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Cardamone F, Piva A, Löser E, Eichenberger B, Romero-Mulero MC, Zenk F, Shields EJ, Cabezas-Wallscheid N, Bonasio R, Tiana G, Zhan Y, Iovino N. Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis. Nat Commun 2025; 16:3007. [PMID: 40148291 PMCID: PMC11950382 DOI: 10.1038/s41467-025-57719-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 03/03/2025] [Indexed: 03/29/2025] Open
Abstract
The establishment of germ layers during early development is crucial for body formation. The Drosophila zygote serves as a model for investigating these transitions in relation to the chromatin landscape. However, the cellular heterogeneity of the blastoderm embryo poses a challenge for gaining mechanistic insights. Using 10× Multiome, we simultaneously analyzed the in vivo epigenomic and transcriptomic states of wild-type, E(z)-, and CBP-depleted embryos during zygotic genome activation at single-cell resolution. We found that pre-zygotic H3K27me3 safeguards tissue-specific gene expression by modulating cis-regulatory elements. Furthermore, we demonstrate that CBP is essential for cell fate specification functioning as a transcriptional activator by stabilizing transcriptional factors binding at key developmental genes. Surprisingly, while CBP depletion leads to transcriptional arrest, chromatin accessibility continues to progress independently through the retention of stalled RNA Polymerase II. Our study reveals fundamental principles of chromatin-mediated gene regulation essential for establishing and maintaining cellular identities during early embryogenesis.
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Affiliation(s)
- Francesco Cardamone
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School of Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Freiburg, Germany
| | - Annamaria Piva
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Eva Löser
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Bastian Eichenberger
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Mari Carmen Romero-Mulero
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Fides Zenk
- Epigenomics of Neurodevelopment, Brain Mind Institute, School of Life Sciences, EPFL - Ecole Polytechnique Federal Lusanne, Ecublens, Switzerland
| | - Emily J Shields
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Laboratory of Stem Cell Biology and Ageing, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
- Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany
| | - Roberto Bonasio
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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2
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Amiri EE, Tenger-Trolander A, Li M, Thomas Julian A, Kasan K, Sanders SA, Blythe S, Schmidt-Ott U. Conservation of symmetry breaking at the level of chromatin accessibility between fly species with unrelated anterior determinants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632851. [PMID: 39868093 PMCID: PMC11760685 DOI: 10.1101/2025.01.13.632851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Establishing the anterior-posterior body axis is a fundamental process during embryogenesis, and the fruit fly, Drosophila melanogaster, provides one of the best-known case studies of this process. In Drosophila, localized mRNA of bicoid serves as anterior determinant (AD). Bicoid engages in a concentration-dependent competition with nucleosomes and initiates symmetry-breaking along the AP axis by promoting chromatin accessibility at the loci of transcription factor (TF) genes that are expressed in the anterior of the embryo. However, ADs of other fly species are unrelated and structurally distinct, and little is known about how they function. We addressed this question in the moth fly, Clogmia albipunctata, in which a maternally expressed transcript isoform of the pair-rule segmentation gene odd-paired is localized in the anterior egg and has been co-opted as AD. We provide a de novo assembly and annotation of the Clogmia genome and describe how knockdown of zelda and maternal odd-paired transcript affect chromatin accessibility and expression of TF-encoding loci. The results of these experiments suggest direct roles of Cal-Zld in opening and closing chromatin during nuclear cleavage cycles and show that Clogmia's maternal odd-paired activity promotes chromatin accessibility and anterior expression during the early phase of zygotic genome activation at Clogmia's homeobrain and sloppy-paired loci. We conclude that unrelated dipteran ADs initiate anterior-posterior axis-specification at the level of enhancer accessibility and that homeobrain and sloppy-paired homologs may serve a more widely conserved role in the initiation of anterior pattern formation given their early anterior expression and function in head development in other insects.
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Affiliation(s)
- Ezra E. Amiri
- The University of Chicago, Department of Organismal Biology and Anatomy, 1027 East 57 Street, Chicago, Illinois 60637, USA
| | - Ayse Tenger-Trolander
- The University of Chicago, Department of Organismal Biology and Anatomy, 1027 East 57 Street, Chicago, Illinois 60637, USA
| | - Muzi Li
- The University of Chicago, Department of Organismal Biology and Anatomy, 1027 East 57 Street, Chicago, Illinois 60637, USA
| | - Alexander Thomas Julian
- Illinois Institute of Technology, Department of Biology, 3105 South Dearborn Street, Chicago, Illinois 60616, USA
| | - Koray Kasan
- The University of Chicago, Department of Organismal Biology and Anatomy, 1027 East 57 Street, Chicago, Illinois 60637, USA
| | - Sheri A. Sanders
- Notre Dame University, 252 Galvin Life Science Center/Freimann Life Science Center, Notre Dame, Indiana 46556, USA
| | - Shelby Blythe
- Northwestern University, Department of Molecular Biosciences, 2205 Tech Drive, Evanston, Illinois 60208, USA
- Northwestern University and The University of Chicago, National Institute for Theory and Mathematics in Biology, 875 North Michigan Avenue, Suite 3500, Chicago, Illinois 60611, USA
| | - Urs Schmidt-Ott
- The University of Chicago, Department of Organismal Biology and Anatomy, 1027 East 57 Street, Chicago, Illinois 60637, USA
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3
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Albright AR, Yan C, Angeles-Albores D, Makushok T, Allen-Henderson J, Marshall WF. Genome-wide analysis of anterior-posterior mRNA regionalization in Stentor coeruleus reveals a role for the microtubule cytoskeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.09.523364. [PMID: 36711710 PMCID: PMC9882060 DOI: 10.1101/2023.01.09.523364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cells have complex and beautiful structures that are important for their function. However, understanding the molecular mechanisms that produce these structures is a challenging problem due to the gap in size scales between molecular interactions and cellular structures. The giant ciliate Stentor coeruleus is a unicellular model organism whose large size, reproducible structure, and ability to heal wounds and regenerate have historically allowed the formation of structure in a single cell to be addressed using methods of experimental embryology. Such studies have shown that specific cellular structures, such as the membranellar band, always form in particular regions of the cell, which raises the question: what is the source of positional information within this organism? By analogy with embryonic development, in which regionalized mRNA is often used to mark position, we asked whether specific regionalized mRNAs might mark position along the anterior-posterior axis of Stentor. By physically bisecting cells and conducting bulk RNA sequencing, we were able to identify sets of messages enriched in either the anterior or posterior half. We then conducted half-cell RNA-sequencing in paired anteriors and posteriors of cells in which the microtubule cytoskeleton was disrupted by RNAi of β-tubulin or dynein intermediate chains. We found that many messages either lost their regionalized distribution or switched to an opposite distribution, such that anterior-enriched messages in control became posterior-enriched in the RNAi cells, or vice versa. This study indicates that mRNA can be regionalized within a single giant cell and that microtubules may play a role, possibly by serving as tracks for the movement of the messages.
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Affiliation(s)
- Ashley R. Albright
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
| | - Connie Yan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
| | | | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
| | - Jamarc Allen-Henderson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
| | - Wallace F. Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Center for Cellular Construction, University of California, San Francisco, San Francisco, CA, USA
- Twitter: @WallaceUCSF
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4
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Ciabrelli F, Atinbayeva N, Pane A, Iovino N. Epigenetic inheritance and gene expression regulation in early Drosophila embryos. EMBO Rep 2024; 25:4131-4152. [PMID: 39285248 PMCID: PMC11467379 DOI: 10.1038/s44319-024-00245-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/13/2024] [Accepted: 08/21/2024] [Indexed: 10/12/2024] Open
Abstract
Precise spatiotemporal regulation of gene expression is of paramount importance for eukaryotic development. The maternal-to-zygotic transition (MZT) during early embryogenesis in Drosophila involves the gradual replacement of maternally contributed mRNAs and proteins by zygotic gene products. The zygotic genome is transcriptionally activated during the first 3 hours of development, in a process known as "zygotic genome activation" (ZGA), by the orchestrated activities of a few pioneer factors. Their decisive role during ZGA has been characterized in detail, whereas the contribution of chromatin factors to this process has been historically overlooked. In this review, we aim to summarize the current knowledge of how chromatin regulation impacts the first stages of Drosophila embryonic development. In particular, we will address the following questions: how chromatin factors affect ZGA and transcriptional silencing, and how genome architecture promotes the integration of these processes early during development. Remarkably, certain chromatin marks can be intergenerationally inherited, and their presence in the early embryo becomes critical for the regulation of gene expression at later stages. Finally, we speculate on the possible roles of these chromatin marks as carriers of epialleles during transgenerational epigenetic inheritance (TEI).
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Affiliation(s)
- Filippo Ciabrelli
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Attilio Pane
- Institute of Biomedical Sciences/UFRJ, 21941902, Rio de Janeiro, Brazil
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.
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5
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Benner L, Muron S, Gomez JG, Oliver B. OVO positively regulates essential maternal pathways by binding near the transcriptional start sites in the Drosophila female germline. eLife 2024; 13:RP94631. [PMID: 39291827 PMCID: PMC11410370 DOI: 10.7554/elife.94631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Differentiation of female germline stem cells into a mature oocyte includes the expression of RNAs and proteins that drive early embryonic development in Drosophila. We have little insight into what activates the expression of these maternal factors. One candidate is the zinc-finger protein OVO. OVO is required for female germline viability and has been shown to positively regulate its own expression, as well as a downstream target, ovarian tumor, by binding to the transcriptional start site (TSS). To find additional OVO targets in the female germline and further elucidate OVO's role in oocyte development, we performed ChIP-seq to determine genome-wide OVO occupancy, as well as RNA-seq comparing hypomorphic and wild type rescue ovo alleles. OVO preferentially binds in close proximity to target TSSs genome-wide, is associated with open chromatin, transcriptionally active histone marks, and OVO-dependent expression. Motif enrichment analysis on OVO ChIP peaks identified a 5'-TAACNGT-3' OVO DNA binding motif spatially enriched near TSSs. However, the OVO DNA binding motif does not exhibit precise motif spacing relative to the TSS characteristic of RNA polymerase II complex binding core promoter elements. Integrated genomics analysis showed that 525 genes that are bound and increase in expression downstream of OVO are known to be essential maternally expressed genes. These include genes involved in anterior/posterior/germ plasm specification (bcd, exu, swa, osk, nos, aub, pgc, gcl), egg activation (png, plu, gnu, wisp, C(3)g, mtrm), translational regulation (cup, orb, bru1, me31B), and vitelline membrane formation (fs(1)N, fs(1)M3, clos). This suggests that OVO is a master transcriptional regulator of oocyte development and is responsible for the expression of structural components of the egg as well as maternally provided RNAs that are required for early embryonic development.
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Affiliation(s)
- Leif Benner
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Savannah Muron
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Jillian G Gomez
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
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6
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Hu Y, Feng B, Wang F. Analysis of maternal effect genes from maternal mRNA in eggs of Sogatella furcifera. Heliyon 2024; 10:e34014. [PMID: 39055844 PMCID: PMC11269863 DOI: 10.1016/j.heliyon.2024.e34014] [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: 01/27/2024] [Revised: 06/07/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
To understand how many kinds of mRNAs in female adults can be transferred into the eggs and the molecular basis of embryonic axis specification in Sogatella furcifera, we performed de novo transcriptome sequencing of six cDNA libraries of female adults and unfertilized eggs. Total 60,306 unigenes were obtained, with an average length of 1114.51 bp and N50 length of 2112 bp. Total 2900 differentially expressed genes with 496 upregulated and 2404 downregulated were found in unfertilized egg compared to female adult. Most of mRNAs in female adult could be passed into its eggs. Total 65 maternal effect genes were identified, including many homologous genes involved in embryonic axis specialization of D. melanogaster. This study provide transcriptome resources to elucidate the functions of maternal effect genes and the molecular basis of embryonic axis specification in S. furcifera in the future.
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Affiliation(s)
- Yang Hu
- State Key Laboratory for Biocontrol and Institute of Entomology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bo Feng
- State Key Laboratory for Biocontrol and Institute of Entomology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fanghai Wang
- State Key Laboratory for Biocontrol and Institute of Entomology, Sun Yat-sen University, Guangzhou, 510275, China
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7
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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8
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Harrison MM, Marsh AJ, Rushlow CA. Setting the stage for development: the maternal-to-zygotic transition in Drosophila. Genetics 2023; 225:iyad142. [PMID: 37616526 PMCID: PMC10550319 DOI: 10.1093/genetics/iyad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/26/2023] Open
Abstract
The zygote has a daunting task ahead of itself; it must develop from a single cell (fertilized egg) into a fully functioning adult with a multitude of different cell types. In the beginning, the zygote has help from its mother, in the form of gene products deposited into the egg, but eventually, it must rely on its own resources to proceed through development. The transfer of developmental control from the mother to the embryo is called the maternal-to-zygotic transition (MZT). All animals undergo this transition, which is defined by two main processes-the degradation of maternal RNAs and the synthesis of new RNAs from the zygote's own genome. Here, we review the regulation of the MZT in Drosophila, but given the broad conservation of this essential process, much of the regulation is shared among metazoans.
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Affiliation(s)
- Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Audrey J Marsh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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9
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Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023; 19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred strain genetic backgrounds, seven associated with a reference quality genome assembly. We develop a method for the quantile normalization of ATAC-seq fragments and test for differences in coverage among genotypes, tissues, and their interaction at 44099 peaks throughout the euchromatic genome. For the strains with reference quality genome assemblies, we correct ATAC-seq profiles for read mis-mapping due to nearby polymorphic structural variants (SVs). Comparing coverage among genotypes without accounting for SVs results in a highly elevated rate (55%) of identifying false positive differences in chromatin state between genotypes. After SV correction, we identify 1050, 30383, and 4508 regions whose peak heights are polymorphic among genotypes, among tissues, or exhibit genotype-by-tissue interactions, respectively. Finally, we identify 3988 candidate causative variants that explain at least 80% of the variance in chromatin state at nearby ATAC-seq peaks.
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Affiliation(s)
- Khoi Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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10
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Dhall JK, Kasturacharya N, Pandit A, Cp L. Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue. STAR Protoc 2023; 4:102153. [PMID: 37074906 PMCID: PMC10148076 DOI: 10.1016/j.xpro.2023.102153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 04/20/2023] Open
Abstract
Transposase-accessible chromatin by sequencing (ATAC-seq) has emerged as an advantageous technique to assess chromatin accessibility owing to the robustness of "tagmentation" process and a relatively faster library preparation. A comprehensive ATAC-seq protocol from Drosophila brain tissue is currently unavailable. Here, we have provided a detailed protocol of ATAC-seq assay from Drosophila brain tissue. Starting from dissection and transposition to amplification of libraries has been elaborated. Furthermore, a robust ATAC-seq analysis pipeline has been presented. The protocol can be easily adapted for other soft tissues.
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Affiliation(s)
- Jasmine Kaur Dhall
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru 560065, India.
| | - Nandashree Kasturacharya
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru 560065, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru 560064, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru 560065, India.
| | - Lakshminarayanan Cp
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru 560065, India
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11
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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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12
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Iwasaki-Yokozawa S, Nanjo R, Akiyama-Oda Y, Oda H. Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider. BMC Biol 2022; 20:223. [PMID: 36203191 PMCID: PMC9535882 DOI: 10.1186/s12915-022-01421-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background
The process of early development varies across the species-rich phylum Arthropoda. Owing to the limited research strategies for dissecting lineage-specific processes of development in arthropods, little is known about the variations in early arthropod development at molecular resolution. The Theridiidae spider, Parasteatoda tepidariorum, has its genome sequenced and could potentially contribute to dissecting early embryonic processes. Results We present genome-wide identification of candidate genes that exhibit locally restricted expression in germ disc forming stage embryos of P. tepidariorum, based on comparative transcriptomes of isolated cells from different regions of the embryo. A subsequent pilot screen by parental RNA interference identifies three genes required for body axis formation. One of them is a GATA-like gene that has been fast evolving after duplication and divergence from a canonical GATA family gene. This gene is designated fuchi nashi (fuchi) after its knockdown phenotypes, where the cell movement toward the formation of a germ disc was reversed. fuchi expression occurs in cells outside a forming germ disc and persists in the endoderm. Transcriptome and chromatin accessibility analyses of fuchi pRNAi embryos suggest that early fuchi activity regulates chromatin state and zygotic gene activation to promote endoderm specification and pattern formation. We also show that there are many uncharacterized genes regulated by fuchi. Conclusions Our genome-based research using an arthropod phylogenetically distant from Drosophila identifies a lineage-specific, fast-evolving gene with key developmental roles in one of the earliest, genome-wide regulatory events, and allows for molecular exploration of the developmental variations in early arthropod embryos. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01421-0.
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Affiliation(s)
- Sawa Iwasaki-Yokozawa
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan
| | - Ryota Nanjo
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan.,Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.
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13
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Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O’Connor-Giles KM, Furlong EEM, Shendure J. The continuum of Drosophila embryonic development at single-cell resolution. Science 2022; 377:eabn5800. [PMID: 35926038 PMCID: PMC9371440 DOI: 10.1126/science.abn5800] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in half a million nuclei from overlapping windows spanning the entirety of embryogenesis. Leveraging developmental asynchronicity within embryo collections, we applied deep neural networks to infer the age of each nucleus, resulting in continuous, multimodal views of molecular and cellular transitions in absolute time. We identify cell lineages; infer their developmental relationships; and link dynamic changes in enhancer usage, transcription factor (TF) expression, and the accessibility of TFs' cognate motifs. With these data, the dynamics of enhancer usage and gene expression can be explored within and across lineages at the scale of minutes, including for precise transitions like zygotic genome activation.
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Affiliation(s)
- Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - James Kentro
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
| | - Riza M. Daza
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alessandro Dulja
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Erica Larschan
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
| | - Kate M. O’Connor-Giles
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Eileen E. M. Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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14
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Keränen SVE, Villahoz-Baleta A, Bruno AE, Halfon MS. REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. INSECTS 2022; 13:618. [PMID: 35886794 PMCID: PMC9323752 DOI: 10.3390/insects13070618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
We provide here an updated description of the REDfly (Regulatory Element Database for Fly) database of transcriptional regulatory elements, a unique resource that provides regulatory annotation for the genome of Drosophila and other insects. The genomic sequences regulating insect gene expression-transcriptional cis-regulatory modules (CRMs, e.g., "enhancers") and transcription factor binding sites (TFBSs)-are not currently curated by any other major database resources. However, knowledge of such sequences is important, as CRMs play critical roles with respect to disease as well as normal development, phenotypic variation, and evolution. Characterized CRMs also provide useful tools for both basic and applied research, including developing methods for insect control. REDfly, which is the most detailed existing platform for metazoan regulatory-element annotation, includes over 40,000 experimentally verified CRMs and TFBSs along with their DNA sequences, their associated genes, and the expression patterns they direct. Here, we briefly describe REDfly's contents and data model, with an emphasis on the new features implemented since 2020. We then provide an illustrated walk-through of several common REDfly search use cases.
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Affiliation(s)
| | - Angel Villahoz-Baleta
- Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14203, USA; (A.V.-B.); (A.E.B.)
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Andrew E. Bruno
- Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14203, USA; (A.V.-B.); (A.E.B.)
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Marc S. Halfon
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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15
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Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos. PLoS One 2022; 17:e0270471. [PMID: 35749552 PMCID: PMC9232161 DOI: 10.1371/journal.pone.0270471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the use of single-nucleus RNA sequencing in Drosophila embryos prior to cellularization, here we look at gene expression in control and insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we provide a resource of candidate differentially expressed genes that might show local changes in gene expression between control and maternal dCTCF null nuclei with no detectable differential expression in bulk. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.
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16
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Gong C, Ruan Y, Zhang Y, Wang Q, Wu Y, Zhan X, He Y, Liu X, Liu X, Pu J, Wang X. Resistance of Sogatella furcifera to triflumezopyrim mediated with the overexpression of CYPSF01 which was regulated by nuclear receptor USP. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 238:113575. [PMID: 35500402 DOI: 10.1016/j.ecoenv.2022.113575] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Sogatella furcifera is one of the main agricultural pests in many Asian countries, bringing about enormous injury. A triflumezopyrim-resistant (Tri) strain of S. furcifera was established through continuous screening in laboratory. The determination of synergist and enzyme activity indicated that P450s, especially for the upregulation expression of CYPSF01, played a key role in the increased resistance, confirmed by RNAi, and the recombinant protein of CYPSF01 and NADPH-P450 reductase was able to degrade triflumezopyrim. CYPSF01 had an obviously co-expression relationship with nuclear receptor ultraspiracle (USP), which were all significantly up-regulated when exposed to triflumezopyrim. Further, a USP-binding motif MA0534.1 was enriched from the upregulated peaks by Assay for Transposase Accessible Chromatin (ATAC-seq) analysis, which exited in the peaks located on the promoter of CYPSF01; the yeast one-hybrid experiments confirmed that USP could bind to the CYPSF01 promoter. And the USP interference significantly down-regulated CYPSF01 expression, and resulted in the significantly increasing sensitivity to triflumezopyrim, its mortality rate increased 28.37%. Therefore, the overexpression of USP could cause to the overexpression of CYPSF01, ultimately resulting in the resistance to triflumezopyrim in S. furcifera.
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Affiliation(s)
- Changwei Gong
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanwei Ruan
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuming Zhang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiulin Wang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yutong Wu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoxu Zhan
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yunfeng He
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinxian Liu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuemei Liu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Pu
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuegui Wang
- College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China.
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17
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Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022; 17:1518-1552. [PMID: 35478247 PMCID: PMC9189070 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.
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Affiliation(s)
- Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lucas Kampman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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18
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Merrill CB, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons. Sci Rep 2022; 12:6043. [PMID: 35411004 PMCID: PMC9001676 DOI: 10.1038/s41598-022-09869-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is rapidly becoming the assay of choice to investigate chromatin-mediated gene regulation, largely because of low input requirements, a fast workflow, and the ability to interrogate the entire genome in an untargeted manner. Many studies using ATAC-seq use mammalian or human-derived tissues, and established protocols work well in these systems. However, ATAC-seq is not yet widely used in Drosophila. Vinegar flies present several advantages over mammalian systems that make them an excellent model for ATAC-seq studies, including abundant genetic tools that allow straightforward targeting, transgene expression, and genetic manipulation that are not available in mammalian models. Because current ATAC-seq protocols are not optimized to use flies, we developed an optimized workflow that accounts for several complicating factors present in Drosophila. We examined parameters affecting nuclei isolation, including input size, freezing time, washing, and possible confounds from retinal pigments. Then, we optimized the enzymatic steps of library construction to account for the smaller Drosophila genome size. Finally, we used our optimized protocol to generate ATAC-seq libraries that meet ENCODE quality metrics. Our optimized protocol enables extensive ATAC-seq experiments in Drosophila, thereby leveraging the advantages of this powerful model system to understand chromatin-mediated gene regulation.
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Affiliation(s)
- Collin B. Merrill
- grid.223827.e0000 0001 2193 0096Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108 USA
| | - Miguel A. Pabon
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA
| | - Austin B. Montgomery
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA
| | - Aylin R. Rodan
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA ,grid.280807.50000 0000 9555 3716Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT 84148 USA
| | - Adrian Rothenfluh
- grid.223827.e0000 0001 2193 0096Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108 USA ,grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Neurobiology, University of Utah, Salt Lake City, UT 84112 USA
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19
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Schmidt-Ott U, Yoon Y. Evolution and loss of ß-catenin and TCF-dependent axis specification in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100877. [PMID: 35104659 PMCID: PMC9133022 DOI: 10.1016/j.cois.2022.100877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Mechanisms and evolution of primary axis specification in insects are discussed in the context of the roles of ß-catenin and TCF in polarizing metazoan embryos. Three hypotheses are presented. First, insects with sequential segmentation and posterior growth use cell-autonomous mechanisms for establishing embryo polarity via the nuclear ratio of ß-catenin and TCF. Second, TCF homologs establish competence for anterior specification. Third, the evolution of simultaneous segmentation mechanisms, also known as long-germ development, resulted in primary axis specification mechanisms that are independent of ß-catenin but reliant on TCF, a condition that preceded the frequent replacement of anterior determinants in long germ insects.
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Affiliation(s)
- Urs Schmidt-Ott
- University of Chicago, Dept. of Organismal Biology and Anatomy, 1027 East 57th Street, Chicago, IL 60637, USA.
| | - Yoseop Yoon
- University of California, Irvine, Dept. of Microbiology and Molecular Genetics, School of Medicine, 811 Health Sciences Rd., Med Sci B262, CA 92617, USA
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20
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Lucas T, Hafer TL, Zhang HG, Molotkova N, Kohwi M. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. Dev Cell 2021; 56:2649-2663.e6. [PMID: 34529940 PMCID: PMC8629127 DOI: 10.1016/j.devcel.2021.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023]
Abstract
The nuclear lamina is typically associated with transcriptional silencing, and peripheral relocation of genes highly correlates with repression. However, the DNA sequences and proteins regulating gene-lamina interactions are largely unknown. Exploiting the developmentally timed hunchback gene movement to the lamina in Drosophila neuroblasts, we identified a 250 bp intronic element (IE) both necessary and sufficient for relocation. The IE can target a reporter transgene to the lamina and silence it. Endogenously, however, hunchback is already repressed prior to relocation. Instead, IE-mediated relocation confers a heritably silenced gene state refractory to activation in descendent neurons, which terminates neuroblast competence to specify early-born identity. Surprisingly, we found that the Polycomb group chromatin factors bind the IE and are required for lamina relocation, revealing a nuclear architectural role distinct from their well-known function in transcriptional repression. Together, our results uncover in vivo mechanisms underlying neuroblast competence and lamina association in heritable gene silencing. In Drosophila neuroblasts, relocation of the hunchback gene locus to the nuclear lamina confers heritable silencing in daughter neurons. Lucas et al. identify a genomic element necessary and sufficient for hunchback gene movement in vivo. Polycomb proteins target this element for lamina relocation, thereby regulating competence, but not hunchback expression.
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Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Terry L Hafer
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Harrison G Zhang
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Natalia Molotkova
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute Mind Brain Behavior, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
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21
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Asma H, Halfon MS. Annotating the Insect Regulatory Genome. INSECTS 2021; 12:591. [PMID: 34209769 PMCID: PMC8305585 DOI: 10.3390/insects12070591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
Abstract
An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotation of newly sequenced insect genomes is an ongoing challenge. We review here the methods being used to identify CRMs in both model and non-model insect species, and focus on two tools that we have developed, REDfly and SCRMshaw. These resources can be paired together in a powerful combination to facilitate insect regulatory annotation over a broad range of species, with an accuracy equal to or better than that of other state-of-the-art methods.
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Affiliation(s)
- Hasiba Asma
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
| | - Marc S. Halfon
- Program in Genetics, Genomics, and Bioinformatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA;
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY 14203, USA
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22
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Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021; 17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
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Affiliation(s)
- Jonathan Liu
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
| | - Donald Hansen
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Meghan Turner
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
| | - Hernan G. Garcia
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California, United States of America
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23
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Fan T, Huang Y. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis. Sci Rep 2021; 11:7896. [PMID: 33846424 PMCID: PMC8042068 DOI: 10.1038/s41598-021-86919-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
This study was conducted to investigate epigenetic landscape across multiple species and identify transcription factors (TFs) and their roles in controlling cell fate decision events during early embryogenesis. We made a comprehensively joint-research of chromatin accessibility of five species during embryogenesis by integration of ATAC-seq and RNA-seq datasets. Regulatory roles of candidate early embryonic TFs were investigated. Widespread accessible chromatin in early embryos overlapped with putative cis-regulatory sequences. Sets of cell-fate-determining TFs were identified. YOX1, a key cell cycle regulator, were found to homologous to clusters of TFs that are involved in neuron and epidermal cell-fate determination. Our research provides an intriguing insight into evolution of cell-fate decision during early embryogenesis among organisms.
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Affiliation(s)
- Tongqiang Fan
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
| | - Youjun Huang
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
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24
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Arguello JR, Abuin L, Armida J, Mika K, Chai PC, Benton R. Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. eLife 2021; 10:63036. [PMID: 33666172 PMCID: PMC7993999 DOI: 10.7554/elife.63036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Determining the molecular properties of neurons is essential to understand their development, function and evolution. Using Targeted DamID (TaDa), we characterize RNA polymerase II occupancy and chromatin accessibility in selected Ionotropic receptor (Ir)-expressing olfactory sensory neurons in Drosophila. Although individual populations represent a minute fraction of cells, TaDa is sufficiently sensitive and specific to identify the expected receptor genes. Unique Ir expression is not consistently associated with differences in chromatin accessibility, but rather to distinct transcription factor profiles. Genes that are heterogeneously expressed across populations are enriched for neurodevelopmental factors, and we identify functions for the POU-domain protein Pdm3 as a genetic switch of Ir neuron fate, and the atypical cadherin Flamingo in segregation of neurons into discrete glomeruli. Together this study reveals the effectiveness of TaDa in profiling rare neural populations, identifies new roles for a transcription factor and a neuronal guidance molecule, and provides valuable datasets for future exploration.
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Affiliation(s)
- J Roman Arguello
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland.,Department of Ecology and Evolution Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Liliane Abuin
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Jan Armida
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Kaan Mika
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Phing Chian Chai
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
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25
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Reddington JP, Garfield DA, Sigalova OM, Karabacak Calviello A, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM. Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis. Dev Cell 2020; 55:648-664.e9. [PMID: 33171098 DOI: 10.1016/j.devcel.2020.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 02/01/2023]
Abstract
Enhancers are essential drivers of cell states, yet the relationship between accessibility, regulatory activity, and in vivo lineage commitment during embryogenesis remains poorly understood. Here, we measure chromatin accessibility in isolated neural and mesodermal lineages across a time course of Drosophila embryogenesis. Promoters, including tissue-specific genes, are often constitutively open, even in contexts where the gene is not expressed. In contrast, the majority of distal elements have dynamic, tissue-specific accessibility. Enhancer priming appears rarely within a lineage, perhaps reflecting the speed of Drosophila embryogenesis. However, many tissue-specific enhancers are accessible in other lineages early on and become progressively closed as embryogenesis proceeds. We demonstrate the usefulness of this tissue- and time-resolved resource to definitively identify single-cell clusters, to uncover predictive motifs, and to identify many regulators of tissue development. For one such predicted neural regulator, l(3)neo38, we generate a loss-of-function mutant and uncover an essential role for neuromuscular junction and brain development.
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Affiliation(s)
- James P Reddington
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Olga M Sigalova
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jacob F Degner
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
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26
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Cartwright EL, Lott SE. Evolved Differences in cis and trans Regulation Between the Maternal and Zygotic mRNA Complements in the Drosophila Embryo. Genetics 2020; 216:805-821. [PMID: 32928902 PMCID: PMC7648588 DOI: 10.1534/genetics.120.303626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 08/26/2020] [Indexed: 11/18/2022] Open
Abstract
How gene expression can evolve depends on the mechanisms driving gene expression. Gene expression is controlled in different ways in different developmental stages; here we ask whether different developmental stages show different patterns of regulatory evolution. To explore the mode of regulatory evolution, we used the early stages of embryonic development controlled by two different genomes, that of the mother and that of the zygote. During embryogenesis in all animals, initial developmental processes are driven entirely by maternally provided gene products deposited into the oocyte. The zygotic genome is activated later, when developmental control is handed off from maternal gene products to the zygote during the maternal-to-zygotic transition. Using hybrid crosses between sister species of Drosophila (Dsimulans, D. sechellia, and D. mauritiana) and transcriptomics, we find that the regulation of maternal transcript deposition and zygotic transcription evolve through different mechanisms. We find that patterns of transcript level inheritance in hybrids, relative to parental species, differ between maternal and zygotic transcripts, and maternal transcript levels are more likely to be conserved. Changes in transcript levels occur predominantly through differences in trans regulation for maternal genes, while changes in zygotic transcription occur through a combination of both cis and trans regulatory changes. Differences in the underlying regulatory landscape in the mother and the zygote are likely the primary determinants for how maternal and zygotic transcripts evolve.
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Affiliation(s)
- Emily L Cartwright
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Susan E Lott
- Department of Evolution and Ecology, University of California, Davis, California 95616
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27
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Serizay J, Dong Y, Jänes J, Chesney M, Cerrato C, Ahringer J. Distinctive regulatory architectures of germline-active and somatic genes in C. elegans. Genome Res 2020; 30:1752-1765. [PMID: 33093068 PMCID: PMC7706728 DOI: 10.1101/gr.265934.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/08/2020] [Indexed: 01/08/2023]
Abstract
RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of Caenorhabditis elegans, covering ∼90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue–specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue–specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies.
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Affiliation(s)
- Jacques Serizay
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jürgen Jänes
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Michael Chesney
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Chiara Cerrato
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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28
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Soluri IV, Zumerling LM, Payan Parra OA, Clark EG, Blythe SA. Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. eLife 2020; 9:e53916. [PMID: 32347792 PMCID: PMC7190358 DOI: 10.7554/elife.53916] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/20/2022] Open
Abstract
Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC-seq on Drosophila embryos during the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of late segmentation network CRMs. opa-driven changes in accessibility are accompanied by equivalent changes in gene expression. Interfering with the timing of opa activity impacts the proper patterning of expression. These results indicate that dynamic systems for chromatin regulation directly impact the reading of embryonic patterning information.
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Affiliation(s)
- Isabella V Soluri
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Lauren M Zumerling
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Omar A Payan Parra
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | - Eleanor G Clark
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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29
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Bozek M, Gompel N. Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity. Bioessays 2020; 42:e1900188. [PMID: 32142172 DOI: 10.1002/bies.201900188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. While the open structure as such is not a specific indicator of enhancer activity, active enhancers display a higher degree of accessibility than the primed and repressed states. Molecular mechanisms that may account for these quantitative differences are discussed. A model that relates molecular events at an enhancer to changes in its activity and accessibility in a developing tissue is also proposed.
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Affiliation(s)
- Marta Bozek
- Department Biochemie, Ludwig-Maximilians Universität München, Genzentrum, 81377, München, Germany
| | - Nicolas Gompel
- Fakultät für Biologie, Ludwig-Maximilians Universität München, Biozentrum, 82152, Planegg-Martinsried, Germany
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30
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Pálfy M, Schulze G, Valen E, Vastenhouw NL. Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLoS Genet 2020; 16:e1008546. [PMID: 31940339 PMCID: PMC6986763 DOI: 10.1371/journal.pgen.1008546] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/28/2020] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remain poorly understood. Here, we generated chromatin accessibility maps with ATAC-seq from genome activation until the onset of lineage specification. During this period, chromatin accessibility increases at regulatory elements. This increase is independent of RNA polymerase II-mediated transcription, with the exception of the hypertranscribed miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors Pou5f3, Sox19b, and Nanog, which are known to be required for zebrafish genome activation, results in decreased accessibility at regulatory elements. Importantly, the accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Our results show that the maternally provided transcription factors Pou5f3, Sox19b, and Nanog open up chromatin and prime genes for activity during zygotic genome activation in zebrafish.
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Affiliation(s)
- Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gunnar Schulze
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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31
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Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Curr Top Dev Biol 2019; 137:1-35. [PMID: 32143740 DOI: 10.1016/bs.ctdb.2019.10.010] [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] [Indexed: 12/13/2022]
Abstract
Although the last 30years have witnessed the mapping of the wiring diagrams of the gene regulatory networks that dictate cell fate and animal body plans, specific understanding building on such network diagrams that shows how DNA regulatory regions control gene expression lags far behind. These networks have yet to yield the predictive power necessary to, for example, calculate how the concentration dynamics of input transcription factors and DNA regulatory sequence prescribes output patterns of gene expression that, in turn, determine body plans themselves. Here, we argue that reaching a predictive understanding of developmental decision-making calls for an interplay between theory and experiment aimed at revealing how the regulation of the processes of the central dogma dictate network connections and how network topology guides cells toward their ultimate developmental fate. To make this possible, it is crucial to break free from the snapshot-based understanding of embryonic development facilitated by fixed-tissue approaches and embrace new technologies that capture the dynamics of developmental decision-making at the single cell level, in living embryos.
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Affiliation(s)
- Hernan G Garcia
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States; Department of Physics, University of California at Berkeley, Berkeley, CA, United States; Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States; Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, United States.
| | - Augusto Berrocal
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States
| | - Gabriella Martini
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, United States
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32
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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: 38] [Impact Index Per Article: 6.3] [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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