1
|
Yuan Y, Chen Q, Brovkina M, Clowney EJ, Yadlapalli S. Clock-dependent chromatin accessibility rhythms regulate circadian transcription. PLoS Genet 2024; 20:e1011278. [PMID: 38805552 DOI: 10.1371/journal.pgen.1011278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 06/07/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. We observed significant oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible at both dawn and dusk, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase at dawn. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.
Collapse
Affiliation(s)
- Ye Yuan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Qianqian Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margarita Brovkina
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - E Josephine Clowney
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Swathi Yadlapalli
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|
2
|
Roggenbuck EC, Hall EA, Hanson IB, Roby AA, Zhang KK, Alkatib KA, Carter JA, Clewner JE, Gelfius AL, Gong S, Gordon FR, Iseler JN, Kotapati S, Li M, Maysun A, McCormick EO, Rastogi G, Sengupta S, Uzoma CU, Wolkov MA, Clowney EJ. Let's talk about sex: Mechanisms of neural sexual differentiation in Bilateria. WIREs Mech Dis 2024; 16:e1636. [PMID: 38185860 DOI: 10.1002/wsbm.1636] [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: 05/09/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
In multicellular organisms, sexed gonads have evolved that facilitate release of sperm versus eggs, and bilaterian animals purposefully combine their gametes via mating behaviors. Distinct neural circuits have evolved that control these physically different mating events for animals producing eggs from ovaries versus sperm from testis. In this review, we will describe the developmental mechanisms that sexually differentiate neural circuits across three major clades of bilaterian animals-Ecdysozoa, Deuterosomia, and Lophotrochozoa. While many of the mechanisms inducing somatic and neuronal sex differentiation across these diverse organisms are clade-specific rather than evolutionarily conserved, we develop a common framework for considering the developmental logic of these events and the types of neuronal differences that produce sex-differentiated behaviors. This article is categorized under: Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development.
Collapse
Affiliation(s)
- Emma C Roggenbuck
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elijah A Hall
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Isabel B Hanson
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyssa A Roby
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine K Zhang
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Kyle A Alkatib
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph A Carter
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jarred E Clewner
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna L Gelfius
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Shiyuan Gong
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Finley R Gordon
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jolene N Iseler
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Samhita Kotapati
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Marilyn Li
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Areeba Maysun
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elise O McCormick
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Geetanjali Rastogi
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Srijani Sengupta
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Chantal U Uzoma
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Madison A Wolkov
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
3
|
Coleman RT, Morantte I, Koreman GT, Cheng ML, Ding Y, Ruta V. A modular circuit architecture coordinates the diversification of courtship strategies in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558080. [PMID: 37745588 PMCID: PMC10516016 DOI: 10.1101/2023.09.16.558080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Identifying a mate is a central imperative for males of most species but poses the challenge of distinguishing a suitable partner from an array of potential male competitors or females of related species. Mate recognition systems are thus subject to strong selective pressures, driving the rapid coevolution of female sensory cues and male sensory preferences. Here we leverage the rapid evolution of female pheromones across the Drosophila genus to gain insight into how males coordinately adapt their detection and interpretation of these chemical cues to hone their mating strategies. While in some Drosophila species females produce unique pheromones that act to attract and arouse their conspecific males, the pheromones of most species are sexually monomorphic such that females possess no distinguishing chemosensory signatures that males can use for mate recognition. By comparing several close and distantly-related Drosophila species, we reveal that D. yakuba males have evolved the distinct ability to use a sexually-monomorphic pheromone, 7-tricosene (7-T), as an excitatory cue to promote courtship, a sensory innovation that enables D. yakuba males to court in the dark thereby expanding their reproductive opportunities. To gain insight into the neural adaptations that enable 7-T to act as an excitatory cue, we compared the functional properties of two key nodes within the pheromone circuits of D. yakuba and a subset of its closest relatives. We show that the instructive role of 7-T in D. yakuba arises from concurrent peripheral and central circuit changes: a distinct subpopulation of sensory neurons has acquired sensitivity to 7-T which in turn selectively signals to a distinct subset of P1 neurons in the central brain that trigger courtship behaviors. Such a modular circuit organization, in which different sensory inputs can independently couple to multiple parallel courtship control nodes, may facilitate the evolution of mate recognition systems by allowing males to take advantage of novel sensory modalities to become aroused. Together, our findings suggest how peripheral and central circuit adaptations can be flexibly linked to underlie the rapid evolution of mate recognition and courtship strategies across species.
Collapse
Affiliation(s)
- Rory T. Coleman
- Laboatory of Neurophysiology and Behavior and Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | - Ianessa Morantte
- Laboatory of Neurophysiology and Behavior and Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | - Gabriel T. Koreman
- Laboatory of Neurophysiology and Behavior and Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | - Megan L. Cheng
- Laboatory of Neurophysiology and Behavior and Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | - Yun Ding
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Vanessa Ruta
- Laboatory of Neurophysiology and Behavior and Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| |
Collapse
|
4
|
Yuan Y, Chen Q, Brovkina M, Clowney EJ, Yadlapalli S. Clock-dependent chromatin accessibility rhythms regulate circadian transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553315. [PMID: 37645872 PMCID: PMC10462003 DOI: 10.1101/2023.08.15.553315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility over the circadian cycle. We observed significant circadian oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible throughout the circadian cycle, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.
Collapse
Affiliation(s)
- Ye Yuan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qianqian Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Margarita Brovkina
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - E Josephine Clowney
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA
| | - Swathi Yadlapalli
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
5
|
Ahmed M, Rajagopalan AE, Pan Y, Li Y, Williams DL, Pedersen EA, Thakral M, Previero A, Close KC, Christoforou CP, Cai D, Turner GC, Clowney EJ. Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body. Curr Biol 2023; 33:2742-2760.e12. [PMID: 37348501 PMCID: PMC10529417 DOI: 10.1016/j.cub.2023.05.064] [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: 02/05/2023] [Revised: 05/02/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.
Collapse
Affiliation(s)
- Maria Ahmed
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adithya E Rajagopalan
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yijie Pan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Donnell L Williams
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik A Pedersen
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Manav Thakral
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Angelica Previero
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kari C Close
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | | | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA; Biophysics LS&A, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA
| | - Glenn C Turner
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
6
|
Palmateer CM, Artikis C, Brovero SG, Friedman B, Gresham A, Arbeitman MN. Single-cell transcriptome profiles of Drosophila fruitless-expressing neurons from both sexes. eLife 2023; 12:e78511. [PMID: 36724009 PMCID: PMC9891730 DOI: 10.7554/elife.78511] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 01/08/2023] [Indexed: 02/02/2023] Open
Abstract
Drosophila melanogaster reproductive behaviors are orchestrated by fruitless neurons. We performed single-cell RNA-sequencing on pupal neurons that produce sex-specifically spliced fru transcripts, the fru P1-expressing neurons. Uniform Manifold Approximation and Projection (UMAP) with clustering generates an atlas containing 113 clusters. While the male and female neurons overlap in UMAP space, more than half the clusters have sex differences in neuron number, and nearly all clusters display sex-differential expression. Based on an examination of enriched marker genes, we annotate clusters as circadian clock neurons, mushroom body Kenyon cell neurons, neurotransmitter- and/or neuropeptide-producing, and those that express doublesex. Marker gene analyses also show that genes that encode members of the immunoglobulin superfamily of cell adhesion molecules, transcription factors, neuropeptides, neuropeptide receptors, and Wnts have unique patterns of enriched expression across the clusters. In vivo spatial gene expression links to the clusters are examined. A functional analysis of fru P1 circadian neurons shows they have dimorphic roles in activity and period length. Given that most clusters are comprised of male and female neurons indicates that the sexes have fru P1 neurons with common gene expression programs. Sex-specific expression is overlaid on this program, to build the potential for vastly different sex-specific behaviors.
Collapse
Affiliation(s)
- Colleen M Palmateer
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Catherina Artikis
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Savannah G Brovero
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Benjamin Friedman
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Alexis Gresham
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Michelle N Arbeitman
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
- Program of Neuroscience, Florida State UniversityTallahasseeUnited States
| |
Collapse
|
7
|
Ahmed M, Rajagopalan AE, Pan Y, Li Y, Williams DL, Pedersen EA, Thakral M, Previero A, Close KC, Christoforou CP, Cai D, Turner GC, Clowney EJ. Hacking brain development to test models of sensory coding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525425. [PMID: 36747712 PMCID: PMC9900841 DOI: 10.1101/2023.01.25.525425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations-computations--that it makes, and what good these computations are for survival. A cardinal method in biology-and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the Drosophila melanogaster mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.
Collapse
Affiliation(s)
- Maria Ahmed
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adithya E. Rajagopalan
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yijie Pan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Donnell L. Williams
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik A. Pedersen
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Manav Thakral
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Angelica Previero
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kari C. Close
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | | | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA
- Biophysics LS&A, University of Michigan, Ann Arbor, MI 48109, United States
- Michigan Neuroscience Institute Affiliate
| | - Glenn C. Turner
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute Affiliate
| |
Collapse
|
8
|
Nanni AV, Martinez N, Graze R, Morse A, Newman JRB, Jain V, Vlaho S, Signor S, Nuzhdin SV, Renne R, McIntyre LM. Sex-biased expression is associated with chromatin state in D. melanogaster and D. simulans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523946. [PMID: 36711631 PMCID: PMC9882225 DOI: 10.1101/2023.01.13.523946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We propose a new model for the association of chromatin state and sex-bias in expression. We hypothesize enrichment of open chromatin in the sex where we see expression bias (OS) and closed chromatin in the opposite sex (CO). In this study of D. melanogaster and D. simulans head tissue, sex-bias in expression is associated with H3K4me3 (open mark) in males for male-biased genes and in females for female-biased genes in both species. Sex-bias in expression is also largely conserved in direction and magnitude between the two species on the X and autosomes. In male-biased orthologs, the sex-bias ratio is more divergent between species if both species have H3K27me2me3 marks in females compared to when either or neither species has H3K27me2me3 in females. H3K27me2me3 marks in females are associated with male-bias in expression on the autosomes in both species, but on the X only in D. melanogaster . In female-biased orthologs the relationship between the species for the sex-bias ratio is similar regardless of the H3K27me2me3 marks in males. Female-biased orthologs are more similar in the ratio of sex-bias than male-biased orthologs and there is an excess of male-bias in expression in orthologs that gain/lose sex-bias. There is an excess of male-bias in sex-limited expression in both species suggesting excess male-bias is due to rapid evolution between the species. The X chromosome has an enrichment in male-limited H3K4me3 in both species and an enrichment of sex-bias in expression compared to the autosomes.
Collapse
Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Natalie Martinez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Rita Graze
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Alison Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremy R B Newman
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Srna Vlaho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| |
Collapse
|
9
|
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: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [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.
Collapse
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
| |
Collapse
|
10
|
Gegenhuber B, Wu MV, Bronstein R, Tollkuhn J. Gene regulation by gonadal hormone receptors underlies brain sex differences. Nature 2022; 606:153-159. [PMID: 35508660 PMCID: PMC9159952 DOI: 10.1038/s41586-022-04686-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023]
Abstract
Oestradiol establishes neural sex differences in many vertebrates1-3 and modulates mood, behaviour and energy balance in adulthood4-8. In the canonical pathway, oestradiol exerts its effects through the transcription factor oestrogen receptor-α (ERα)9. Although ERα has been extensively characterized in breast cancer, the neuronal targets of ERα, and their involvement in brain sex differences, remain largely unknown. Here we generate a comprehensive map of genomic ERα-binding sites in a sexually dimorphic neural circuit that mediates social behaviours. We conclude that ERα orchestrates sexual differentiation of the mouse brain through two mechanisms: establishing two male-biased neuron types and activating a sustained male-biased gene expression program. Collectively, our findings reveal that sex differences in gene expression are defined by hormonal activation of neuronal steroid receptors. The molecular targets we identify may underlie the effects of oestradiol on brain development, behaviour and disease.
Collapse
Affiliation(s)
- B Gegenhuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring Harbor, NY, USA
| | - M V Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - R Bronstein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - J Tollkuhn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| |
Collapse
|
11
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
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
| |
Collapse
|
12
|
Sato K, Yamamoto D. Mutually exclusive expression of sex-specific and non-sex-specific fruitless gene products in the Drosophila central nervous system. Gene Expr Patterns 2022; 43:119232. [DOI: 10.1016/j.gep.2022.119232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 11/04/2022]
|
13
|
Lin D, Guo Y, Chen X, Yang H, Li Q, Liu Q, Luo F, Meng K, Yang S, Cheng X, Ma W, Chen X, Wang M, Zhao Y. Identification and expression pattern of the sex determination gene fruitless-like in Cherax quadricarinatus. Comp Biochem Physiol B Biochem Mol Biol 2021; 259:110704. [PMID: 34920111 DOI: 10.1016/j.cbpb.2021.110704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/24/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
The fruitless (fru) gene has an important function in the courtship behavior and sex determination pathway of Drosophila melanogaster; however, the fru gene has never been reported in shrimps. In this study, the fruitless-like gene was identified in Cherax quadricarinatus (Cqfru) and is reported here for the first time. A sequence analysis revealed a conserved BTB domain in Cqfru which is the same as fru in D. melanogaster. An analysis of the expression level of Cqfru showed that it was highly expressed in the gastrula stage during embryonic development. Furthermore, in situ hybridization and expression distribution in tissues showed that its sexually dimorphic expression may be focused on the hepatopancreas, brains, and gonads. The gonads, brains, and hepatopancreas of males had a higher expression level of Cqfru than those of females; however, the expression level of the abdominal ganglion was found to be higher in females than in males in this study. The results of an RNA interference treatment showed that a knockdown of Cqfru reduced the expression of the insulin-like androgenic gland hormone (IAG) and tumor necrosis factor (TNF). The characteristic fru gene in shrimps is reported here for the first time, with the results providing basic information for research into the sex-determination mechanism in C. quadricarinatus.
Collapse
Affiliation(s)
- Dawei Lin
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Yongjun Guo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Huizan Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Fuli Luo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Kui Meng
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Songting Yang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Xinquan Cheng
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Wenming Ma
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, People's Republic of China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Moran Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China.
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China.
| |
Collapse
|
14
|
Goodwin SF, Hobert O. Molecular Mechanisms of Sexually Dimorphic Nervous System Patterning in Flies and Worms. Annu Rev Cell Dev Biol 2021; 37:519-547. [PMID: 34613817 DOI: 10.1146/annurev-cellbio-120319-115237] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Male and female brains display anatomical and functional differences. Such differences are observed in species across the animal kingdom, including humans, but have been particularly well-studied in two classic animal model systems, the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Here we summarize recent advances in understanding how the worm and fly brain acquire sexually dimorphic features during development. We highlight the advantages of each system, illustrating how the precise anatomical delineation of sexual dimorphisms in worms has enabled recent analysis into how these dimorphisms become specified during development, and how focusing on sexually dimorphic neurons in the fly has enabled an increasingly detailed understanding of sex-specific behaviors.
Collapse
Affiliation(s)
- Stephen F Goodwin
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford OX1 3SR, United Kingdom;
| | - Oliver Hobert
- Department of Biological Sciences and Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA;
| |
Collapse
|
15
|
Glastad KM, Ju L, Berger SL. Tramtrack acts during late pupal development to direct ant caste identity. PLoS Genet 2021; 17:e1009801. [PMID: 34550980 PMCID: PMC8489709 DOI: 10.1371/journal.pgen.1009801] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/04/2021] [Accepted: 09/01/2021] [Indexed: 11/17/2022] Open
Abstract
A key question in the rising field of neuroepigenetics is how behavioral plasticity is established and maintained in the developing CNS of multicellular organisms. Behavior is controlled through systemic changes in hormonal signaling, cell-specific regulation of gene expression, and changes in neuronal connections in the nervous system, however the link between these pathways is unclear. In the ant Camponotus floridanus, the epigenetic corepressor CoREST is a central player in experimentally-induced reprogramming of caste-specific behavior, from soldier (Major worker) to forager (Minor worker). Here, we show this pathway is engaged naturally on a large genomic scale during late pupal development targeting multiple genes differentially expressed between castes, and central to this mechanism is the protein tramtrack (ttk), a DNA binding partner of CoREST. Caste-specific differences in DNA binding of ttk co-binding with CoREST correlate with caste-biased gene expression both in the late pupal stage and immediately after eclosion. However, we find a unique set of exclusive Minor-bound genes that show ttk pre-binding in the late pupal stage preceding CoREST binding, followed by caste-specific gene repression on the first day of eclosion. In addition, we show that ttk binding correlates with neurogenic Notch signaling, and that specific ttk binding between castes is enriched for regulatory sites associated with hormonal function. Overall our findings elucidate a pathway of transcription factor binding leading to a repressive epigenetic axis that lies at the crux of development and hormonal signaling to define worker caste identity in C. floridanus.
Collapse
Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania United States of America.,Epigenetics Institute; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania United States of America
| | - Linyang Ju
- Epigenetics Institute; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania United States of America.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania United States of America
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania United States of America.,Epigenetics Institute; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania United States of America.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania United States of America
| |
Collapse
|