, Batut PJ, Ryabichko S, Gregor T, Levine MS. Transcriptional coupling of distant regulatory genes in living embryos. Nature 2022; 605:754-760. [PMID: 35508662 PMCID: PMC9886134 DOI: 10.1038/s41586-022-04680-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 03/23/2022] [Indexed: 02/01/2023]
Abstract
The prevailing view of metazoan gene regulation is that individual genes are independently regulated by their own dedicated sets of transcriptional enhancers. Past studies have reported long-range gene-gene associations1-3, but their functional importance in regulating transcription remains unclear. Here we used quantitative single-cell live imaging methods to provide a demonstration of co-dependent transcriptional dynamics of genes separated by large genomic distances in living Drosophila embryos. We find extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases. Regulatory interconnectivity depends on promoter-proximal tethering elements, and perturbations in these elements uncouple transcription and alter the bursting dynamics of distant genes, suggesting a role of genome topology in the formation and stability of co-transcriptional hubs. Transcriptional coupling is detected throughout the fly genome and encompasses a broad spectrum of conserved developmental processes, suggesting a general strategy for long-range integration of gene activity.
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Affiliation(s)
- Michal Levo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - João Raimundo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xin Yang Bing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zachary Sisco
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Philippe J. Batut
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sergey Ryabichko
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA,Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, Paris, France,Corresponding authors
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Corresponding authors
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5
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Yang TH, Yang YC, Tu KC. regCNN: identifying Drosophila genome-wide cis-regulatory modules via integrating the local patterns in epigenetic marks and transcription factor binding motifs. Comput Struct Biotechnol J 2022; 20:296-308. [PMID: 35035784 PMCID: PMC8724954 DOI: 10.1016/j.csbj.2021.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Transcription regulation in metazoa is controlled by the binding events of transcription factors (TFs) or regulatory proteins on specific modular DNA regulatory sequences called cis-regulatory modules (CRMs). Understanding the distributions of CRMs on a genomic scale is essential for constructing the metazoan transcriptional regulatory networks that help diagnose genetic disorders. While traditional reporter-assay CRM identification approaches can provide an in-depth understanding of functions of some CRM, these methods are usually cost-inefficient and low-throughput. It is generally believed that by integrating diverse genomic data, reliable CRM predictions can be made. Hence, researchers often first resort to computational algorithms for genome-wide CRM screening before specific experiments. However, current existing in silico methods for searching potential CRMs were restricted by low sensitivity, poor prediction accuracy, or high computation time from TFBS composition combinatorial complexity. To overcome these obstacles, we designed a novel CRM identification pipeline called regCNN by considering the base-by-base local patterns in TF binding motifs and epigenetic profiles. On the test set, regCNN shows an accuracy/auROC of 84.5%/92.5% in CRM identification. And by further considering local patterns in epigenetic profiles and TF binding motifs, it can accomplish 4.7% (92.5%–87.8%) improvement in the auROC value over the average value-based pure multi-layer perceptron model. We also demonstrated that regCNN outperforms all currently available tools by at least 11.3% in auROC values. Finally, regCNN is verified to be robust against its resizing window hyperparameter in dealing with the variable lengths of CRMs. The model of regCNN can be downloaded athttp://cobisHSS0.im.nuk.edu.tw/regCNN/.
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Ya-Chiao Yang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Kai-Chi Tu
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
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6
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Li L, Waymack R, Gad M, Wunderlich Z. Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo. Genetics 2021; 219:6372693. [PMID: 34849867 DOI: 10.1093/genetics/iyab154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/12/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene's overall expression pattern.
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Affiliation(s)
- Lily Li
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Waymack
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mario Gad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.,Department of Biology, Boston University, Boston, MA 02215, USA
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7
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Graham PL, Fischer MD, Giri A, Pick L. The fushi tarazu zebra element is not required for Drosophila viability or fertility. G3-GENES GENOMES GENETICS 2021; 11:6358135. [PMID: 34518886 PMCID: PMC8527495 DOI: 10.1093/g3journal/jkab300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022]
Abstract
Expression of genes in precisely controlled spatiotemporal patterns is essential for embryonic development. Much of our understanding of mechanisms regulating gene expression comes from the study of cis-regulatory elements (CREs) that direct expression of reporter genes in transgenic organisms. This reporter-transgene approach identifies genomic regions sufficient to drive expression but fails to provide information about quantitative and qualitative contributions to endogenous expression, although such conclusions are often inferred. Here we evaluated the endogenous function of a classic Drosophila CRE, the fushi tarazu (ftz) zebra element. ftz is a pair-rule segmentation gene expressed in seven stripes during embryogenesis, necessary for formation of alternate body segments. Reporter transgenes identified the promoter-proximal zebra element as a major driver of the seven ftz stripes. We generated a precise genomic deletion of the zebra element (ftzΔZ) to assess its role in the context of native chromatin and neighboring CREs, expecting large decreases in ftz seven-stripe expression. However, significant reduction in expression was found for only one stripe, ftz stripe 4, expressed at ∼25% of wild type levels in ftzΔZ homozygotes. Defects in corresponding regions of ftzΔZ mutants suggest this level of expression borders the threshold required to promote morphological segmentation. Further, we established true-breeding lines of homozygous ftzΔZ flies, demonstrating that the body segments missing in the mutants are not required for viability or fertility. These results highlight the different types of conclusions drawn from different experimental designs and emphasize the importance of examining transcriptional regulatory mechanisms in the context of the native genomic environment.
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Affiliation(s)
- Patricia L Graham
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Matthew D Fischer
- Graduate Program in Molecular & Cell Biology, University of Maryland, College Park, MD 20742, USA
| | - Abhigya Giri
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Leslie Pick
- Department of Entomology, University of Maryland, College Park, MD 20742, USA.,Graduate Program in Molecular & Cell Biology, University of Maryland, College Park, MD 20742, USA
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8
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Shlemov A, Alexandrov T, Golyandina N, Holloway D, Baumgartner S, Spirov AV. Quantification reveals early dynamics in Drosophila maternal gradients. PLoS One 2021; 16:e0244701. [PMID: 34411119 PMCID: PMC8376041 DOI: 10.1371/journal.pone.0244701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 07/16/2021] [Indexed: 11/18/2022] Open
Abstract
The Bicoid (Bcd) protein is a primary determinant of early anterior-posterior (AP) axis specification in Drosophila embryogenesis. This morphogen is spatially distributed in an anterior-high gradient, and affects particular AP cell fates in a concentration-dependent manner. The early distribution and dynamics of the bicoid (bcd) mRNA, the source for the Bcd protein gradient, is not well understood, leaving a number of open questions for how Bcd positional information develops and is regulated. Confocal microscope images of whole early embryos, stained for bcd mRNA or the Staufen (Stau) protein involved in its transport, were processed to extract quantitative AP intensity profiles at two depths (apical-under the embryo surface but above the nuclear layer; and basal-below the nuclei). Each profile was quantified by a two- (or three-) exponential equation. The parameters of these equations were used to analyze the early developmental dynamics of bcd. Analysis of 1D profiles was compared with 2D intensity surfaces from the same images. This approach reveals strong early changes in bcd and Stau, which appear to be coordinated. We can unambiguously discriminate three stages in early development using the exponential parameters: pre-blastoderm (1-9 cleavage cycle, cc), syncytial blastoderm (10-13 cc) and cellularization (from 14A cc). Key features which differ in this period are how fast the first exponential (anterior component) of the apical profile drops with distance and whether it is higher or lower than the basal first exponential. We can further discriminate early and late embryos within the pre-blastoderm stage, depending on how quickly the anterior exponential drops. This relates to the posterior-wards spread of bcd in the first hour of development. Both bcd and Stau show several redistributions in the head cytoplasm, quite probably related to nuclear activity: first shifting inwards towards the core plasm, forming either protrusions (early pre-blastoderm) or round aggregations (early nuclear cleavage cycles, cc, 13 and 14), then moving to the embryo surface and spreading posteriorly. These movements are seen both with the 2D surface study and the 1D profile analysis. The continued spreading of bcd can be tracked from the time of nuclear layer formation (later pre-blastoderm) to the later syncytial blastoderm stages by the progressive loss of steepness of the apical anterior exponential (for both bcd and Stau). Finally, at the beginning of cc14 (cellularization stage) we see a distinctive flip from the basal anterior gradient being higher to the apical gradient being higher (for both bcd and Stau). Quantitative analysis reveals substantial (and correlated) bcd and Stau redistributions during early development, supporting that the distribution and dynamics of bcd mRNA are key factors in the formation and maintenance of the Bcd protein morphogenetic gradient. This analysis reveals the complex and dynamic nature of bcd redistribution, particularly in the head cytoplasm. These resemble observations in oogenesis; their role and significance have yet to be clarified. The observed co-localization during redistribution of bcd and Stau may indicate the involvement of active transport.
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Affiliation(s)
- Alex Shlemov
- Laboratory for Algorithmic Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nina Golyandina
- Faculty of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - David Holloway
- Mathematics Department, British Columbia Institute of Technology, Burnaby, British Columbia, Canada
| | - Stefan Baumgartner
- Department of Experimental Medical Sciences, Lund University, Lund, Sweden
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander V. Spirov
- Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, New York, United States of America
- Lab Modelling Evolution, The I.M. Sechenov Institute of Evolutionary Physiology & Biochemistry, St. Petersburg, Russia
- * E-mail:
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9
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Ghotbi E, Ye P, Ervin T, Kum A, Benes J, Jones RS. Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator. SCIENCE ADVANCES 2021; 7:7/29/eabg1556. [PMID: 34272248 PMCID: PMC8284896 DOI: 10.1126/sciadv.abg1556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Polycomb-group (PcG) proteins are epigenetic regulators that maintain the transcriptional repression of target genes following their initial repression by transcription factors. PcG target genes are repressed in some cells, but active in others. Therefore, a mechanism must exist by which PcG proteins distinguish between the repressed and active states and only assemble repressive chromatin environments at target genes that are repressed. Here, we present experimental evidence that the repressed state of a Drosophila PcG target gene, giant (gt), is not identified by the presence of a repressor. Rather, de novo establishment of PcG-mediated silencing at gt is the default state that is prevented by the presence of an activator or coactivator, which may inhibit the catalytic activity of Polycomb-repressive complex 2 (PRC2).
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Affiliation(s)
- Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Piao Ye
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Taylor Ervin
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Anni Kum
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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10
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Abstract
Shadow enhancers are seemingly redundant transcriptional cis-regulatory elements that regulate the same gene and drive overlapping expression patterns. Recent studies have shown that shadow enhancers are remarkably abundant and control most developmental gene expression in both invertebrates and vertebrates, including mammals. Shadow enhancers might provide an important mechanism for buffering gene expression against mutations in non-coding regulatory regions of genes implicated in human disease. Technological advances in genome editing and live imaging have shed light on how shadow enhancers establish precise gene expression patterns and confer phenotypic robustness. Shadow enhancers can interact in complex ways and may also help to drive the formation of transcriptional hubs within the nucleus. Despite their apparent redundancy, the prevalence and evolutionary conservation of shadow enhancers underscore their key role in emerging metazoan gene regulatory networks.
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11
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Jana T, Brodsky S, Barkai N. Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites. Trends Genet 2021; 37:421-432. [PMID: 33414013 DOI: 10.1016/j.tig.2020.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors (TFs) regulate gene expression by binding DNA sequences recognized by their DNA-binding domains (DBDs). DBD-recognized motifs are short and highly abundant in genomes. The ability of TFs to bind a specific subset of motif-containing sites, and to do so rapidly upon activation, is fundamental for gene expression in all eukaryotes. Despite extensive interest, our understanding of the TF-target search process is fragmented; although binding specificity and detection speed are two facets of this same process, trade-offs between them are rarely addressed. In this opinion article, we discuss potential speed-specificity trade-offs in the context of existing models. We further discuss the recently described 'distributed specificity' paradigm, suggesting that intrinsically disordered regions (IDRs) promote specificity while reducing the TF-target search time.
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Affiliation(s)
- Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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12
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Makashov AA, Myasnikova EM, Spirov AV. Fuzzy Linguistic Modeling of the Regulation of Drosophila Segmentation Genes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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Ghotbi E, Lackey K, Wong V, Thompson KT, Caston EG, Haddadi M, Benes J, Jones RS. Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene. Genetics 2020; 214:623-634. [PMID: 31919108 PMCID: PMC7054010 DOI: 10.1534/genetics.119.302981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/06/2020] [Indexed: 11/18/2022] Open
Abstract
Polycomb-group (PcG) proteins are evolutionarily conserved epigenetic regulators whose primary function is to maintain the transcriptional repression of target genes. Recruitment of Drosophila melanogaster PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs). The functions or necessity for more than one PRE at a gene are not clear and individual PREs at some loci may have distinct regulatory roles. Various combinations of sequence-specific DNA-binding proteins are present at a given PRE, but only Pleiohomeotic (Pho) is present at all strong PREs. The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2. This observation indicated a possible dependence of PRE2 on PRE1 for PcG recruitment; however, we find here that PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites, Phol binding is less so and appears to play a minimal role in recruiting other PcG proteins to gt Another PRE-binding protein, Sp1/Kruppel-like factor, is dependent on the presence of Pho for PRE1 binding. Further, we show that, in addition to silencing gene expression, PcG proteins dampen transcription of an active gene.
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Affiliation(s)
- Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Kristina Lackey
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Vicki Wong
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Katie T Thompson
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Evan G Caston
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Minna Haddadi
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
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14
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Johnson HE, Toettcher JE. Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo. Dev Cell 2019; 48:361-370.e3. [PMID: 30753836 DOI: 10.1016/j.devcel.2019.01.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/27/2018] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
The Erk mitogen-activated protein kinase plays diverse roles in animal development. Its widespread reuse raises a conundrum: when a single kinase like Erk is activated, how does a developing cell know which fate to adopt? We combine optogenetic control with genetic perturbations to dissect Erk-dependent fates in the early Drosophila embryo. We find that Erk activity is sufficient to "posteriorize" 88% of the embryo, inducing gut endoderm-like gene expression and morphogenetic movements in all cells within this region. Gut endoderm fate adoption requires at least 1 h of signaling, whereas a 30-min Erk pulse specifies a distinct ectodermal cell type, intermediate neuroblasts. We find that the endoderm-ectoderm cell fate switch is controlled by the cumulative load of Erk activity, not the duration of a single pulse. The fly embryo thus harbors a classic example of dynamic control, where the temporal profile of Erk signaling selects between distinct physiological outcomes.
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Affiliation(s)
- Heath E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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15
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Bozek M, Cortini R, Storti AE, Unnerstall U, Gaul U, Gompel N. ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Res 2019; 29:771-783. [PMID: 30962180 PMCID: PMC6499308 DOI: 10.1101/gr.242362.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization is not well understood. We profiled chromatin accessibility with ATAC-seq in narrow, genetically tagged domains along the antero-posterior axis in the Drosophila blastoderm. We demonstrate that one-quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable intervals, and their accessibility changes correlate with their regulatory activity. In an embryonic domain where an enhancer receives a net activating TF input and promotes transcription, it displays elevated accessibility in comparison to a domain where it receives a net repressive input. We propose that differential accessibility is a signature of patterning cis-regulatory elements in the Drosophila blastoderm and discuss potential mechanisms by which accessibility of enhancers may be modulated by activator and repressor TFs.
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Affiliation(s)
- Marta Bozek
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Roberto Cortini
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Andrea Ennio Storti
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Ulrich Unnerstall
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Ulrike Gaul
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Nicolas Gompel
- Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, 82152 Planegg-Martinsried, Germany
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16
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Fernandez-Valverde SL, Aguilera F, Ramos-Díaz RA. Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era. Integr Comp Biol 2019; 58:640-653. [PMID: 29917089 DOI: 10.1093/icb/icy061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The advent of high-throughput sequencing (HTS) technologies has revolutionized the way we understand the transformation of genetic information into morphological traits. Elucidating the network of interactions between genes that govern cell differentiation through development is one of the core challenges in genome research. These networks are known as developmental gene regulatory networks (dGRNs) and consist largely of the functional linkage between developmental control genes, cis-regulatory modules, and differentiation genes, which generate spatially and temporally refined patterns of gene expression. Over the last 20 years, great advances have been made in determining these gene interactions mainly in classical model systems, including human, mouse, sea urchin, fruit fly, and worm. This has brought about a radical transformation in the fields of developmental biology and evolutionary biology, allowing the generation of high-resolution gene regulatory maps to analyze cell differentiation during animal development. Such maps have enabled the identification of gene regulatory circuits and have led to the development of network inference methods that can recapitulate the differentiation of specific cell-types or developmental stages. In contrast, dGRN research in non-classical model systems has been limited to the identification of developmental control genes via the candidate gene approach and the characterization of their spatiotemporal expression patterns, as well as to the discovery of cis-regulatory modules via patterns of sequence conservation and/or predicted transcription-factor binding sites. However, thanks to the continuous advances in HTS technologies, this scenario is rapidly changing. Here, we give a historical overview on the architecture and elucidation of the dGRNs. Subsequently, we summarize the approaches available to unravel these regulatory networks, highlighting the vast range of possibilities of integrating multiple technical advances and theoretical approaches to expand our understanding on the global gene regulation during animal development in non-classical model systems. Such new knowledge will not only lead to greater insights into the evolution of molecular mechanisms underlying cell identity and animal body plans, but also into the evolution of morphological key innovations in animals.
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Affiliation(s)
- Selene L Fernandez-Valverde
- CONACYT, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - René Alexander Ramos-Díaz
- CONACYT, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
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17
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Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster. Biophysics (Nagoya-shi) 2019; 63:43-51. [PMID: 30739944 DOI: 10.1134/s0006350918010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene regulatory networks control the complex programs that drive development. Deciphering the connections between transcription factors (TFs) and target genes is challenging, in part because TFs bind to thousands of places in the genome but control expression through a subset of these binding events. We hypothesize that we can combine natural variation of expression levels and predictions of TF binding sites to identify TF targets. We gather RNA-seq data from 71 genetically distinct F1 Drosophila melanogaster embryos and calculate the correlations between TF and potential target genes' expression levels, which we call "regulatory strength." To separate direct and indirect TF targets, we hypothesize that direct TF targets will have a preponderance of binding sites in their upstream regions. Using 14 TFs active during embryogenesis, we find that 12 TFs showed a significant correlation between their binding strength and regulatory strength on downstream targets, and 10 TFs showed a significant correlation between the number of binding sites and the regulatory effect on target genes. The general roles, e.g. bicoid's role as an activator, and the particular interactions we observed between our TFs, e.g. twist's role as a repressor of sloppy paired and odd paired, generally coincide with the literature.
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Affiliation(s)
- Noha M Osman
- University of Southern California, Los Angeles, CA.,National Research Centre, Dokki, Giza, Egypt
| | | | - Srna Vlaho
- University of Southern California, Los Angeles, CA
| | | | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA.,Saint Petersburg Polytechnical University, St Petersburg, Russia
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18
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Alhaj Abed J, Ghotbi E, Ye P, Frolov A, Benes J, Jones RS. De novo recruitment of Polycomb-group proteins in Drosophila embryos. Development 2018; 145:dev.165027. [PMID: 30389849 DOI: 10.1242/dev.165027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/29/2018] [Indexed: 12/24/2022]
Abstract
Polycomb-group (PcG)-mediated transcriptional repression of target genes can be delineated into two phases. First, following initial repression of target genes by gene-specific transcription factors, PcG proteins recognize the repressed state and assume control of the genes' repression. Second, once the silenced state is established, PcG proteins may maintain repression through an indefinite number of cell cycles. Little is understood about how PcG proteins initially recognize the repressed state of target genes and the steps leading to de novo establishment of PcG-mediated repression. We describe a genetic system in which a Drosophila PcG target gene, giant (gt), is ubiquitously repressed during early embryogenesis by a maternally expressed transcription factor, and show the temporal recruitment of components of three PcG protein complexes: PhoRC, PRC1 and PRC2. We show that de novo PcG recruitment follows a temporal hierarchy in which PhoRC stably localizes at the target gene at least 1 h before stable recruitment of PRC2 and concurrent trimethylation of histone H3 at lysine 27 (H3K27me3). The presence of PRC2 and increased levels of H3K27me3 are found to precede stable binding by PRC1.
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Affiliation(s)
- Jumana Alhaj Abed
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Piao Ye
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Alexander Frolov
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
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19
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Zoller B, Little SC, Gregor T. Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. Cell 2018; 175:835-847.e25. [PMID: 30340044 PMCID: PMC6779125 DOI: 10.1016/j.cell.2018.09.056] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 07/02/2018] [Accepted: 09/26/2018] [Indexed: 01/14/2023]
Abstract
How transcriptional bursting relates to gene regulation is a central question that has persisted for more than a decade. Here, we measure nascent transcriptional activity in early Drosophila embryos and characterize the variability in absolute activity levels across expression boundaries. We demonstrate that boundary formation follows a common transcription principle: a single control parameter determines the distribution of transcriptional activity, regardless of gene identity, boundary position, or enhancer-promoter architecture. We infer the underlying bursting kinetics and identify the key regulatory parameter as the fraction of time a gene is in a transcriptionally active state. Unexpectedly, both the rate of polymerase initiation and the switching rates are tightly constrained across all expression levels, predicting synchronous patterning outcomes at all positions in the embryo. These results point to a shared simplicity underlying the apparently complex transcriptional processes of early embryonic patterning and indicate a path to general rules in transcriptional regulation.
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Affiliation(s)
- Benjamin Zoller
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Shawn C Little
- Department of Molecular Biology and Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas Gregor
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France.
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20
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Datta RR, Ling J, Kurland J, Ren X, Xu Z, Yucel G, Moore J, Shokri L, Baker I, Bishop T, Struffi P, Levina R, Bulyk ML, Johnston RJ, Small S. A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites. Genes Dev 2018; 32:723-736. [PMID: 29764918 PMCID: PMC6004077 DOI: 10.1101/gad.311985.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/17/2018] [Indexed: 11/25/2022]
Abstract
Datta et al. define three major classes of enhancers that are differentially sensitive to binding and transcriptional activation by Bicoid (Bcd) and Orthodenticle (Otd). The specific activities of enhancers in each class are mediated by DNA motif variants preferentially bound by Bcd or Otd and the presence or absence of sites for cofactors that interact with these proteins. The K50 (lysine at amino acid position 50) homeodomain (HD) protein Orthodenticle (Otd) is critical for anterior patterning and brain and eye development in most metazoans. In Drosophila melanogaster, another K50HD protein, Bicoid (Bcd), has evolved to replace Otd's ancestral function in embryo patterning. Bcd is distributed as a long-range maternal gradient and activates transcription of a large number of target genes, including otd. Otd and Bcd bind similar DNA sequences in vitro, but how their transcriptional activities are integrated to pattern anterior regions of the embryo is unknown. Here we define three major classes of enhancers that are differentially sensitive to binding and transcriptional activation by Bcd and Otd. Class 1 enhancers are initially activated by Bcd, and activation is transferred to Otd via a feed-forward relay (FFR) that involves sequential binding of the two proteins to the same DNA motif. Class 2 enhancers are activated by Bcd and maintained by an Otd-independent mechanism. Class 3 enhancers are never bound by Bcd, but Otd binds and activates them in a second wave of zygotic transcription. The specific activities of enhancers in each class are mediated by DNA motif variants preferentially bound by Bcd or Otd and the presence or absence of sites for cofactors that interact with these proteins. Our results define specific patterning roles for Bcd and Otd and provide mechanisms for coordinating the precise timing of gene expression patterns during embryonic development.
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Affiliation(s)
- Rhea R Datta
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Jia Ling
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Jesse Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaotong Ren
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Zhe Xu
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Gozde Yucel
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Jackie Moore
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Leila Shokri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Isabel Baker
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Timothy Bishop
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Paolo Struffi
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Rimma Levina
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Stephen Small
- Center for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, USA
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21
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Haines JE, Eisen MB. Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo. PLoS Genet 2018; 14:e1007367. [PMID: 29727464 PMCID: PMC5955596 DOI: 10.1371/journal.pgen.1007367] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 05/16/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of open chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear how regions of activity are established during early embryogenesis, and if they are the product of spatially restricted or ubiquitous processes. To shed light on this question, we probed chromatin accessibility across the anterior-posterior axis (A-P) of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is highly similar between the two halves, with regions that manifest significant accessibility in one half of the embryo almost always accessible in the other half, even for promoters that are active in exclusively one half of the embryo. These data support previous studies that show that chromatin accessibility is not a direct result of activity, and point to a role for ubiquitous factors or processes in establishing chromatin accessibility at promoters in the early embryo. However, in concordance with similar works, we find that at enhancers active exclusively in one half of the embryo, we observe a significant skew towards greater accessibility in the region of their activity, highlighting the role of patterning factors such as Bicoid in this process.
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Affiliation(s)
- Jenna E. Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States of America
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States of America
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22
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True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy. Nat Commun 2018; 9:1605. [PMID: 29686282 PMCID: PMC5913336 DOI: 10.1038/s41467-018-03977-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/16/2018] [Indexed: 01/31/2023] Open
Abstract
The complex patterns of gene expression in metazoans are controlled by selective binding of transcription factors (TFs) to regulatory DNA. To improve the quantitative understanding of this process, we have developed a novel method that uses fluorescence anisotropy measurements in a controlled delivery system to determine TF-DNA binding energies in solution with high sensitivity and throughput. Owing to its large dynamic range, the method, named high performance fluorescence anisotropy (HiP-FA), allows for reliable quantification of both weak and strong binding; binding specificities are calculated on the basis of equilibrium constant measurements for mutational DNA variants. We determine the binding preference landscapes for 26 TFs and measure high absolute affinities, but mostly lower binding specificities than reported by other methods. The revised binding preferences give rise to improved predictions of in vivo TF occupancy and enhancer expression. Our approach provides a powerful new tool for the systems-biological analysis of gene regulation. Methods to measure selective transcription factor-DNA binding often lack sensitivity and are not performed in solution. Here the authors develop a method to perform fluorescence anisotropy measurements of transcription factor-DNA binding energies with high sensitivity and throughput.
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23
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Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG. Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PLoS One 2017; 12:e0184657. [PMID: 28898266 PMCID: PMC5595321 DOI: 10.1371/journal.pone.0184657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022] Open
Abstract
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression. The analysis reveals that the sequence variants increase (decrease) gene expression if located within binding sites of repressors (activators). We show that the sign of SNP influence (activation or repression) may change in time and space and elucidate the origin of this change in specific examples. The thermodynamic modeling approach predicts non-local and non-linear effects arising from SNPs, and combinations of SNPs, in individual fly genotypes. Simulation of individual fly genotypes using our model reveals that this non-linearity reduces to almost additive inputs from multiple SNPs. Further, we see signatures of the action of purifying selection in the gap gene regulatory regions. To infer the specific targets of purifying selection, we analyze the patterns of polymorphism in the data at two phenotypic levels: the strengths of binding and expression. We find that combinations of SNPs show evidence of being under selective pressure, while individual SNPs do not. The model predicts that SNPs appear to accumulate in the genotypes of the natural population in a way biased towards small increases in activating action on the expression pattern. Taken together, these results provide a systems-level view of how genetic variation translates to the level of gene regulatory networks via combinatorial SNP effects.
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Affiliation(s)
- Vitaly V. Gursky
- Theoretical Department, Ioffe Institute, Saint Petersburg, Russia
- Systems Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
- * E-mail:
| | - Konstantin N. Kozlov
- Systems Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ivan V. Kulakovskiy
- Engelhardt Institute of Molecular Biology, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Asif Zubair
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Paul Marjoram
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - David S. Lawrie
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Sergey V. Nuzhdin
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Maria G. Samsonova
- Systems Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, Saint Petersburg, Russia
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24
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Hannon CE, Blythe SA, Wieschaus EF. Concentration dependent chromatin states induced by the bicoid morphogen gradient. eLife 2017; 6:28275. [PMID: 28891464 PMCID: PMC5624782 DOI: 10.7554/elife.28275] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/08/2017] [Indexed: 12/29/2022] Open
Abstract
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset of its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations. This may be a common property of developmental transcription factors that must gain early access to their target enhancers while the chromatin state of the genome is being remodeled during large-scale transitions in the gene regulatory landscape.
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Affiliation(s)
- Colleen E Hannon
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, United States
| | - Shelby A Blythe
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, United States
| | - Eric F Wieschaus
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, United States
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25
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Sex combs reduced (Scr) regulatory region of Drosophila revisited. Mol Genet Genomics 2017; 292:773-787. [DOI: 10.1007/s00438-017-1309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/08/2017] [Indexed: 10/19/2022]
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26
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Combs PA, Eisen MB. Genome-wide measurement of spatial expression in patterning mutants of Drosophila melanogaster. F1000Res 2017; 6:41. [PMID: 28299188 PMCID: PMC5325077 DOI: 10.12688/f1000research.9720.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2016] [Indexed: 11/20/2022] Open
Abstract
Patterning in the
Drosophila melanogaster embryo is affected by multiple maternal factors, but the effect of these factors on spatial gene expression has not been systematically analyzed. Here we characterize the effect of the maternal factors Zelda, Hunchback and Bicoid by cryosectioning wildtype and mutant blastoderm stage embryos and sequencing mRNA from each slice. The resulting atlas of spatial gene expression highlights the intersecting roles of these factors in regulating spatial patterns, and serves as a resource for researchers studying spatial patterning in the early embryo. We identify a large number of genes with both expected and unexpected patterning changes, and through integrated analysis of transcription factor binding data identify common themes in genes with complex dependence on these transcription factors.
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Affiliation(s)
- Peter A Combs
- Graduate Program in Biophysics, University of California, Berkley, USA
| | - Michael B Eisen
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, USA
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27
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Retinal Expression of the Drosophila eyes absent Gene Is Controlled by Several Cooperatively Acting Cis-regulatory Elements. PLoS Genet 2016; 12:e1006462. [PMID: 27930646 PMCID: PMC5145141 DOI: 10.1371/journal.pgen.1006462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/04/2016] [Indexed: 12/15/2022] Open
Abstract
The eyes absent (eya) gene of the fruit fly, Drosophila melanogaster, is a member of an evolutionarily conserved gene regulatory network that controls eye formation in all seeing animals. The loss of eya leads to the complete elimination of the compound eye while forced expression of eya in non-retinal tissues is sufficient to induce ectopic eye formation. Within the developing retina eya is expressed in a dynamic pattern and is involved in tissue specification/determination, cell proliferation, apoptosis, and cell fate choice. In this report we explore the mechanisms by which eya expression is spatially and temporally governed in the developing eye. We demonstrate that multiple cis-regulatory elements function cooperatively to control eya transcription and that spacing between a pair of enhancer elements is important for maintaining correct gene expression. Lastly, we show that the loss of eya expression in sine oculis (so) mutants is the result of massive cell death and a progressive homeotic transformation of retinal progenitor cells into head epidermis. Activation of a gene requires interactions between enhancer and promoter elements. It has been known for some time that transcription of a gene expressed in a complex pattern or in multiple tissues is regulated by an array of enhancers. Recent studies have also demonstrated that multiple enhancers can regulate a single expression pattern within a single tissue. In this study we asked how the expression pattern of eyes absent (eya) is regulated at the level of the enhancer in the developing retina. We found that several adjacently positioned enhancer elements function cooperatively to control temporal and spatial expression of eya and that the spacing between two of these cis-regulatory elements is important to their function. This study shows the importance of enhancer cooperation and architecture in regulating complex and dynamically changing expression patterns.
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28
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Acevedo-Luna N, Mariño-Ramírez L, Halbert A, Hansen U, Landsman D, Spouge JL. Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. BMC Bioinformatics 2016; 17:479. [PMID: 27871221 PMCID: PMC5117513 DOI: 10.1186/s12859-016-1354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/11/2016] [Indexed: 11/24/2022] Open
Abstract
Background Transcription factors (TFs) form complexes that bind regulatory modules (RMs) within DNA, to control specific sets of genes. Some transcription factor binding sites (TFBSs) near the transcription start site (TSS) display tight positional preferences relative to the TSS. Furthermore, near the TSS, RMs can co-localize TFBSs with each other and the TSS. The proportion of TFBS positional preferences due to TFBS co-localization within RMs is unknown, however. ChIP experiments confirm co-localization of some TFBSs genome-wide, including near the TSS, but they typically examine only a few TFs at a time, using non-physiological conditions that can vary from lab to lab. In contrast, sequence analysis can examine many TFs uniformly and methodically, broadly surveying the co-localization of TFBSs with tight positional preferences relative to the TSS. Results Our statistics found 43 significant sets of human motifs in the JASPAR TF Database with positional preferences relative to the TSS, with 38 preferences tight (±5 bp). Each set of motifs corresponded to a gene group of 135 to 3304 genes, with 42/43 (98%) gene groups independently validated by DAVID, a gene ontology database, with FDR < 0.05. Motifs corresponding to two TFBSs in a RM should co-occur more than by chance alone, enriching the intersection of the gene groups corresponding to the two TFs. Thus, a gene-group intersection systematically enriched beyond chance alone provides evidence that the two TFs participate in an RM. Of the 903 = 43*42/2 intersections of the 43 significant gene groups, we found 768/903 (85%) pairs of gene groups with significantly enriched intersections, with 564/768 (73%) intersections independently validated by DAVID with FDR < 0.05. A user-friendly web site at http://go.usa.gov/3kjsH permits biologists to explore the interaction network of our TFBSs to identify candidate subunit RMs. Conclusions Gene duplication and convergent evolution within a genome provide obvious biological mechanisms for replicating an RM near the TSS that binds a particular TF subunit. Of all intersections of our 43 significant gene groups, 85% were significantly enriched, with 73% of the significant enrichments independently validated by gene ontology. The co-localization of TFBSs within RMs therefore likely explains much of the tight TFBS positional preferences near the TSS. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1354-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Acevedo-Luna
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Armand Halbert
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Ulla Hansen
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - John L Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J. Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biol 2016; 17:196. [PMID: 27678375 PMCID: PMC5037609 DOI: 10.1186/s13059-016-1057-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear. RESULTS Using DV patterning as a test system, we develop a simple and effective method to identify tissue-specific enhancers de novo. We sample a broad set of candidate enhancer regions using data on CREB-binding protein co-factor binding or ATAC-seq chromatin accessibility, and then identify those regions with significant differences in histone acetylation between tissues. This method identifies hundreds of novel DV enhancers and outperforms ChIP-seq data of relevant transcription factors when benchmarked with mRNA expression data and transgenic reporter assays. These DV enhancers allow the de novo discovery of the relevant transcription factor motifs involved in DV patterning and contain additional motifs that are evolutionarily conserved and for which the corresponding transcription factors are expressed in a DV-biased fashion. Finally, we identify novel target genes of the regulatory network, implicating morphogenesis genes as early targets of DV patterning. CONCLUSIONS Taken together, our approach has expanded our knowledge of the DV patterning network even further and is a general method to identify enhancers in any developmental system, including mammalian development.
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Affiliation(s)
- Nina Koenecke
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,Present address: Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Malini Natarajan
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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30
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Ma J, He F, Xie G, Deng WM. Maternal AP determinants in the Drosophila oocyte and embryo. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:562-81. [PMID: 27253156 DOI: 10.1002/wdev.235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/24/2016] [Accepted: 03/13/2016] [Indexed: 12/12/2022]
Abstract
An animal embryo cannot initiate its journey of forming a new life on its own. It must rely on maternally provided resources and inputs to kick-start its developmental process. In Drosophila, the initial polarities of the embryo along both the anterior-posterior (AP) and dorsal-ventral (DV) axes are also specified by maternal determinants. Over the past several decades, genetic and molecular studies have identified and characterized such determinants, as well as the zygotic genetic regulatory networks that control patterning in the early embryo. Extensive studies of oogenesis have also led to a detailed knowledge of the cellular and molecular interactions that control the formation of a mature egg. Despite these efforts, oogenesis and embryogenesis have been studied largely as separate problems, except for qualitative aspects with regard to maternal regulation of the asymmetric localization of maternal determinants. Can oogenesis and embryogenesis be viewed from a unified perspective at a quantitative level, and can that improve our understanding of how robust embryonic patterning is achieved? Here, we discuss the basic knowledge of the regulatory mechanisms controlling oogenesis and embryonic patterning along the AP axis. We explore properties of the maternal Bicoid gradient in relation to embryo size in search for a unified framework for robust AP patterning. WIREs Dev Biol 2016, 5:562-581. doi: 10.1002/wdev.235 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jun Ma
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, OH, USA.,Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Feng He
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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31
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Rothschild JB, Tsimiklis P, Siggia ED, François P. Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution. PLoS Genet 2016; 12:e1006052. [PMID: 27227405 PMCID: PMC4882032 DOI: 10.1371/journal.pgen.1006052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/23/2016] [Indexed: 12/23/2022] Open
Abstract
Molecular evolution is an established technique for inferring gene homology but regulatory DNA turns over so rapidly that inference of ancestral networks is often impossible. In silico evolution is used to compute the most parsimonious path in regulatory space for anterior-posterior patterning linking two Dipterian species. The expression pattern of gap genes has evolved between Drosophila (fly) and Anopheles (mosquito), yet one of their targets, eve, has remained invariant. Our model predicts that stripe 5 in fly disappears and a new posterior stripe is created in mosquito, thus eve stripe modules 3+7 and 4+6 in fly are homologous to 3+6 and 4+5 in mosquito. We can place Clogmia on this evolutionary pathway and it shares the mosquito homologies. To account for the evolution of the other pair-rule genes in the posterior we have to assume that the ancestral Dipterian utilized a dynamic method to phase those genes in relation to eve. The last common ancestor of the fruit fly (Drosophila) and mosquito (Anopheles) lived more than 200 Million years ago. Can we use available data on insects alive today to infer what their ancestor looked like? In this manuscript, we focus on early embryonic development, when stripes of genetic expression appear and define the location of insect segments (“segmentation”). We use an evolutionary algorithm to reconstruct and predict dynamics of genes controlling stripes in the last common ancestor of fly and mosquito. We predict a new and different combinatorial logic of stripe formation in mosquito compared to fly, which is fully consistent with development of intermediate species such as moth-fly (Clogmia). Our simulations further suggest that the dynamics of gene expression in this last common ancestor were similar to other insects, such as wasps (Nasonia). Our method illustrates how computational methods inspired by machine learning and non-linear physics can be used to infer gene dynamics in species that disappeared millions of years ago.
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Affiliation(s)
- Jeremy B. Rothschild
- Physics Department, McGill University, Ernest Rutherford Physics Building, Montreal, Quebec, Canada
| | - Panagiotis Tsimiklis
- Physics Department, McGill University, Ernest Rutherford Physics Building, Montreal, Quebec, Canada
| | - Eric D. Siggia
- Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America
| | - Paul François
- Physics Department, McGill University, Ernest Rutherford Physics Building, Montreal, Quebec, Canada
- * E-mail:
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32
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El-Sherif E, Levine M. Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo. Curr Biol 2016; 26:1164-9. [PMID: 27112292 DOI: 10.1016/j.cub.2016.02.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Drosophila patterning genes often contain pairs of primary and shadow enhancers that possess overlapping activities [1-5]. It has been suggested that this regulatory "redundancy" helps ensure reliable activation of gene expression under stressful conditions such as increases in temperature [4, 5]. There is also evidence that shadow enhancers help produce sharp on/off boundaries of gene expression in response to small changes in the levels of regulatory factors, such as the maternal Bicoid gradient [6, 7]. Here, we use live-imaging methods to visualize the temporal dynamics of the gap genes Kruppel and knirps, which are essential for the patterning of the thorax and abdomen, respectively [8, 9]. Previous analyses of fixed embryos suggested anterior shifts of the Kruppel and knirps expression patterns [10]. Here, we use computational visualization methods to reveal the precise temporal dynamics of these shifts and further suggest that shadow enhancers are crucial for this process. We discuss potential mechanisms for enhancer dominance, whereby one enhancer represses the other to foster temporal dynamics.
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Affiliation(s)
- Ezzat El-Sherif
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Levine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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33
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Hoermann A, Cicin-Sain D, Jaeger J. A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila. Dev Biol 2016; 411:325-338. [DOI: 10.1016/j.ydbio.2016.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/22/2015] [Accepted: 01/08/2016] [Indexed: 01/05/2023]
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34
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Chen M, Wang C, Wang W, Ji G, Hu B, Du M, Liu G, Li Z, Wang W, Lin X, Zheng W, Chen J. De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus. PLoS One 2016; 11:e0145825. [PMID: 26731763 PMCID: PMC4711587 DOI: 10.1371/journal.pone.0145825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 01/09/2023] Open
Abstract
The horseshoe crab Tachypleus tridentatus is a unique marine species and a potential model for marine invertebrate. Limited genomic and transcriptional data are currently available to understand the molecular mechanisms underlying the embryonic development of T. tridentatus. Here, we reported for the first time the de novo transcriptome assembly for T. tridentatus at embryonic developmental stage using Illumina RNA-seq platform. Approximate 38 million reads were obtained and further assembled into 133,212 unigenes. Sequence homology analysis against public databases revealed that 33,796 unigenes could be annotated with gene descriptions. Of the annotated unigenes, we identified a number of key components of several conserved metazoan signaling pathways (Hedgehog, Wnt, TGF-beta and Notch pathways) and other important regulatory genes involved in embryonic development. Targeted searching of Pax family genes which play critical roles in the formation of tissue and organ during embryonic development identified a complete set of Pax family genes. Moreover, the full length T. tridentatus Pax1/9a (TtPax1/9a) and Pax1/9b (TtPax1/9b) cDNA sequences were determined based on the transcriptome, demonstrating the immediate application of our database. Using quantitative real time PCR, we analyzed the expression patterns of TtPax1/9a and TtPax1/9b in different tissues of horseshoe crab. Taking advantage of Drosophila model, we further found that TtPax1/9b, but not TtPax1/9a, can partly rescue the Drosophila homolog Poxm dysfunction-caused lethality at the larval stage. Our study provides the embryonic transcriptome of T. tridentatus which could be immediately used for gene discovery and characterization, functional genomics studies in T. tridentatus. This transcriptome database will also facilitate the investigations of molecular mechanisms underlying embryonic development of T. tridentatus and other marine arthropods as well.
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Affiliation(s)
- Mingliang Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Chenying Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Wei Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Gubiao Ji
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Bin Hu
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Mi Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Guosheng Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Weiyi Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Xiangzhi Lin
- Center of Marine Biotechnology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Weibing Zheng
- Center of Marine Biotechnology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
- * E-mail:
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35
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Kozlov K, Gursky VV, Kulakovskiy IV, Dymova A, Samsonova M. Analysis of functional importance of binding sites in the Drosophila gap gene network model. BMC Genomics 2015; 16 Suppl 13:S7. [PMID: 26694511 PMCID: PMC4686791 DOI: 10.1186/1471-2164-16-s13-s7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. RESULTS We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. CONCLUSIONS The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.
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Affiliation(s)
- Konstantin Kozlov
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
| | - Vitaly V Gursky
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
- Ioffe Institute, 26 Polytechnicheskaya, 194021 St.Petersburg, Russia
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, 32 Vavilova, 119991 Moscow, Russia
| | - Arina Dymova
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
| | - Maria Samsonova
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
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Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Res 2015; 25:1703-14. [PMID: 26335633 PMCID: PMC4617966 DOI: 10.1101/gr.192542.115] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/20/2015] [Indexed: 11/25/2022]
Abstract
The Drosophila genome activator Vielfaltig (Vfl), also known as Zelda (Zld), is thought to prime enhancers for activation by patterning transcription factors (TFs). Such priming is accompanied by increased chromatin accessibility, but the mechanisms by which this occurs are poorly understood. Here, we analyze the effect of Zld on genome-wide nucleosome occupancy and binding of the patterning TF Dorsal (Dl). Our results show that early enhancers are characterized by an intrinsically high nucleosome barrier. Zld tackles this nucleosome barrier through local depletion of nucleosomes with the effect being dependent on the number and position of Zld motifs. Without Zld, Dl binding decreases at enhancers and redistributes to open regions devoid of enhancer activity. We propose that Zld primes enhancers by lowering the high nucleosome barrier just enough to assist TFs in accessing their binding motifs and promoting spatially controlled enhancer activation if the right patterning TFs are present. We envision that genome activators in general will utilize this mechanism to activate the zygotic genome in a robust and precise manner.
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37
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Jiang P, Ludwig MZ, Kreitman M, Reinitz J. Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. Dev Biol 2015; 405:173-81. [PMID: 26129990 PMCID: PMC4529771 DOI: 10.1016/j.ydbio.2015.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 11/28/2022]
Abstract
The evolution of canalized traits is a central question in evolutionary biology. Natural variation in highly conserved traits can provide clues about their evolutionary potential. Here we investigate natural variation in a conserved trait-even-skipped (eve) expression at the cellular blastoderm stage of embryonic development in Drosophila melanogaster. Expression of the pair-rule gene eve was quantitatively measured in three inbred lines derived from a natural population of D. melanogaster. One line showed marked differences in the spacing, amplitude and timing of formation of the characteristic seven-striped pattern over a 50-min period prior to the onset of gastrulation. Stripe 5 amplitude and the width of the interstripe between stripes 4 and 5 were both reduced in this line, while the interstripe distance between stripes 3 and 4 was increased. Engrailed expression in stage 10 embryos revealed a statistically significant increase in the length of parasegment 6 and a decrease in the length of parasegments 8 and 9. These changes are larger than those previously reported between D. melanogaster and D. pseudoobscura, two species that are thought to have diverged from a common ancestor over 25 million years ago. This line harbors a rare 448 bp deletion in the first intron of knirps (kni). This finding suggested that reduced Kni levels caused the deviant eve expression, and indeed we observed lower levels of Kni protein at early cycle 14A in L2 compared to the other two lines. A second of the three lines displayed an approximately 20% greater level of expression for all seven eve stripes. The three lines are each viable and fertile, and none display a segmentation defect as adults, suggesting that early-acting variation in eve expression is ameliorated by developmental buffering mechanisms acting later in development. Canalization of the segmentation pathway may reduce the fitness consequences of genetic variation, thus allowing the persistence of mutations with unexpectedly strong gene expression phenotypes.
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Affiliation(s)
- Pengyao Jiang
- Department of Ecology & Evolution, University of Chicago, IL 60637, USA.
| | - Michael Z Ludwig
- Department of Ecology & Evolution, University of Chicago, IL 60637, USA; Institute for Genomics & Systems Biology, Chicago, IL 60637, USA
| | - Martin Kreitman
- Department of Ecology & Evolution, University of Chicago, IL 60637, USA; Institute for Genomics & Systems Biology, Chicago, IL 60637, USA
| | - John Reinitz
- Department of Ecology & Evolution, University of Chicago, IL 60637, USA; Institute for Genomics & Systems Biology, Chicago, IL 60637, USA; Department of Statistics, University of Chicago, IL 60637, USA; Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA
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Kazemian M, Suryamohan K, Chen JY, Zhang Y, Samee MAH, Halfon MS, Sinha S. Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. Genome Biol Evol 2015; 6:2301-20. [PMID: 25173756 PMCID: PMC4217690 DOI: 10.1093/gbe/evu184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many genes familiar from Drosophila development, such as the so-called gap, pair-rule, and segment polarity genes, play important roles in the development of other insects and in many cases appear to be deployed in a similar fashion, despite the fact that Drosophila-like "long germband" development is highly derived and confined to a subset of insect families. Whether or not these similarities extend to the regulatory level is unknown. Identification of regulatory regions beyond the well-studied Drosophila has been challenging as even within the Diptera (flies, including mosquitoes) regulatory sequences have diverged past the point of recognition by standard alignment methods. Here, we demonstrate that methods we previously developed for computational cis-regulatory module (CRM) discovery in Drosophila can be used effectively in highly diverged (250-350 Myr) insect species including Anopheles gambiae, Tribolium castaneum, Apis mellifera, and Nasonia vitripennis. In Drosophila, we have successfully used small sets of known CRMs as "training data" to guide the search for other CRMs with related function. We show here that although species-specific CRM training data do not exist, training sets from Drosophila can facilitate CRM discovery in diverged insects. We validate in vivo over a dozen new CRMs, roughly doubling the number of known CRMs in the four non-Drosophila species. Given the growing wealth of Drosophila CRM annotation, these results suggest that extensive regulatory sequence annotation will be possible in newly sequenced insects without recourse to costly and labor-intensive genome-scale experiments. We develop a new method, Regulus, which computes a probabilistic score of similarity based on binding site composition (despite the absence of nucleotide-level sequence alignment), and demonstrate similarity between functionally related CRMs from orthologous loci. Our work represents an important step toward being able to trace the evolutionary history of gene regulatory networks and defining the mechanisms underlying insect evolution.
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Affiliation(s)
- Majid Kazemian
- Department of Computer Science, University of Illinois at Urbana-Champaign Laboratory of Molecular Immunology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Kushal Suryamohan
- Department of Biochemistry, University at Buffalo-State University of New York NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York
| | - Jia-Yu Chen
- Department of Computer Science, University of Illinois at Urbana-Champaign
| | - Yinan Zhang
- Department of Computer Science, University of Illinois at Urbana-Champaign
| | | | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York Department of Biological Sciences, University at Buffalo-State University of New York Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign Institute of Genomic Biology, University of Illinois at Urbana-Champaign
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Bahrami-Samani E, Vo DT, de Araujo PR, Vogel C, Smith AD, Penalva LOF, Uren PJ. Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015; 6:291-310. [PMID: 25515586 PMCID: PMC4397117 DOI: 10.1002/wrna.1274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022]
Abstract
Co- and post-transcriptional regulation of gene expression is complex and multifaceted, spanning the complete RNA lifecycle from genesis to decay. High-throughput profiling of the constituent events and processes is achieved through a range of technologies that continue to expand and evolve. Fully leveraging the resulting data is nontrivial, and requires the use of computational methods and tools carefully crafted for specific data sources and often intended to probe particular biological processes. Drawing upon databases of information pre-compiled by other researchers can further elevate analyses. Within this review, we describe the major co- and post-transcriptional events in the RNA lifecycle that are amenable to high-throughput profiling. We place specific emphasis on the analysis of the resulting data, in particular the computational tools and resources available, as well as looking toward future challenges that remain to be addressed.
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Affiliation(s)
- Emad Bahrami-Samani
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Dat T. Vo
- Children’s Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX
| | - Patricia Rosa de Araujo
- Children’s Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Andrew D. Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
| | - Luiz O. F. Penalva
- Children’s Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX
| | - Philip J. Uren
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA
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Mead ME, Stanton BC, Kruzel EK, Hull CM. Targets of the Sex Inducer homeodomain proteins are required for fungal development and virulence in Cryptococcus neoformans. Mol Microbiol 2015; 95:804-18. [PMID: 25476490 PMCID: PMC4339537 DOI: 10.1111/mmi.12898] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2014] [Indexed: 01/14/2023]
Abstract
In the yeast Saccharomyces cerevisiae, the regulation of cell types by homeodomain transcription factors is a key paradigm; however, many questions remain regarding this class of developmental regulators in other fungi. In the human fungal pathogen Cryptococcus neoformans, the homeodomain transcription factors Sxi1α and Sxi2a are required for sexual development that produces infectious spores, but the molecular mechanisms by which they drive this process are unknown. To better understand homeodomain control of fungal development, we determined the targets of the Sxi2a-Sxi1α heterodimer using whole genome expression analyses paired with in silico and in vitro binding site identification methods. We identified Sxi-regulated genes that contained a site bound directly by the Sxi proteins that is required for full regulation in vivo. Among the targets of the Sxi2a-Sxi1α complex were many genes known to be involved in sexual reproduction, as well as several well-studied virulence genes. Our findings suggest that genes involved in sexual development are also important in mammalian disease. Our work advances the understanding of how homeodomain transcription factors control complex developmental events and suggests an intimate link between fungal development and virulence.
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Affiliation(s)
- Matthew E Mead
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53706, USA
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Abstract
BACKGROUND The detailed analysis of transcriptional regulation is crucially important for understanding biological processes. The gap gene network in Drosophila attracts large interest among researches studying mechanisms of transcriptional regulation. It implements the most upstream regulatory layer of the segmentation gene network. The knowledge of molecular mechanisms involved in gap gene regulation is far less complete than that of genetics of the system. Mathematical modeling goes beyond insights gained by genetics and molecular approaches. It allows us to reconstruct wild-type gene expression patterns in silico, infer underlying regulatory mechanism and prove its sufficiency. RESULTS We developed a new model that provides a dynamical description of gap gene regulatory systems, using detailed DNA-based information, as well as spatial transcription factor concentration data at varying time points. We showed that this model correctly reproduces gap gene expression patterns in wild type embryos and is able to predict gap expression patterns in Kr mutants and four reporter constructs. We used four-fold cross validation test and fitting to random dataset to validate the model and proof its sufficiency in data description. The identifiability analysis showed that most model parameters are well identifiable. We reconstructed the gap gene network topology and studied the impact of individual transcription factor binding sites on the model output. We measured this impact by calculating the site regulatory weight as a normalized difference between the residual sum of squares error for the set of all annotated sites and for the set with the site of interest excluded. CONCLUSIONS The reconstructed topology of the gap gene network is in agreement with previous modeling results and data from literature. We showed that 1) the regulatory weights of transcription factor binding sites show very weak correlation with their PWM score; 2) sites with low regulatory weight are important for the model output; 3) functional important sites are not exclusively located in cis-regulatory elements, but are rather dispersed through regulatory region. It is of importance that some of the sites with high functional impact in hb, Kr and kni regulatory regions coincide with strong sites annotated and verified in Dnase I footprint assays.
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Affiliation(s)
- Konstantin Kozlov
- St.Petersburg State Polytechnical University, Polytekhnicheskaya 29, 195251 St.Petersburg, Russia
| | - Vitaly Gursky
- Ioffe Physical-Technical Institute, RAS, Polytekhnicheskaya 26, 194021 St.Petersburg, Russia
| | - Ivan Kulakovskiy
- Engelhardt Institute of Molecular Biology, RAS, Vavilov 32, 119991 Moscow, Russia
| | - Maria Samsonova
- St.Petersburg State Polytechnical University, Polytekhnicheskaya 29, 195251 St.Petersburg, Russia
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Mensch J, Serra F, Lavagnino NJ, Dopazo H, Hasson E. Positive selection in nucleoporins challenges constraints on early expressed genes in Drosophila development. Genome Biol Evol 2014; 5:2231-41. [PMID: 24171912 PMCID: PMC3845637 DOI: 10.1093/gbe/evt156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Developmental conservation among related species is a common generalization known as von Baer’s third law and implies that early stages of development are the most refractory to change. The “hourglass model” is an alternative view that proposes that middle stages are the most constrained during development. To investigate this issue, we undertook a genomic approach and provide insights into how natural selection operates on genes expressed during the first 24 h of Drosophila ontogeny in the six species of the melanogaster group for which whole genome sequences are available. Having studied the rate of evolution of more than 2,000 developmental genes, our results showed differential selective pressures at different moments of embryogenesis. In many Drosophila species, early zygotic genes evolved slower than maternal genes indicating that mid-embryogenesis is the stage most refractory to evolutionary change. Interestingly, positively selected genes were found in all embryonic stages even during the period with the highest developmental constraint, emphasizing that positive selection and negative selection are not mutually exclusive as it is often mistakenly considered. Among the fastest evolving genes, we identified a network of nucleoporins (Nups) as part of the maternal transcriptome. Specifically, the acceleration of Nups was driven by positive selection only in the more recently diverged species. Because many Nups are involved in hybrid incompatibilities between species of the Drosophila melanogaster subgroup, our results link rapid evolution of early developmental genes with reproductive isolation. In summary, our study revealed that even within functional groups of genes evolving under strong negative selection many positively selected genes could be recognized. Understanding these exceptions to the broad evolutionary conservation of early expressed developmental genes can shed light into relevant processes driving the evolution of species divergence.
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Affiliation(s)
- Julián Mensch
- Departamento de Ecología, Genética y Evolución-IEGEBA (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Xie Y, Li X, Zhang X, Mei S, Li H, Urso A, Zhu S. The Drosophila Sp8 transcription factor Buttonhead prevents premature differentiation of intermediate neural progenitors. eLife 2014; 3. [PMID: 25285448 PMCID: PMC4221738 DOI: 10.7554/elife.03596] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/28/2014] [Indexed: 11/13/2022] Open
Abstract
Intermediate neural progenitor cells (INPs) need to avoid differentiation and cell cycle exit while maintaining restricted developmental potential, but mechanisms preventing differentiation and cell cycle exit of INPs are not well understood. In this study, we report that the Drosophila homolog of mammalian Sp8 transcription factor Buttonhead (Btd) prevents premature differentiation and cell cycle exit of INPs in Drosophila larval type II neuroblast (NB) lineages. We show that the loss of Btd leads to elimination of mature INPs due to premature differentiation of INPs into terminally dividing ganglion mother cells. We provide evidence to demonstrate that Btd prevents the premature differentiation by suppressing the expression of the homeodomain protein Prospero in immature INPs. We further show that Btd functions cooperatively with the Ets transcription factor Pointed P1 to promote the generation of INPs. Thus, our work reveals a critical mechanism that prevents premature differentiation and cell cycle exit of Drosophila INPs.
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Affiliation(s)
- Yonggang Xie
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, United States
| | - Xiaosu Li
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, United States
| | - Xian Zhang
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, United States
| | - Shaolin Mei
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, United States
| | - Hongyu Li
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, United States
| | | | - Sijun Zhu
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, United States
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Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PLoS One 2014; 9:e91924. [PMID: 24786295 PMCID: PMC4006794 DOI: 10.1371/journal.pone.0091924] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/18/2014] [Indexed: 11/23/2022] Open
Abstract
Changes in regulatory DNA contribute to phenotypic differences within and between taxa. Comparative studies show that many transcription factor binding sites (TFBS) are conserved between species whereas functional studies reveal that some mutations segregating within species alter TFBS function. Consistently, in this analysis of 13 regulatory elements in Drosophila melanogaster populations, single base and insertion/deletion polymorphism are rare in characterized regulatory elements. Experimentally defined TFBS are nearly devoid of segregating mutations and, as has been shown before, are quite conserved. For instance 8 of 11 Hunchback binding sites in the stripe 3+7 enhancer of even-skipped are conserved between D. melanogaster and Drosophila virilis. Oddly, we found a 72 bp deletion that removes one of these binding sites (Hb8), segregating within D. melanogaster. Furthermore, a 45 bp deletion polymorphism in the spacer between the stripe 3+7 and stripe 2 enhancers, removes another predicted Hunchback site. These two deletions are separated by ∼250 bp, sit on distinct haplotypes, and segregate at appreciable frequency. The Hb8Δ is at 5 to 35% frequency in the new world, but also shows cosmopolitan distribution. There is depletion of sequence variation on the Hb8Δ-carrying haplotype. Quantitative genetic tests indicate that Hb8Δ affects developmental time, but not viability of offspring. The Eve expression pattern differs between inbred lines, but the stripe 3 and 7 boundaries seem unaffected by Hb8Δ. The data reveal segregating variation in regulatory elements, which may reflect evolutionary turnover of characterized TFBS due to drift or co-evolution.
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45
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Xu Z, Chen H, Ling J, Yu D, Struffi P, Small S. Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila. Genes Dev 2014; 28:608-21. [PMID: 24637116 PMCID: PMC3967049 DOI: 10.1101/gad.234534.113] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Drosophila transcription factor Bicoid (Bcd) binds thousands of genomic sites during early embryogenesis, but it is unclear how many of these binding events are functionally important. Here, Small and colleagues test the role of the maternal factor Zelda (Zld) in Bcd-mediated binding and transcription. Embryos lacking Zld show enhanced Bcd binding to a subset of genomic locations, causing early activation of target genes normally silent until later stages. This study demonstrates a critical role for Zld in controlling Bcd binding and target gene activation in the early embryo. In vivo cross-linking studies suggest that the Drosophila transcription factor Bicoid (Bcd) binds to several thousand sites during early embryogenesis, but it is not clear how many of these binding events are functionally important. In contrast, reporter gene studies have identified >60 Bcd-dependent enhancers, all of which contain clusters of the consensus binding sequence TAATCC. These studies also identified clusters of TAATCC motifs (inactive fragments) that failed to drive Bcd-dependent activation. In general, active fragments showed higher levels of Bcd binding in vivo and were enriched in predicted binding sites for the ubiquitous maternal protein Zelda (Zld). Here we tested the role of Zld in Bcd-mediated binding and transcription. Removal of Zld function and mutations in Zld sites caused significant reductions in Bcd binding to known enhancers and variable effects on the activation and spatial positioning of Bcd-dependent expression patterns. Also, insertion of Zld sites converted one of six inactive fragments into a Bcd-responsive enhancer. Genome-wide binding experiments in zld mutants showed variable effects on Bcd-binding peaks, ranging from strong reductions to significantly enhanced levels of binding. Increases in Bcd binding caused the precocious Bcd-dependent activation of genes that are normally not expressed in early embryos, suggesting that Zld controls the genome-wide binding profile of Bcd at the qualitative level and is critical for selecting target genes for activation in the early embryo. These results underscore the importance of combinatorial binding in enhancer function and provide data that will help predict regulatory activities based on DNA sequence.
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Affiliation(s)
- Zhe Xu
- Department of Biology, New York University, New York, New York 10003, USA
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46
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Rouault H, Santolini M, Schweisguth F, Hakim V. Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. Nucleic Acids Res 2014; 42:6128-45. [PMID: 24682824 PMCID: PMC4041412 DOI: 10.1093/nar/gku209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cis-regulatory modules (CRMs) and motifs play a central role in tissue and condition-specific gene expression. Here we present Imogene, an ensemble of statistical tools that we have developed to facilitate their identification and implemented in a publicly available software. Starting from a small training set of mammalian or fly CRMs that drive similar gene expression profiles, Imogene determines de novocis-regulatory motifs that underlie this co-expression. It can then predict on a genome-wide scale other CRMs with a regulatory potential similar to the training set. Imogene bypasses the need of large datasets for statistical analyses by making central use of the information provided by the sequenced genomes of multiple species, based on the developed statistical tools and explicit models for transcription factor binding site evolution. We test Imogene on characterized tissue-specific mouse developmental CRMs. Its ability to identify CRMs with the same specificity based on its de novo created motifs is comparable to that of previously evaluated ‘motif-blind’ methods. We further show, both in flies and in mammals, that Imogene de novo generated motifs are sufficient to discriminate CRMs related to different developmental programs. Notably, purely relying on sequence data, Imogene performs as well in this discrimination task as a previously reported learning algorithm based on Chromatin Immunoprecipitation (ChIP) data for multiple transcription factors at multiple developmental stages.
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Affiliation(s)
- Hervé Rouault
- Developmental and Stem Cell Biology Department, Institut Pasteur, F-75015 Paris, France CNRS, URA2578, F-75015 Paris, France
| | - Marc Santolini
- Laboratoire de Physique Statistique, CNRS, École Normale Supérieure, Université P. et M. Curie, Université Paris-Diderot
| | - François Schweisguth
- Developmental and Stem Cell Biology Department, Institut Pasteur, F-75015 Paris, France CNRS, URA2578, F-75015 Paris, France
| | - Vincent Hakim
- Laboratoire de Physique Statistique, CNRS, École Normale Supérieure, Université P. et M. Curie, Université Paris-Diderot
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Samee MAH, Sinha S. Quantitative modeling of a gene's expression from its intergenic sequence. PLoS Comput Biol 2014; 10:e1003467. [PMID: 24604095 PMCID: PMC3945089 DOI: 10.1371/journal.pcbi.1003467] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 12/18/2013] [Indexed: 11/18/2022] Open
Abstract
Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1) combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2) independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were "shut down" by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference between enhancer activities was a possible factor necessitating enhancer independence in our model.
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Affiliation(s)
- Md. Abul Hassan Samee
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (MAHS); (SS)
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (MAHS); (SS)
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Rosenberg MI, Brent AE, Payre F, Desplan C. Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes. eLife 2014; 3:e01440. [PMID: 24599282 PMCID: PMC3941026 DOI: 10.7554/elife.01440] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Embryonic anterior-posterior patterning is well understood in Drosophila, which uses 'long germ' embryogenesis, in which all segments are patterned before cellularization. In contrast, most insects use 'short germ' embryogenesis, wherein only head and thorax are patterned in a syncytial environment while the remainder of the embryo is generated after cellularization. We use the wasp Nasonia (Nv) to address how the transition from short to long germ embryogenesis occurred. Maternal and gap gene expression in Nasonia suggest long germ embryogenesis. However, the Nasonia pair-rule genes even-skipped, odd-skipped, runt and hairy are all expressed as early blastoderm pair-rule stripes and late-forming posterior stripes. Knockdown of Nv eve, odd or h causes loss of alternate segments at the anterior and complete loss of abdominal segments. We propose that Nasonia uses a mixed mode of segmentation wherein pair-rule genes pattern the embryo in a manner resembling Drosophila at the anterior and ancestral Tribolium at the posterior. DOI: http://dx.doi.org/10.7554/eLife.01440.001.
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Affiliation(s)
- Miriam I Rosenberg
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
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49
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Heffer A, Grubbs N, Mahaffey J, Pick L. The evolving role of the orphan nuclear receptor ftz-f1, a pair-rule segmentation gene. Evol Dev 2014; 15:406-17. [PMID: 24261442 DOI: 10.1111/ede.12050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Segmentation is a critical developmental process that occurs by different mechanisms in diverse taxa. In insects, there are three common modes of embryogenesis-short-, intermediate-, and long-germ development-which differ in the number of segments specified at the blastoderm stage. While genes involved in segmentation have been extensively studied in the long-germ insect Drosophila melanogaster (Dm), it has been found that their expression and function in segmentation in short- and intermediate-germ insects often differ. Drosophila ftz-f1 encodes an orphan nuclear receptor that functions as a maternally expressed pair-rule segmentation gene, responsible for the formation of alternate body segments during Drosophila embryogenesis. Here we investigated the expression and function of ftz-f1 in the short-germ beetle, Tribolium castaneum (Tc). We found that Tc-ftz-f1 is expressed in stripes in Tribolium embryos. These stripes overlap alternate Tc-Engrailed (Tc-En) stripes, indicative of a pair-rule expression pattern. To test whether Tc-ftz-f1 has pair-rule function, we utilized embryonic RNAi, injecting double-stranded RNA corresponding to Tc-ftz-f1 coding or non-coding regions into early Tribolium embryos. Knockdown of Tc-ftz-f1 produced pair-rule segmentation defects, evidenced by loss of expression of alternate En stripes. In addition, a later role for Tc-ftz-f1 in cuticle formation was revealed. These results identify a new pair-rule gene in Tribolium and suggest that its role in segmentation may be shared among holometabolous insects. Interestingly, while Tc-ftz-f1 is expressed in pair-rule stripes, the gene is ubiquitously expressed in Drosophila embryos. Thus, the pair-rule function of ftz-f1 is conserved despite differences in expression patterns of ftz-f1 genes in different lineages. This suggests that ftz-f1 expression changed after the divergence of lineages leading to extant beetles and flies, likely due to differences in cis-regulatory sequences. We propose that the dependence of Dm-Ftz-F1 on interaction with the homeodomain protein Ftz which is expressed in stripes in Drosophila, loosened constraints on Dm-ftz-f1 expression, allowing for ubiquitous expression of this pair-rule gene in Drosophila.
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Affiliation(s)
- Alison Heffer
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
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Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res 2013; 42:2976-87. [PMID: 24335146 PMCID: PMC3950668 DOI: 10.1093/nar/gkt1249] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Recent advances in technology have led to a dramatic increase in the number of available transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of these data sets is an important step in understanding the underlying mechanisms of regulation. Here we provide a systematic motif analysis for 427 human ChIP-seq data sets using motifs curated from the literature and also discovered de novo using five established motif discovery tools. We use a systematic pipeline for calculating motif enrichment in each data set, providing a principled way for choosing between motif variants found in the literature and for flagging potentially problematic data sets. Our analysis confirms the known specificity of 41 of the 56 analyzed factor groups and reveals motifs of potential cofactors. We also use cell type-specific binding to find factors active in specific conditions. The resource we provide is accessible both for browsing a small number of factors and for performing large-scale systematic analyses. We provide motif matrices, instances and enrichments in each of the ENCODE data sets. The motifs discovered here have been used in parallel studies to validate the specificity of antibodies, understand cooperativity between data sets and measure the variation of motif binding across individuals and species.
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Affiliation(s)
- Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA and Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02139, USA
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