1
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Bing X, Ke W, Fujioka M, Kurbidaeva A, Levitt S, Levine M, Schedl P, Jaynes JB. Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. eLife 2024; 13:RP94070. [PMID: 39110499 PMCID: PMC11305675 DOI: 10.7554/elife.94070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Two different models have been proposed to explain how the endpoints of chromatin looped domains ('TADs') in eukaryotic chromosomes are determined. In the first, a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop. In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of MicroC to analyze how TADs are organized, and experimental manipulations of the even skipped TAD boundary, homie, to test the predictions of the 'loop-extrusion' and the 'boundary-pairing' models. Our findings are incompatible with the loop-extrusion model, and instead suggest that the endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their partners, either head-to-head or head-to-tail, with varying degrees of specificity. Although our experiments do not address how partners find each other, the mechanism is unlikely to require loop extrusion.
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Affiliation(s)
- Xinyang Bing
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Amina Kurbidaeva
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Sarah Levitt
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Mike Levine
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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2
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Ke W, Fujioka M, Schedl P, Jaynes JB. Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties. eLife 2024; 13:RP94114. [PMID: 39110491 PMCID: PMC11305674 DOI: 10.7554/elife.94114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT orientation), and homie forward (same orientation as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: in MicroC experiments, the eve TAD is a 'volcano' triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the 'new' eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve triangle peak is converted to a pair of 'clouds' of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.
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Affiliation(s)
- Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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3
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Vidaurre V, Song A, Li T, Ku WL, Zhao K, Qian J, Chen X. The Drosophila histone methyltransferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation. Development 2024; 151:dev202729. [PMID: 39007366 DOI: 10.1242/dev.202729] [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: 01/25/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Many tissue-specific adult stem cell lineages maintain a balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase Set1 regulates early-stage male germ cells in Drosophila. Early-stage germline-specific knockdown of Set1 results in temporally progressive defects, arising as germ cell loss and developing into overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage non-cell-autonomously. Additionally, wild-type Set1, but not the catalytically inactive Set1, rescues the Set1 knockdown phenotypes, highlighting the functional importance of the methyltransferase activity of Set1. Further, RNA-sequencing experiments reveal key signaling pathway components, such as the JAK-STAT pathway gene Stat92E and the BMP pathway gene Mad, which are upregulated upon Set1 knockdown. Genetic interaction assays support the functional relationships between Set1 and JAK-STAT or BMP pathways, as both Stat92E and Mad mutations suppress the Set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The phenotype of germ cell loss followed by over-proliferation when inhibiting a histone methyltransferase also raises concerns about using their inhibitors in cancer therapy.
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Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Annabelle Song
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taibo Li
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Wai Lim Ku
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20814, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20814, USA
| | - Jiang Qian
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
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4
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Marsh JI, Johri P. Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection. Mol Biol Evol 2024; 41:msae118. [PMID: 38874402 PMCID: PMC11245712 DOI: 10.1093/molbev/msae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.
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Affiliation(s)
- Jacob I Marsh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
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Kim BY, Gellert HR, Church SH, Suvorov A, Anderson SS, Barmina O, Beskid SG, Comeault AA, Crown KN, Diamond SE, Dorus S, Fujichika T, Hemker JA, Hrcek J, Kankare M, Katoh T, Magnacca KN, Martin RA, Matsunaga T, Medeiros MJ, Miller DE, Pitnick S, Schiffer M, Simoni S, Steenwinkel TE, Syed ZA, Takahashi A, Wei KHC, Yokoyama T, Eisen MB, Kopp A, Matute D, Obbard DJ, O’Grady PM, Price DK, Toda MJ, Werner T, Petrov DA. Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS Biol 2024; 22:e3002697. [PMID: 39024225 PMCID: PMC11257246 DOI: 10.1371/journal.pbio.3002697] [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: 11/06/2023] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
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Affiliation(s)
- Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Hannah R. Gellert
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Samuel H. Church
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut United States of America
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Sean S. Anderson
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Sofia G. Beskid
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Aaron A. Comeault
- School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom
| | - K. Nicole Crown
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sarah E. Diamond
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Takako Fujichika
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - James A. Hemker
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Jan Hrcek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Toru Katoh
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan
| | - Karl N. Magnacca
- Hawaii Invertebrate Program, Division of Forestry & Wildlife, Honolulu, Hawaii, United States of America
| | - Ryan A. Martin
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Teruyuki Matsunaga
- Department of Complexity Science and Engineering, The University of Tokyo, Tokyo, Japan
| | - Matthew J. Medeiros
- Pacific Biosciences Research Center, University of Hawaiʻi, Mānoa, Hawaii, United States of America
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Michele Schiffer
- Daintree Rainforest Observatory, James Cook University, Townsville, Australia
| | - Sara Simoni
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Zeeshan A. Syed
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Kevin H-C. Wei
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Tsuya Yokoyama
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Michael B. Eisen
- Department of Cell and Molecular Biology, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Daniel Matute
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Darren J. Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick M. O’Grady
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
| | - Donald K. Price
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | | | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
- CZ Biohub, Investigator, San Francisco, California, United States of America
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6
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Long T, Mohapatra P, Ballou S, Menuz K. Odorant receptor co-receptors affect expression of tuning receptors in Drosophila. Front Cell Neurosci 2024; 18:1390557. [PMID: 38832356 PMCID: PMC11145718 DOI: 10.3389/fncel.2024.1390557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/01/2024] [Indexed: 06/05/2024] Open
Abstract
Insects detect odorants using two large families of heteromeric receptors, the Odorant Receptors (ORs) and Ionotropic Receptors (IRs). Most OR and IR genes encode odorant-binding "tuning" subunits, whereas four (Orco, Ir8a, Ir25a, and Ir76b) encode co-receptor subunits required for receptor function. Olfactory neurons are thought to degenerate in the absence of Orco in ants and bees, and limited data suggest this may happen to some olfactory neurons in Drosophila fruit flies as well. Here, we thoroughly examined the role of co-receptors on olfactory neuron survival in Drosophila. Leveraging knowledge that olfactory neuron classes are defined by the expression of different tuning receptors, we used tuning receptor expression in antennal transcriptomes as a proxy for the survival of distinct olfactory neuron classes. Consistent with olfactory neuron degeneration, expression of many OR-family tuning receptors is decreased in Orco mutants relative to controls, and transcript loss is progressive with age. The effects of Orco are highly receptor-dependent, with expression of some receptor transcripts nearly eliminated and others unaffected. Surprisingly, further studies revealed that olfactory neuron classes with reduced tuning receptor expression generally survive in Orco mutant flies. Furthermore, there is little apoptosis or neuronal loss in the antenna of these flies. We went on to investigate the effects of IR family co-receptor mutants using similar approaches and found that expression of IR tuning receptors is decreased in the absence of Ir8a and Ir25a, but not Ir76b. As in Orco mutants, Ir8a-dependent olfactory neurons mostly endure despite near-absent expression of associated tuning receptors. Finally, we used differential expression analysis to identify other antennal genes whose expression is changed in IR and OR co-receptor mutants. Taken together, our data indicate that odorant co-receptors are necessary for maintaining expression of many tuning receptors at the mRNA level. Further, most Drosophila olfactory neurons persist in OR and IR co-receptor mutants, suggesting that the impact of co-receptors on neuronal survival may vary across insect species.
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Affiliation(s)
- Teng Long
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Pratyajit Mohapatra
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Sydney Ballou
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Karen Menuz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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7
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565184. [PMID: 38076814 PMCID: PMC10705541 DOI: 10.1101/2023.11.01.565184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2023]
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 Health, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Savannah Muron
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jillian G Gomez
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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8
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Baril T, Galbraith J, Hayward A. Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline. Mol Biol Evol 2024; 41:msae068. [PMID: 38577785 PMCID: PMC11003543 DOI: 10.1093/molbev/msae068] [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: 11/24/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.
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Affiliation(s)
- Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - James Galbraith
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
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9
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Mishra P, Rundle HD, Agrawal AF. The evolution of sexual dimorphism in gene expression in response to a manipulation of mate competition. Evolution 2024; 78:746-757. [PMID: 38270064 DOI: 10.1093/evolut/qpae004] [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: 08/16/2023] [Revised: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
Many genes are differentially expressed between males and females and patterns of sex-biased gene expression (SBGE) vary among species. Some of this variation is thought to have evolved in response to differences in mate competition among species that cause varying patterns of sex-specific selection. We used experimental evolution to test this by quantifying SBGE and sex-specific splicing in 15 Drosophila melanogaster populations that evolved for 104 generations in mating treatments that removed mate competition via enforced monogamy, or allowed mate competition in either small, simple, or larger, structurally more complex mating environments. Consistent with sex-specific selection affecting SBGE, initially sex-biased genes diverged in expression more among treatments than unbiased genes, and there was greater expression divergence for male- than female-biased genes. It has been suggested the transcriptome should be "feminized" under monogamy because of the removal of sexual selection on males; we did not observe this, likely because selection differs in additional ways between monogamy vs. polygamy. Significant divergence in average expression dimorphism between treatments was observed and, in some treatment comparisons, the direction of the divergence differed across different sex-bias categories. There was not a generalized reduction in expression dimorphism under enforced monogamy.
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Affiliation(s)
- Prashastha Mishra
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Howard D Rundle
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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10
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Robben M, Ramesh B, Pau S, Meletis D, Luber J, Demuth J. scRNA-seq Reveals Novel Genetic Pathways and Sex Chromosome Regulation in Tribolium Spermatogenesis. Genome Biol Evol 2024; 16:evae059. [PMID: 38513111 PMCID: PMC10980526 DOI: 10.1093/gbe/evae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High-throughput single-cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded in nonmodel systems by a lack of known genes that can reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species like Drosophila melanogaster. Using single-cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component clustering, and SNP-based haploid/diploid phasing. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. Our results indicate that molecular pathways underlying spermatogenesis in Coleoptera are substantially diverged from those in Diptera. We also show that most genes on the X chromosome experience meiotic sex chromosome inactivation. Temporal expression of Drosophila MSL complex homologs coupled with spatial analysis of potential chromatin entry sites further suggests that the dosage compensation machinery may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.
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Affiliation(s)
- Michael Robben
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Balan Ramesh
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Shana Pau
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Demetra Meletis
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jacob Luber
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Jeffery Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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11
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Lafuente E, Duneau D, Beldade P. Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation. Mol Ecol 2024; 33:e17294. [PMID: 38366327 DOI: 10.1111/mec.17294] [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: 09/13/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.
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Affiliation(s)
- E Lafuente
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - D Duneau
- UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - P Beldade
- cE3c (Center for Ecology, Evolution and Environmental Changes) & CHANGE (Global Change and Sustainability Institute), FCUL, Lisboa, Portugal
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12
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Vidaurre V, Song A, Li T, Ku WL, Zhao K, Qian J, Chen X. The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580277. [PMID: 38405894 PMCID: PMC10888844 DOI: 10.1101/2024.02.14.580277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Many cell types come from tissue-specific adult stem cells that maintain the balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase, Set1, regulates early-stage male germ cell proliferation and differentiation in Drosophila. Early-stage germline-specific knockdown of set1 results in a temporally progressed defects, arising as germ cell loss and developing to overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage in a non-cell-autonomous manner. Additionally, wild-type Set1, but not the catalytically inactive Set1, could rescue the set1 knockdown phenotypes, highlighting the functional importance of the methyl-transferase activity of the Set1 enzyme. Further, RNA-seq experiments reveal key signaling pathway components, such as the JAK-STAT pathway gene stat92E and the BMP pathway gene mad, that are upregulated upon set1 knockdown. Genetic interaction assays support the functional relationships between set1 and JAK-STAT or BMP pathways, as mutations of both the stat92E and mad genes suppress the set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The germ cell loss followed by over-proliferation phenotypes when inhibiting a histone methyl-transferase raise concerns about using their inhibitors in cancer therapy.
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Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Annabelle Song
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Taibo Li
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wai Lim Ku
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, United States of America
| | - Jiang Qian
- Department of Ophthalmology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Xin Chen
- Howard Hughes Medical Institute, Baltimore, Maryland, United States of America
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, United States of America
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13
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Wheeler DW, Kopsick JD, Sutton N, Tecuatl C, Komendantov AO, Nadella K, Ascoli GA. Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. eLife 2024; 12:RP90597. [PMID: 38345923 PMCID: PMC10942544 DOI: 10.7554/elife.90597] [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] [Indexed: 02/15/2024] Open
Abstract
Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Previously, Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression (Wheeler et al., 2015). Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
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Affiliation(s)
- Diek W Wheeler
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Jeffrey D Kopsick
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason UniversityFairfaxUnited States
| | - Nate Sutton
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Carolina Tecuatl
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Alexander O Komendantov
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Kasturi Nadella
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason UniversityFairfaxUnited States
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14
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Blum JA, Wells M, Huxley-Reicher Z, Johnson JE, Bateman JR. Transvection between nonallelic genomic positions in Drosophila. G3 (BETHESDA, MD.) 2024; 14:jkad255. [PMID: 37949840 PMCID: PMC10849331 DOI: 10.1093/g3journal/jkad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
In Drosophila, pairing of maternal and paternal homologous chromosomes can permit trans-interactions between enhancers on one homolog and promoters on another, an example of transvection. Although trans-interactions have been observed at many loci in the Drosophila genome and in other organisms, the parameters that govern enhancer action in trans remain poorly understood. Using a transgenic reporter system, we asked whether enhancers and promoters at nonallelic, but nearby, genomic positions can communication in trans. Using one transgenic insertion carrying the synthetic enhancer GMR and another nearby insertion carrying the hsp70 promoter driving a fluorescent reporter, we show that transgenes separated by 2.6 kb of linear distance can support enhancer action in trans at the 53F8 locus. Furthermore, transvection between the nonallelic insertions can be augmented by a small deletion flanking one insert, likely via changes to the paired configuration of the homologs. Subsequent analyses of other insertions in 53F8 that carry different transgenic sequences demonstrate that the capacity to support transvection between nonallelic sites varies greatly, suggesting that factors beyond the linear distance between insertion sites play an important role. Finally, analysis of transvection between nearby nonallelic sites at other genomic locations shows evidence of position effects, where one locus supported GMR action in trans over a linear distance of over 10 kb, whereas another locus showed no evidence of transvection over a span <200 bp. Overall, our data demonstrate that transvection between nonallelic sites represents a complex interplay between genomic context, interallelic distance, and promoter identity.
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Affiliation(s)
- Jacob A Blum
- Biology Department, 2 Polar Loop, Bowdoin College, Brunswick, ME 04011, USA
| | - Michelle Wells
- Biology Department, 2 Polar Loop, Bowdoin College, Brunswick, ME 04011, USA
| | | | - Justine E Johnson
- Biology Department, 2 Polar Loop, Bowdoin College, Brunswick, ME 04011, USA
| | - Jack R Bateman
- Biology Department, 2 Polar Loop, Bowdoin College, Brunswick, ME 04011, USA
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15
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Hu W, Li M, Xiao H, Guan L. Essential genes identification model based on sequence feature map and graph convolutional neural network. BMC Genomics 2024; 25:47. [PMID: 38200437 PMCID: PMC10777564 DOI: 10.1186/s12864-024-09958-w] [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: 06/18/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Essential genes encode functions that play a vital role in the life activities of organisms, encompassing growth, development, immune system functioning, and cell structure maintenance. Conventional experimental techniques for identifying essential genes are resource-intensive and time-consuming, and the accuracy of current machine learning models needs further enhancement. Therefore, it is crucial to develop a robust computational model to accurately predict essential genes. RESULTS In this study, we introduce GCNN-SFM, a computational model for identifying essential genes in organisms, based on graph convolutional neural networks (GCNN). GCNN-SFM integrates a graph convolutional layer, a convolutional layer, and a fully connected layer to model and extract features from gene sequences of essential genes. Initially, the gene sequence is transformed into a feature map using coding techniques. Subsequently, a multi-layer GCN is employed to perform graph convolution operations, effectively capturing both local and global features of the gene sequence. Further feature extraction is performed, followed by integrating convolution and fully-connected layers to generate prediction results for essential genes. The gradient descent algorithm is utilized to iteratively update the cross-entropy loss function, thereby enhancing the accuracy of the prediction results. Meanwhile, model parameters are tuned to determine the optimal parameter combination that yields the best prediction performance during training. CONCLUSIONS Experimental evaluation demonstrates that GCNN-SFM surpasses various advanced essential gene prediction models and achieves an average accuracy of 94.53%. This study presents a novel and effective approach for identifying essential genes, which has significant implications for biology and genomics research.
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Affiliation(s)
- Wenxing Hu
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Mengshan Li
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China.
| | - Haiyang Xiao
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Lixin Guan
- College of Physics and Electronic Information, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
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16
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Fischer MD, Graham P, Pick L. The ftz upstream element drives late ftz stripes but is not required for regulation of Ftz target genes. Dev Biol 2024; 505:141-147. [PMID: 37977522 PMCID: PMC10843599 DOI: 10.1016/j.ydbio.2023.11.004] [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: 10/10/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
The regulation of gene expression in precise, rapidly changing spatial patterns is essential for embryonic development. Multiple enhancers have been identified for the evolving expression patterns of the cascade of Drosophila segmentation genes that establish the basic body plan of the fly. Classic reporter transgene experiments identified multiple cis-regulatory elements (CREs) that are sufficient to direct various aspects of the evolving expression pattern of the pair-rule gene fushi tarazu (ftz). These include enhancers that coordinately activate expression in all seven stripes and stripe-specific elements that activate expression in one or more ftz stripes. Of the two 7-stripe enhancers, analysis of reporter transgenes demonstrated that the upstream element (UPS) is autoregulatory, requiring direct binding of Ftz protein to direct striped expression. Here, we asked about the endogenous role of the UPS by precisely deleting this 7-stripe enhancer. In ftzΔUPS7S homozygotes, ftz stripes appear in the same order as wildtype, and all but stripe 4 are expressed at wildtype levels by the end of the cellular blastoderm stage. This suggests that the zebra element and UPS harbor information to direct stripe 4 expression, although previous deletion analyses failed to identify a stripe-specific CRE within these two 7-stripe enhancers. However, the UPS is necessary for late ftz stripe expression, with all 7 stripes decaying earlier than wildtype in ftzΔUPS7S homozygotes. Despite this premature loss of ftz expression, downstream target gene regulation proceeds as in wildtype, and segmentation is unperturbed in the overwhelming majority of animals. We propose that this late-acting enhancer provides a buffer against perturbations in gene expression but is not required for establishment of Ftz cell fates. Overall, our results demonstrate that multiple enhancers, each directing distinct aspects of an overall gene expression pattern, contribute to fine-tuning the complex patterns necessary for embryonic development.
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Affiliation(s)
- Matthew D Fischer
- Department of Pathology and Laboratory Medicine, 3501 Civic Center Boulevard, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Patricia Graham
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD, 20742, USA
| | - Leslie Pick
- Department of Entomology, 4291 Fieldhouse Drive, University of Maryland, College Park, MD, 20742, USA.
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17
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Hopkins BR, Angus-Henry A, Kim BY, Carlisle JA, Thompson A, Kopp A. Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547128. [PMID: 37425821 PMCID: PMC10327216 DOI: 10.1101/2023.06.29.547128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accelerating availability of high-quality genomes now allows us to test how these proteins are evolving at fine taxonomic scales. Here, we use genomes from 264 species to chart the evolutionary history of Sex Peptide (SP), a potent regulator of female post-mating responses in Drosophila melanogaster. We infer that SP first evolved in the Drosophilinae subfamily and has followed markedly different evolutionary trajectories in different lineages. Outside of the Sophophora-Lordiphosa, SP exists largely as a single-copy gene with independent losses in several lineages. Within the Sophophora-Lordiphosa, the SP gene family has repeatedly and independently expanded. Up to seven copies, collectively displaying extensive sequence variation, are present in some species. Despite these changes, SP expression remains restricted to the male reproductive tract. Alongside, we document considerable interspecific variation in the presence and morphology of seminal microcarriers that, despite the critical role SP plays in microcarrier assembly in D. melanogaster, appear to be independent of changes in the presence/absence or sequence of SP. We end by providing evidence that SP's evolution is decoupled from that of its receptor, SPR, in which we detect no evidence of correlated diversifying selection. Collectively, our work describes the divergent evolutionary trajectories that a novel gene has taken following its origin and finds a surprisingly weak coevolutionary signal between a supposedly sexually antagonistic protein and its receptor.
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Affiliation(s)
- Ben R. Hopkins
- Department of Evolution and Ecology, University of California – Davis, CA, USA
| | - Aidan Angus-Henry
- Department of Evolution and Ecology, University of California – Davis, CA, USA
| | | | - Jolie A. Carlisle
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California – Davis, CA, USA
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California – Davis, CA, USA
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18
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Clifton BD, Hariyani I, Kimura A, Luo F, Nguyen A, Ranz JM. Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages. Commun Biol 2023; 6:1069. [PMID: 37864070 PMCID: PMC10589255 DOI: 10.1038/s42003-023-05427-4] [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: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023] Open
Abstract
How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
| | - Imtiyaz Hariyani
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Fangning Luo
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Alvin Nguyen
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
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19
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Wierzbicki F, Kofler R. The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model. BMC Biol 2023; 21:224. [PMID: 37858221 PMCID: PMC10588112 DOI: 10.1186/s12915-023-01727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e., the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model. RESULTS Here, we test the trap model from a population genetics perspective. Our simulations show that the composition of regions that act as transposon traps (i.e., potentially piRNA clusters) ought to deviate from regions that have no effect on TE activity. We investigated TEs in five Drosophila melanogaster strains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, the distribution of the number of TE insertions in piRNA clusters is also much broader than expected. CONCLUSIONS We found that the observed composition of piRNA clusters is not in agreement with expectations under the simple trap model. Dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may account for these deviations.
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Affiliation(s)
- Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.
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20
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Oliveira DS, Fablet M, Larue A, Vallier A, Carareto CA, Rebollo R, Vieira C. ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements. Nucleic Acids Res 2023; 51:9764-9784. [PMID: 37615575 PMCID: PMC10570057 DOI: 10.1093/nar/gkad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.
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Affiliation(s)
- Daniel S Oliveira
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Institut Universitaire de France (IUF), Paris, Île-de-FranceF-75231, France
| | - Anaïs Larue
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Claudia M A Carareto
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
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21
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Kim BY, Gellert HR, Church SH, Suvorov A, Anderson SS, Barmina O, Beskid SG, Comeault AA, Crown KN, Diamond SE, Dorus S, Fujichika T, Hemker JA, Hrcek J, Kankare M, Katoh T, Magnacca KN, Martin RA, Matsunaga T, Medeiros MJ, Miller DE, Pitnick S, Simoni S, Steenwinkel TE, Schiffer M, Syed ZA, Takahashi A, Wei KHC, Yokoyama T, Eisen MB, Kopp A, Matute D, Obbard DJ, O'Grady PM, Price DK, Toda MJ, Werner T, Petrov DA. Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560517. [PMID: 37873137 PMCID: PMC10592941 DOI: 10.1101/2023.10.02.560517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
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Affiliation(s)
| | | | - Samuel H Church
- Department of Ecology and Evolutionary Biology, Yale University, USA
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, USA
| | - Sean S Anderson
- Department of Biology, University of North Carolina Chapel Hill, USA
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis, USA
| | | | - Aaron A Comeault
- School of Environmental and Natural Sciences, Bangor University, UK
| | - K Nicole Crown
- Department of Biology, Case Western Reserve University, USA
| | | | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, USA
| | - Takako Fujichika
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - James A Hemker
- Department of Developmental Biology, Stanford University, USA
| | - Jan Hrcek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Czechia
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Toru Katoh
- Department of Biological Sciences, Hokkaido University, Japan
| | - Karl N Magnacca
- Hawaii Invertebrate Program, Division of Forestry & Wildlife, State of Hawaii, USA
| | - Ryan A Martin
- Department of Biology, Case Western Reserve University, USA
| | - Teruyuki Matsunaga
- Department of Complexity Science and Engineering, The University of Tokyo, Japan
| | | | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics; Department of Laboratory Medicine and Pathology, University of Washington, USA
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, USA
| | - Sara Simoni
- Department of Biology, Stanford University, USA
| | | | - Michele Schiffer
- Daintree Rainforest Observatory, James Cook University, Australia
| | - Zeeshan A Syed
- Center for Reproductive Evolution, Department of Biology, Syracuse University, USA
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Kevin H-C Wei
- Department of Zoology, The University of British Columbia
| | | | - Michael B Eisen
- Department of Cell and Molecular Biology, University of California Berkeley, United States
- Howard Hughes Medical Institute,University of California Berkeley, United States
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, USA
| | - Daniel Matute
- Department of Biology, University of North Carolina Chapel Hill, USA
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, UK
| | | | - Donald K Price
- School of Life Sciences, University of Nevada Las Vegas, USA
| | | | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, USA
- CZ Biohub, Investigator
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22
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Garcia-Vaquero ML, Heim M, Flix B, Pereira M, Palin L, Marques TM, Pinto FR, de Las Rivas J, Voigt A, Besse F, Gama-Carvalho M. Analysis of asymptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration. BMC Genomics 2023; 24:576. [PMID: 37759179 PMCID: PMC10523761 DOI: 10.1186/s12864-023-09562-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Spinal Muscular Atrophy (SMA) and Amyotrophic Lateral Sclerosis (ALS) share phenotypic and molecular commonalities, including the fact that they can be caused by mutations in ubiquitous proteins involved in RNA metabolism, namely SMN, TDP-43 and FUS. Although this suggests the existence of common disease mechanisms, there is currently no model to explain the resulting motor neuron dysfunction. In this work we generated a parallel set of Drosophila models for adult-onset RNAi and tagged neuronal expression of the fly orthologues of the three human proteins, named Smn, TBPH and Caz, respectively. We profiled nuclear and cytoplasmic bound mRNAs using a RIP-seq approach and characterized the transcriptome of the RNAi models by RNA-seq. To unravel the mechanisms underlying the common functional impact of these proteins on neuronal cells, we devised a computational approach based on the construction of a tissue-specific library of protein functional modules, selected by an overall impact score measuring the estimated extent of perturbation caused by each gene knockdown. RESULTS Transcriptome analysis revealed that the three proteins do not bind to the same RNA molecules and that only a limited set of functionally unrelated transcripts is commonly affected by their knock-down. However, through our integrative approach we were able to identify a concerted effect on protein functional modules, albeit acting through distinct targets. Most strikingly, functional annotation revealed that these modules are involved in critical cellular pathways for motor neurons, including neuromuscular junction function. Furthermore, selected modules were found to be significantly enriched in orthologues of human neuronal disease genes. CONCLUSIONS The results presented here show that SMA and ALS disease-associated genes linked to RNA metabolism functionally converge on neuronal protein complexes, providing a new hypothesis to explain the common motor neuron phenotype. The functional modules identified represent promising biomarkers and therapeutic targets, namely given their alteration in asymptomatic settings.
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Affiliation(s)
- Marina L Garcia-Vaquero
- BioISI - Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
- Department of Medicine and Cytometry General Service-15 Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), CIBERONC, 16 37007, Salamanca, Spain
| | - Marjorie Heim
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, 06108, Nice, Inserm, France
| | - Barbara Flix
- Department of Neurology, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Marcelo Pereira
- BioISI - Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Lucile Palin
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, 06108, Nice, Inserm, France
| | - Tânia M Marques
- BioISI - Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Francisco R Pinto
- BioISI - Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Javier de Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), 37007, Salamanca, Spain
| | - Aaron Voigt
- Department of Neurology, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
- JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH RWTH Aachen University, 52074, Aachen, Germany
| | - Florence Besse
- Institut de Biologie Valrose, Université Côte d'Azur, CNRS, 06108, Nice, Inserm, France
| | - Margarida Gama-Carvalho
- BioISI - Institute for Biosystems and Integrative Sciences, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal.
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23
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Langmüller AM, Nolte V, Dolezal M, Schlötterer C. The genomic distribution of transposable elements is driven by spatially variable purifying selection. Nucleic Acids Res 2023; 51:9203-9213. [PMID: 37560917 PMCID: PMC10516647 DOI: 10.1093/nar/gkad635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023] Open
Abstract
It is widely accepted that the genomic distribution of transposable elements (TEs) mainly reflects the outcome of purifying selection and insertion bias (1). Nevertheless, the relative importance of these two evolutionary forces could not be tested thoroughly. Here, we introduce an experimental system, which allows separating purifying selection from TE insertion bias. We used experimental evolution to study the TE insertion patterns in Drosophila simulans founder populations harboring 1040 insertions of an active P-element. After 10 generations at a large population size, we detected strong selection against P-element insertions. The exception were P-element insertions in genomic regions for which a strong insertion bias has been proposed (2-4). Because recurrent P-element insertions cannot explain this pattern, we conclude that purifying selection, with variable strength along the chromosomes, is the major determinant of the genomic distribution of P-elements. Genomic regions with relaxed purifying selection against P-element insertions exhibit normal levels of purifying selection against base substitutions. This suggests that different types of purifying selection operate on base substitutions and P-element insertions. Our results highlight the power of experimental evolution to understand basic evolutionary processes, which are difficult to infer from patterns of natural variation alone.
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Affiliation(s)
- Anna M Langmüller
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
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24
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Rosales-Vega M, Reséndez-Pérez D, Zurita M, Vázquez M. TnaA, a trithorax group protein, modulates wingless expression in different regions of the Drosophila wing imaginal disc. Sci Rep 2023; 13:15162. [PMID: 37704704 PMCID: PMC10499800 DOI: 10.1038/s41598-023-42169-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: 02/09/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
wingless expression is exquisitely regulated by different factors and enhancers in the imaginal wing discs of Drosophila melanogaster in four domains: the dorsal band, the dorso-ventral boundary, and the inner and outer ring domains. tonalli is a trithorax group gene that encodes a putative SUMO E3 ligase that binds to chromatin to regulate the expression of its targets, including the Hox genes. However, its role in modulating gene expression is barely known. Here, we show that TnaA modulates the wingless expression at two domains of the wing disc, the dorso-ventral boundary and the inner ring. At first, tonalli interacts genetically with Notch to form the wing margin. In the inner ring domain, TnaA modulates wingless transcription. When the dosage of TnaA increases in or near the inner ring since early larval stages, this domain expands with a rapid increase in wingless expression. TnaA occupies the wingless Inner Ring Enhancer at the wing disc, meanwhile it does not affect wingless expression directed by the Ventral Disc Enhancer in leg discs, suggesting that TnaA acts as a wingless enhancer-specific factor. We describe for the first time the presence of TnaA at the Inner Ring Enhancer as a specific regulator of wingless in the development of wing boundaries.
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Affiliation(s)
- Marco Rosales-Vega
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Diana Reséndez-Pérez
- Departamento de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, Mexico
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
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25
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Benner L, Muron S, Oliver B. Female germline expression of OVO transcription factor bridges Drosophila generations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554887. [PMID: 37662231 PMCID: PMC10473757 DOI: 10.1101/2023.08.25.554887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
OVO is required for karyotypically female germ cell viability but has no known function in the male germline in Drosophila. ovo is autoregulated by two antagonistic isoforms, OVO-A and OVO-B. All ovo- alleles were created as partial revertants of the antimorphic ovoD1 allele. Creation of new targeted alleles in an ovo+ background indicated that disrupting the germline-specific exon extension of ovo-B leads to an arrested egg chamber phenotype, rather than germ cell death. RNA-seq analysis, including >1K full length cDNAs, indicates that ovo utilizes a number of unannotated splice variations in the extended exon and a minor population of ovo-B transcripts utilizes an alternative splice. This indicates that classical ovo alleles such as ovoD1rv23, are not truly null for ovo, and are likely to be weak antimorphs. To generate bonafide nulls, we deleted the ovo-A and ovo-B promoters showing that only ovo-B is required for female germ cell viability and there is an early and polyphasic developmental requirement for ovo-B in the female germline. To visualize OVO expression and localization, we endogenously tagged ovo and found nuclear OVO in all differentiating female germ cells throughout oogenesis in adults. We also found that OVO is maternally deposited into the embryo, where it showed nuclear localization in newly formed pole cells. Maternal OVO persisted in embryonic germ cells until zygotic OVO expression was detectable, suggesting that there is continuous nuclear OVO expression in the female germline in the transition from one generation to the next.
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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 Health, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Savannah Muron
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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26
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Ibragimov A, Bing XY, Shidlovskii YV, Levine M, Georgiev P, Schedl P. lncRNA read-through regulates the BX-C insulator Fub-1. eLife 2023; 12:e84711. [PMID: 37643473 PMCID: PMC10497285 DOI: 10.7554/elife.84711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Though long non-coding RNAs (lncRNAs) represent a substantial fraction of the Pol II transcripts in multicellular animals, only a few have known functions. Here we report that the blocking activity of the Bithorax complex (BX-C) Fub-1 boundary is segmentally regulated by its own lncRNA. The Fub-1 boundary is located between the Ultrabithorax (Ubx) gene and the bxd/pbx regulatory domain, which is responsible for regulating Ubx expression in parasegment PS6/segment A1. Fub-1 consists of two hypersensitive sites, HS1 and HS2. HS1 is an insulator while HS2 functions primarily as an lncRNA promoter. To activate Ubx expression in PS6/A1, enhancers in the bxd/pbx domain must be able to bypass Fub-1 blocking activity. We show that the expression of the Fub-1 lncRNAs in PS6/A1 from the HS2 promoter inactivates Fub-1 insulating activity. Inactivation is due to read-through as the HS2 promoter must be directed toward HS1 to disrupt blocking.
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Affiliation(s)
- Airat Ibragimov
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of SciencesMoscowRussian Federation
| | - Xin Yang Bing
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Yulii V Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of SciencesMoscowRussian Federation
- Department of Biology and General Genetics, Sechenov UniversityMoscowRussian Federation
| | - Michael Levine
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of SciencesMoscowRussian Federation
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
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27
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Corpuz RL, Bellinger MR, Veillet A, Magnacca KN, Price DK. The Transmission Patterns of the Endosymbiont Wolbachia within the Hawaiian Drosophilidae Adaptive Radiation. Genes (Basel) 2023; 14:1545. [PMID: 37628597 PMCID: PMC10454618 DOI: 10.3390/genes14081545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023] Open
Abstract
The evolution of endosymbionts and their hosts can lead to highly dynamic interactions with varying fitness effects for both the endosymbiont and host species. Wolbachia, a ubiquitous endosymbiont of arthropods and nematodes, can have both beneficial and detrimental effects on host fitness. We documented the occurrence and patterns of transmission of Wolbachia within the Hawaiian Drosophilidae and examined the potential contributions of Wolbachia to the rapid diversification of their hosts. Screens for Wolbachia infections across a minimum of 140 species of Hawaiian Drosophila and Scaptomyza revealed species-level infections of 20.0%, and across all 399 samples, a general infection rate of 10.3%. Among the 44 Wolbachia strains we identified using a modified Wolbachia multi-locus strain typing scheme, 30 (68.18%) belonged to supergroup B, five (11.36%) belonged to supergroup A, and nine (20.45%) had alleles with conflicting supergroup assignments. Co-phylogenetic reconciliation analysis indicated that Wolbachia strain diversity within their endemic Hawaiian Drosophilidae hosts can be explained by vertical (e.g., co-speciation) and horizontal (e.g., host switch) modes of transmission. Results from stochastic character trait mapping suggest that horizontal transmission is associated with the preferred oviposition substrate of the host, but not the host's plant family or island of occurrence. For Hawaiian Drosophilid species of conservation concern, with 13 species listed as endangered and 1 listed as threatened, knowledge of Wolbachia strain types, infection status, and potential for superinfection could assist with conservation breeding programs designed to bolster population sizes, especially when wild populations are supplemented with laboratory-reared, translocated individuals. Future research aimed at improving the understanding of the mechanisms of Wolbachia transmission in nature, their impact on the host, and their role in host species formation may shed light on the influence of Wolbachia as an evolutionary driver, especially in Hawaiian ecosystems.
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Affiliation(s)
- Renée L. Corpuz
- Department of Biology, Tropical Conservation Biology and Environmental Science, University of Hawaii at Hilo, 200 West Kāwili Street, Hilo, HI 96720, USA (D.K.P.)
| | - M. Renee Bellinger
- Department of Biology, Tropical Conservation Biology and Environmental Science, University of Hawaii at Hilo, 200 West Kāwili Street, Hilo, HI 96720, USA (D.K.P.)
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, P.O. Box 44, Hawaii National Park, HI 96718, USA
| | - Anne Veillet
- Department of Biology, Tropical Conservation Biology and Environmental Science, University of Hawaii at Hilo, 200 West Kāwili Street, Hilo, HI 96720, USA (D.K.P.)
| | - Karl N. Magnacca
- Department of Land and Natural Resources, Division of Forestry & Wildlife, Native Ecosystem Protection and Management, Hawaii Invertebrate Program, 1151 Punchbowl Street Rm. 325, Honolulu, HI 96813, USA;
| | - Donald K. Price
- Department of Biology, Tropical Conservation Biology and Environmental Science, University of Hawaii at Hilo, 200 West Kāwili Street, Hilo, HI 96720, USA (D.K.P.)
- School of Life Sciences, University of Nevada, Las Vegas, NV 89557, USA
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28
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Jalloh B, Lancaster CL, Rounds JC, Brown BE, Leung SW, Banerjee A, Morton DJ, Bienkowski RS, Fasken MB, Kremsky IJ, Tegowski M, Meyer K, Corbett A, Moberg K. The Drosophila Nab2 RNA binding protein inhibits m 6A methylation and male-specific splicing of Sex lethal transcript in female neuronal tissue. eLife 2023; 12:e64904. [PMID: 37458420 PMCID: PMC10351920 DOI: 10.7554/elife.64904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
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Affiliation(s)
- Binta Jalloh
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Carly L Lancaster
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory UniversityAtlantaUnited States
| | - J Christopher Rounds
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Brianna E Brown
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
| | - Sara W Leung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ayan Banerjee
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Derrick J Morton
- Department of Biology, Emory UniversityAtlantaUnited States
- Emory Institutional Research and Academic Career Development Award (IRACDA), Fellowships in Research and Science Teaching (FIRST) Postdoctoral FellowshipAtlantaUnited States
| | - Rick S Bienkowski
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Milo B Fasken
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | - Matthew Tegowski
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
| | - Kate Meyer
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Anita Corbett
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ken Moberg
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
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29
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Sun J, Liu WK, Ellsworth C, Sun Q, Pan Y, Huang YC, Deng WM. Integrating lipid metabolism, pheromone production and perception by Fruitless and Hepatocyte Nuclear Factor 4. SCIENCE ADVANCES 2023; 9:eadf6254. [PMID: 37390217 PMCID: PMC10313179 DOI: 10.1126/sciadv.adf6254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/30/2023] [Indexed: 07/02/2023]
Abstract
Sexual attraction and perception are crucial for mating and reproductive success. In Drosophila melanogaster, the male-specific isoform of Fruitless (Fru), FruM, is a known master neuro-regulator of innate courtship behavior to control the perception of sex pheromones in sensory neurons. Here, we show that the non-sex-specific Fru isoform (FruCOM) is necessary for pheromone biosynthesis in hepatocyte-like oenocytes for sexual attraction. Loss of FruCOM in oenocytes resulted in adults with reduced levels of cuticular hydrocarbons (CHCs), including sex pheromones, and show altered sexual attraction and reduced cuticular hydrophobicity. We further identify Hepatocyte nuclear factor 4 (Hnf4) as a key target of FruCOM in directing fatty acid conversion to hydrocarbons. Fru or Hnf4 depletion in oenocytes disrupts lipid homeostasis, resulting in a sex-dimorphic CHC profile that differs from doublesex- and transformer-dependent CHC dimorphism. Thus, Fru couples pheromone perception and production in separate organs to regulate chemosensory communications and ensure efficient mating behavior.
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Affiliation(s)
- Jie Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Wen-Kan Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Calder Ellsworth
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Qian Sun
- Department of Entomology, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yufeng Pan
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Yi-Chun Huang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Wu-Min Deng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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30
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Grešová K, Martinek V, Čechák D, Šimeček P, Alexiou P. Genomic benchmarks: a collection of datasets for genomic sequence classification. BMC Genom Data 2023; 24:25. [PMID: 37127596 PMCID: PMC10150520 DOI: 10.1186/s12863-023-01123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Recently, deep neural networks have been successfully applied in many biological fields. In 2020, a deep learning model AlphaFold won the protein folding competition with predicted structures within the error tolerance of experimental methods. However, this solution to the most prominent bioinformatic challenge of the past 50 years has been possible only thanks to a carefully curated benchmark of experimentally predicted protein structures. In Genomics, we have similar challenges (annotation of genomes and identification of functional elements) but currently, we lack benchmarks similar to protein folding competition. RESULTS Here we present a collection of curated and easily accessible sequence classification datasets in the field of genomics. The proposed collection is based on a combination of novel datasets constructed from the mining of publicly available databases and existing datasets obtained from published articles. The collection currently contains nine datasets that focus on regulatory elements (promoters, enhancers, open chromatin region) from three model organisms: human, mouse, and roundworm. A simple convolution neural network is also included in a repository and can be used as a baseline model. Benchmarks and the baseline model are distributed as the Python package 'genomic-benchmarks', and the code is available at https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks . CONCLUSIONS Deep learning techniques revolutionized many biological fields but mainly thanks to the carefully curated benchmarks. For the field of Genomics, we propose a collection of benchmark datasets for the classification of genomic sequences with an interface for the most commonly used deep learning libraries, implementation of the simple neural network and a training framework that can be used as a starting point for future research. The main aim of this effort is to create a repository for shared datasets that will make machine learning for genomics more comparable and reproducible while reducing the overhead of researchers who want to enter the field, leading to healthy competition and new discoveries.
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Affiliation(s)
- Katarína Grešová
- Centre for Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Vlastimil Martinek
- Centre for Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Čechák
- Centre for Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Petr Šimeček
- Centre for Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia.
| | - Panagiotis Alexiou
- Centre for Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
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Jéssica Paloma ÁR, Juan Rafael RE. Activation of the Cap'n'collar C pathway (Nrf2 pathway in vertebrates) signaling in insulin pathway compromised Drosophila melanogaster flies ameliorates the diabetic state upon pro-oxidant conditions. Gen Comp Endocrinol 2023; 335:114229. [PMID: 36781022 DOI: 10.1016/j.ygcen.2023.114229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
The insulin pathway is a crucial central system for metabolism and growth. The Nrf2 signaling pathway functions to counteract oxidative stress. Here we sought to study the consequences of an oxidative stress challenge to insulin compromised and control adult flies of different ages, varying the activation state of the Nrf2 pathway in flies, the Cap'n'collar C pathway. For this, we employed two different pro-oxidative conditions: 3 % hydrogen peroxide or 20 mM paraquat laced in the food. In both cases, wild type (control) flies die within a few days, yet there are significant differences between males and females, and also within flies of different ages (seven versus thirty days old flies). We repeated the same conditions with young (seven days old) flies that were heterozygous for a loss-of-function mutation in Keap1. There were no significant differences. We then tested two hypomorphic viable conditions of the insulin pathway (heteroallelic combination for the insulin receptor and the S6 Kinase), challenged in the same way: Whereas they also die in the pro-oxidant conditions, they fare significantly better when heterozygous for Keap1, in contrast to controls. We also monitored locomotion in all of these conditions, and, in general, found significant differences between flies without and with a mutant allele (heterozygous) for Keap1. Our results point to altered oxidative stress conditions in diabetic flies. These findings suggest that modest activation of the Cap'n'collar C pathway may be a treatment for diabetic symptoms.
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Affiliation(s)
- Álvarez-Rendón Jéssica Paloma
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Programa de posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Riesgo-Escovar Juan Rafael
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Programa de posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Mexico.
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32
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Li H, Berent E, Hadjipanteli S, Galey M, Muhammad-Lahbabi N, Miller DE, Crown KN. Heterozygous inversion breakpoints suppress meiotic crossovers by altering recombination repair outcomes. PLoS Genet 2023; 19:e1010702. [PMID: 37053290 PMCID: PMC10128924 DOI: 10.1371/journal.pgen.1010702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/25/2023] [Accepted: 03/15/2023] [Indexed: 04/15/2023] Open
Abstract
Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D. melanogaster. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs outside of the proximal inversion breakpoint are distributed in a distance-dependent manner, with strongest suppression near the inversion breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, are not suppressed near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break formation. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.
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Affiliation(s)
- Haosheng Li
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Erica Berent
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Savannah Hadjipanteli
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Nigel Muhammad-Lahbabi
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
| | - K Nicole Crown
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
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33
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Zhao H, Moberg KH, Veraksa A. Hippo pathway and Bonus control developmental cell fate decisions in the Drosophila eye. Dev Cell 2023; 58:416-434.e12. [PMID: 36868234 PMCID: PMC10023510 DOI: 10.1016/j.devcel.2023.02.005] [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: 09/08/2021] [Revised: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023]
Abstract
The canonical function of the Hippo signaling pathway is the regulation of organ growth. How this pathway controls cell-fate determination is less well understood. Here, we identify a function of the Hippo pathway in cell-fate decisions in the developing Drosophila eye, exerted through the interaction of Yorkie (Yki) with the transcriptional regulator Bonus (Bon), an ortholog of mammalian transcriptional intermediary factor 1/tripartite motif (TIF1/TRIM) family proteins. Instead of controlling tissue growth, Yki and Bon promote epidermal and antennal fates at the expense of the eye fate. Proteomic, transcriptomic, and genetic analyses reveal that Yki and Bon control these cell-fate decisions by recruiting transcriptional and post-transcriptional co-regulators and by repressing Notch target genes and activating epidermal differentiation genes. Our work expands the range of functions and regulatory mechanisms under Hippo pathway control.
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Affiliation(s)
- Heya Zhao
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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Solorzano J, Carrillo-de Santa Pau E, Laguna T, Busturia A. A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila. Dev Biol 2023; 495:63-75. [PMID: 36596335 DOI: 10.1016/j.ydbio.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 01/02/2023]
Abstract
Characterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore for the presence of gene regulatory circuits between two large groups of transcriptional regulators: the epigenetic group of the Polycomb/trithorax (PcG/trxG) proteins and the microRNAs (miRNAs). We have searched genome-wide for miRNA targets in PcG/trxG transcripts as well as for Polycomb Response Elements (PREs) in miRNA genes. Our results show that 10% of the analyzed miRNAs could be controlling PcG/trxG gene expression, while 40% of those miRNAs are putatively controlled by the selected set of PcG/trxG proteins. The integration of these analyses has resulted in the predicted existence of 3 classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits. In the first class, miRNA-PcG circuits are defined by miRNAs that reciprocally crosstalk with PcG. In the second, miRNA-trxG circuits are defined by miRNAs that reciprocally crosstalk with trxG. In the third class, miRNA-PcG/trxG shared circuits are defined by miRNAs that crosstalk with both PcG and trxG regulators. These putative regulatory circuits may uncover a novel mechanism in Drosophila for the control of PcG/trxG and miRNAs levels of expression. The computational framework developed here for Drosophila melanogaster can serve as a model case for similar analyses in other species. Moreover, our work provides, for the first time, a new and useful resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression.
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Affiliation(s)
- Jacobo Solorzano
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, 28049, Madrid, Spain; Centre de Recherches en Cancerologie de Toulouse, 2 Av. Hubert Curien, 31100, Toulouse, France
| | - Enrique Carrillo-de Santa Pau
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, CEI UAM+CSIC, 28049, Madrid, Spain
| | - Teresa Laguna
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, CEI UAM+CSIC, 28049, Madrid, Spain.
| | - Ana Busturia
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, 28049, Madrid, Spain.
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35
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Baisgaard AE, Koldby KM, Kristensen TN, Nyegaard M, Rohde PD. Functionally Validating Evolutionary Conserved Risk Genes for Parkinson's Disease in Drosophila melanogaster. INSECTS 2023; 14:168. [PMID: 36835737 PMCID: PMC9958964 DOI: 10.3390/insects14020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Parkinson's disease (PD) is a heterogeneous and complex neurodegenerative disorder and large-scale genetic studies have identified >130 genes associated with PD. Although genomic studies have been decisive for our understanding of the genetic contributions underlying PD, these associations remain as statistical associations. Lack of functional validation limits the biological interpretation; however, it is labour extensive, expensive, and time consuming. Therefore, the ideal biological system for functionally validating genetic findings must be simple. The study aim was to assess systematically evolutionary conserved PD-associated genes using Drosophila melanogaster. From a literature review, a total of 136 genes have found to be associated with PD in GWAS studies, of which 11 are strongly evolutionary conserved between Homo sapiens and D. melanogaster. By ubiquitous gene expression knockdown of the PD-genes in D. melanogaster, the flies' escape response was investigated by assessing their negative geotaxis response, a phenotype that has previously been used to investigate PD in D. melanogaster. Gene expression knockdown was successful in 9/11 lines, and phenotypic consequences were observed in 8/9 lines. The results provide evidence that genetically modifying expression levels of PD genes in D. melanogaster caused reduced climbing ability of the flies, potentially supporting their role in dysfunctional locomotion, a hallmark of PD.
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Affiliation(s)
- Amalie Elton Baisgaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | | | | | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
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36
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Babišová K, Mentelová L, Geisseová TK, Beňová-Liszeková D, Beňo M, Chase BA, Farkaš R. Apocrine secretion in the salivary glands of Drosophilidae and other dipterans is evolutionarily conserved. Front Cell Dev Biol 2023; 10:1088055. [PMID: 36712974 PMCID: PMC9880899 DOI: 10.3389/fcell.2022.1088055] [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: 11/03/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
Apocrine secretion is a transport and secretory mechanism that remains only partially characterized, even though it is evolutionarily conserved among all metazoans, including humans. The excellent genetic model organism Drosophila melanogaster holds promise for elucidating the molecular mechanisms regulating this fundamental metazoan process. Two prerequisites for such investigations are to clearly define an experimental system to investigate apocrine secretion and to understand the evolutionarily and functional contexts in which apocrine secretion arose in that system. To this end, we recently demonstrated that, in D. melanogaster, the prepupal salivary glands utilize apocrine secretion prior to pupation to deliver innate immune and defense components to the exuvial fluid that lies between the metamorphosing pupae and its chitinous case. This finding provided a unique opportunity to appraise how this novel non-canonical and non-vesicular transport and secretory mechanism is employed in different developmental and evolutionary contexts. Here we demonstrate that this apocrine secretion, which is mechanistically and temporarily separated from the exocytotic mechanism used to produce the massive salivary glue secretion (Sgs), is shared across Drosophilidae and two unrelated dipteran species. Screening more than 30 species of Drosophila from divergent habitats across the globe revealed that apocrine secretion is a widespread and evolutionarily conserved cellular mechanism used to produce exuvial fluid. Species with longer larval and prepupal development than D. melanogaster activate apocrine secretion later, while smaller and more rapidly developing species activate it earlier. In some species, apocrine secretion occurs after the secretory material is first concentrated in cytoplasmic structures of unknown origin that we name "collectors." Strikingly, in contrast to the widespread use of apocrine secretion to provide exuvial fluid, not all species use exocytosis to produce the viscid salivary glue secretion that is seen in D. melanogaster. Thus, apocrine secretion is the conserved mechanism used to realize the major function of the salivary gland in fruitflies and related species: it produces the pupal exuvial fluid that provides an active defense against microbial invasion during pupal metamorphosis.
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Affiliation(s)
- Klaudia Babišová
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Mentelová
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia,Department of Genetics, Comenius University, Bratislava, Slovakia
| | - Terézia Klaudia Geisseová
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Denisa Beňová-Liszeková
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Milan Beňo
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Bruce A. Chase
- Department of Biology, University of Nebraska, Omaha, NE, United States
| | - Robert Farkaš
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia,*Correspondence: Robert Farkaš,
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37
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Pallares LF, Lea AJ, Han C, Filippova EV, Andolfatto P, Ayroles JF. Dietary stress remodels the genetic architecture of lifespan variation in outbred Drosophila. Nat Genet 2023; 55:123-129. [PMID: 36550361 DOI: 10.1038/s41588-022-01246-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Evolutionary theory suggests that lifespan-reducing alleles should be purged from the gene pool, and yet decades of genome-wide association and model organism studies have shown that they persist. One potential explanation is that alleles that regulate lifespan do so only in certain environmental contexts. We exposed outbred Drosophila to control and high-sugar diets and genotyped more than 10,000 adult flies to track allele frequency changes over the course of a single adult lifespan. We identified thousands of lifespan-associated alleles associated with early versus late-life trade-offs, late-onset effects and genotype-by-environment interactions. Remarkably, a third of lifespan-associated genetic variation had environmentally dependent effects on lifespan. We find that lifespan-reducing alleles are often recently derived, have stronger effects on a high-sugar diet and show signatures of selection in wild Drosophila populations, consistent with the evolutionary mismatch hypothesis. Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan variation and the evolutionary processes that shape this key trait.
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Affiliation(s)
- Luisa F Pallares
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Amanda J Lea
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Clair Han
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Elena V Filippova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| | - Julien F Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA.
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38
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Lewerentz J, Johansson AM, Stenberg P. The path to immortalization of cells starts by managing stress through gene duplications. Exp Cell Res 2023; 422:113431. [PMID: 36423660 DOI: 10.1016/j.yexcr.2022.113431] [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: 06/27/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
The genomes of immortalized cell lines (and cancer cells) are characterized by multiple types of aberrations, ranging from single nucleotide polymorphisms (SNPs) to structural rearrangements that have accumulated over time. Consequently, it is difficult to estimate the relative impact of different aberrations, the order of events, and which gene functions were under selective pressure at the early stage towards cellular immortalization. Here, we have established novel cell cultures derived from Drosophila melanogaster embryos that were sampled at multiple time points over a one-year period. Using short-read DNA sequencing, we show that copy-number gain in preferentially stress-related genes were acquired in a dominant fraction of cells in 300-days old cultures. Furthermore, transposable elements were active in cells of all cultures. Only a few (<1%) SNPs could be followed over time, and these showed no trend to increase or decrease. We conclude that the early cellular responses of a novel culture comprise sequence duplication and transposable element activity. During immortalization, positive selection first occurs on genes that are related to stress response before shifting to genes that are related to growth.
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Affiliation(s)
- Jacob Lewerentz
- Department of Molecular Biology, Umeå University, Umeå, Västerbotten, SE-901 87, Sweden.
| | - Anna-Mia Johansson
- Department of Molecular Biology, Umeå University, Umeå, Västerbotten, SE-901 87, Sweden
| | - Per Stenberg
- Department of Ecology and Environmental Sciences, Umeå University, Umeå, Västerbotten, SE-901 87, Sweden
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Ren M, Yang Y, Heng KHY, Ng LY, Chong CYY, Ng YT, Gorur-Shandilya S, Lee RMQ, Lim KL, Zhang J, Koh TW. MED13 and glycolysis are conserved modifiers of α-synuclein-associated neurodegeneration. Cell Rep 2022; 41:111852. [PMID: 36543134 DOI: 10.1016/j.celrep.2022.111852] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
α-Synuclein (α-syn) is important in synucleinopathies such as Parkinson's disease (PD). While genome-wide association studies (GWASs) of synucleinopathies have identified many risk loci, the underlying genes have not been shown for most loci. Using Drosophila, we screened 3,471 mutant chromosomes for genetic modifiers of α-synuclein and identified 12 genes. Eleven modifiers have human orthologs associated with diseases, including MED13 and CDC27, which lie within PD GWAS loci. Drosophila Skd/Med13 and glycolytic enzymes are co-upregulated by α-syn-associated neurodegeneration. While elevated α-syn compromises mitochondrial function, co-expressing skd/Med13 RNAi and α-syn synergistically increase the ratio of oxidized-to-reduced glutathione. The resulting neurodegeneration can be suppressed by overexpressing a glycolytic enzyme or treatment with deferoxamine, suggesting that compensatory glycolysis is neuroprotective. In addition, the functional relationship between α-synuclein, MED13, and glycolytic enzymes is conserved between flies and mice. We propose that hypoxia-inducible factor and MED13 are part of a druggable pathway for PD.
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Affiliation(s)
- Mengda Ren
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308207, Singapore; National Neuroscience Institute, Singapore 308433, Singapore
| | - Ying Yang
- Department of Pathology, Zhejiang University First Affiliated Hospital and School of Medicine, Hangzhou, Zhejiang 310002, China
| | | | - Lu Yi Ng
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Yan Ting Ng
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Rachel Min Qi Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308207, Singapore; National Neuroscience Institute, Singapore 308433, Singapore
| | - Jing Zhang
- Department of Pathology, Zhejiang University First Affiliated Hospital and School of Medicine, Hangzhou, Zhejiang 310002, China; China National Health and Disease Human Brain Tissue Resource Center, Hangzhou, Zhejiang 310002, China
| | - Tong-Wey Koh
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
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40
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Andreyeva EN, Emelyanov AV, Nevil M, Sun L, Vershilova E, Hill CA, Keogh MC, Duronio RJ, Skoultchi AI, Fyodorov DV. Drosophila SUMM4 complex couples insulator function and DNA replication control. eLife 2022; 11:e81828. [PMID: 36458689 PMCID: PMC9917439 DOI: 10.7554/elife.81828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Asynchronous replication of chromosome domains during S phase is essential for eukaryotic genome function, but the mechanisms establishing which domains replicate early versus late in different cell types remain incompletely understood. Intercalary heterochromatin domains replicate very late in both diploid chromosomes of dividing cells and in endoreplicating polytene chromosomes where they are also underreplicated. Drosophila SNF2-related factor SUUR imparts locus-specific underreplication of polytene chromosomes. SUUR negatively regulates DNA replication fork progression; however, its mechanism of action remains obscure. Here, we developed a novel method termed MS-Enabled Rapid protein Complex Identification (MERCI) to isolate a stable stoichiometric native complex SUMM4 that comprises SUUR and a chromatin boundary protein Mod(Mdg4)-67.2. Mod(Mdg4) stimulates SUUR ATPase activity and is required for a normal spatiotemporal distribution of SUUR in vivo. SUUR and Mod(Mdg4)-67.2 together mediate the activities of gypsy insulator that prevent certain enhancer-promoter interactions and establish euchromatin-heterochromatin barriers in the genome. Furthermore, SuUR or mod(mdg4) mutations reverse underreplication of intercalary heterochromatin. Thus, SUMM4 can impart late replication of intercalary heterochromatin by attenuating the progression of replication forks through euchromatin/heterochromatin boundaries. Our findings implicate a SNF2 family ATP-dependent motor protein SUUR in the insulator function, reveal that DNA replication can be delayed by a chromatin barrier, and uncover a critical role for architectural proteins in replication control. They suggest a mechanism for the establishment of late replication that does not depend on an asynchronous firing of late replication origins.
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Affiliation(s)
- Evgeniya N Andreyeva
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | | | - Markus Nevil
- UNC-SPIRE, University of North CarolinaChapel HillUnited States
| | - Lu Sun
- EpiCypherDurhamUnited States
| | - Elena Vershilova
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Christina A Hill
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillUnited States
- Department of Biology, University of North CarolinaChapel HillUnited States
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of MedicineBronxUnited States
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41
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Miyao A, Yamanouchi U. Transposable element finder (TEF): finding active transposable elements from next generation sequencing data. BMC Bioinformatics 2022; 23:500. [PMID: 36418944 PMCID: PMC9682801 DOI: 10.1186/s12859-022-05011-3] [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: 03/29/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Detection of newly transposed events by transposable elements (TEs) from next generation sequence (NGS) data is difficult, due to their multiple distribution sites over the genome containing older TEs. The previously reported Transposon Insertion Finder (TIF) detects TE transpositions on the reference genome from NGS short reads using end sequences of target TE. TIF requires the sequence of target TE and is not able to detect transpositions for TEs with an unknown sequence. RESULT The new algorithm Transposable Element Finder (TEF) enables the detection of TE transpositions, even for TEs with an unknown sequence. TEF is a finding tool of transposed TEs, in contrast to TIF as a detection tool of transposed sites for TEs with a known sequence. The transposition event is often accompanied with a target site duplication (TSD). Focusing on TSD, two algorithms to detect both ends of TE, TSDs and target sites are reported here. One is based on the grouping with TSDs and direct comparison of k-mers from NGS without similarity search. The other is based on the junction mapping of TE end sequence candidates. Both methods succeed to detect both ends and TSDs of known active TEs in several tests with rice, Arabidopsis and Drosophila data and discover several new TEs in new locations. PCR confirmed the detected transpositions of TEs in several test cases in rice. CONCLUSIONS TEF detects transposed TEs with TSDs as a result of TE transposition, sequences of both ends and their inserted positions of transposed TEs by direct comparison of NGS data between two samples. Genotypes of transpositions are verified by counting of junctions of head and tail, and non-insertion sequences in NGS reads. TEF is easy to run and independent of any TE library, which makes it useful to detect insertions from unknown TEs bypassed by common TE annotation pipelines.
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Affiliation(s)
- Akio Miyao
- grid.416835.d0000 0001 2222 0432Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8518 Japan
| | - Utako Yamanouchi
- grid.416835.d0000 0001 2222 0432Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8518 Japan
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42
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Parker MT, Soanes BK, Kusakina J, Larrieu A, Knop K, Joy N, Breidenbach F, Sherwood AV, Barton GJ, Fica SM, Davies BH, Simpson GG. m 6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site. eLife 2022; 11:e78808. [PMID: 36409063 PMCID: PMC9803359 DOI: 10.7554/elife.78808] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022] Open
Abstract
Alternative splicing of messenger RNAs is associated with the evolution of developmentally complex eukaryotes. Splicing is mediated by the spliceosome, and docking of the pre-mRNA 5' splice site into the spliceosome active site depends upon pairing with the conserved ACAGA sequence of U6 snRNA. In some species, including humans, the central adenosine of the ACAGA box is modified by N6 methylation, but the role of this m6A modification is poorly understood. Here, we show that m6A modified U6 snRNA determines the accuracy and efficiency of splicing. We reveal that the conserved methyltransferase, FIONA1, is required for Arabidopsis U6 snRNA m6A modification. Arabidopsis fio1 mutants show disrupted patterns of splicing that can be explained by the sequence composition of 5' splice sites and cooperative roles for U5 and U6 snRNA in splice site selection. U6 snRNA m6A influences 3' splice site usage. We generalise these findings to reveal two major classes of 5' splice site in diverse eukaryotes, which display anti-correlated interaction potential with U5 snRNA loop 1 and the U6 snRNA ACAGA box. We conclude that U6 snRNA m6A modification contributes to the selection of degenerate 5' splice sites crucial to alternative splicing.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Beth K Soanes
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Jelena Kusakina
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Antoine Larrieu
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Nisha Joy
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Friedrich Breidenbach
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld UniversityBielefeldGermany
| | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Sebastian M Fica
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Brendan H Davies
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of LeedsLeedsUnited Kingdom
| | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- Cell & Molecular Sciences, James Hutton InstituteInvergowrieUnited Kingdom
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43
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Wang Z, Lincoln S, Nguyen AD, Li W, Young MW. Chronic sleep loss disrupts rhythmic gene expression in Drosophila. Front Physiol 2022; 13:1048751. [PMID: 36467698 PMCID: PMC9716074 DOI: 10.3389/fphys.2022.1048751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022] Open
Abstract
Genome-wide profiling of rhythmic gene expression has offered new avenues for studying the contribution of circadian clock to diverse biological processes. Sleep has been considered one of the most important physiological processes that are regulated by the circadian clock, however, the effects of chronic sleep loss on rhythmic gene expression remain poorly understood. In the present study, we exploited Drosophila sleep mutants insomniac 1 (inc 1 ) and wide awake D2 (wake D2 ) as models for chronic sleep loss. We profiled the transcriptomes of head tissues collected from 4-week-old wild type flies, inc 1 and wake D2 at timepoints around the clock. Analysis of gene oscillation revealed a substantial loss of rhythmicity in inc 1 and wake D2 compared to wild type flies, with most of the affected genes common to both mutants. The disruption of gene oscillation was not due to changes in average gene expression levels. We also identified a subset of genes whose loss of rhythmicity was shared among animals with chronic sleep loss and old flies, suggesting a contribution of aging to chronic, sleep-loss-induced disruption of gene oscillation.
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Affiliation(s)
- Zikun Wang
- Laboratory of Genetics, The Rockefeller University, New York, NY, United States
| | - Samantha Lincoln
- Laboratory of Genetics, The Rockefeller University, New York, NY, United States
| | - Andrew D. Nguyen
- Laboratory of Genetics, The Rockefeller University, New York, NY, United States
| | - Wanhe Li
- Laboratory of Genetics, The Rockefeller University, New York, NY, United States
- Department of Biology, Center for Biological Clocks Research, Texas A&M University, College Station, United States
| | - Michael W. Young
- Laboratory of Genetics, The Rockefeller University, New York, NY, United States
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44
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Li J, Wang J, Zhang P, Wang R, Mei Y, Sun Z, Fei L, Jiang M, Ma L, E W, Chen H, Wang X, Fu Y, Wu H, Liu D, Wang X, Li J, Guo Q, Liao Y, Yu C, Jia D, Wu J, He S, Liu H, Ma J, Lei K, Chen J, Han X, Guo G. Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types. Nat Genet 2022; 54:1711-1720. [PMID: 36229673 DOI: 10.1038/s41588-022-01197-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Despite extensive efforts to generate and analyze reference genomes, genetic models to predict gene regulation and cell fate decisions are lacking for most species. Here, we generated whole-body single-cell transcriptomic landscapes of zebrafish, Drosophila and earthworm. We then integrated cell landscapes from eight representative metazoan species to study gene regulation across evolution. Using these uniformly constructed cross-species landscapes, we developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory sequences at the single-cell level. We systematically compared cell-type-specific transcription factors to reveal conserved genetic regulation in vertebrates and invertebrates. Our work provides a valuable resource and offers a new strategy for studying regulatory grammar in diverse biological systems.
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Affiliation(s)
- Jiaqi Li
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuqing Mei
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongyi Sun
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hanyu Wu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daiyuan Liu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueyi Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingyu Li
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qile Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuan Liao
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danmei Jia
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital School of Medicine, Zhejiang University, Hangzhou, China
| | - Shibo He
- College of Control Science and Engineering, Zhejiang University, Hangzhou, China
| | - Huanju Liu
- Women's Hospital and Institute of Genetics, Zhenjiang University School of Medicine, Hangzhou, China
| | - Jun Ma
- Women's Hospital and Institute of Genetics, Zhenjiang University School of Medicine, Hangzhou, China
| | - Kai Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiming Chen
- College of Control Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China. .,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China. .,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China. .,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China.
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45
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Vitelline Membrane Protein 26 Mutagenesis, Using CRISPR/Cas9, Results in Egg Collapse in Plutella xylostella. Int J Mol Sci 2022; 23:ijms23179538. [PMID: 36076934 PMCID: PMC9455775 DOI: 10.3390/ijms23179538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/13/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Vitelline membrane proteins (VMPs) are the main proteins that form the inner shell (vitelline membrane layer) of insect eggs and are an integral part of egg formation and embryo development. Here, we characterized the molecular structure and expression patterns of the VMP26 gene and analyzed its reproductive functions in diamondback moth, Plutella xylostella (L.), a worldwide migratory pest of cruciferous plants. The PxVMP26 gene was shown to be a single exon gene that contained an open reading frame of 852 base pairs (bp) encoding 283 amino acids. Both qPCR and western blot analyses showed that PxVMP26 was specifically expressed in female adults and was significantly highly expressed in the ovary. Further anatomical analysis indicated that the expression level of PxVMP26 in the ovarian tube with an incomplete yolk was significantly higher than that in the ovarian tube with a complete yolk. CRISPR/Cas9-induced PxVMP26 knockout successfully created two homozygous strains with 8- and 46-bp frameshift mutations. The expression deficiency of the PxVMP26 protein was detected in the mutant strains using immunofluorescence and western blot. No significant difference was found in the number of eggs laid within three days between wild and mutant individuals, but there was a lower egg hatchability. The loss of the PxVMP26 gene changed the mean egg size, damaged the structure of the vitelline membrane, and increased the proportion of abnormal eggs due to water loss, resulting in egg collapse. This first analysis of the roles of the VMP gene in the oocyte formation and embryonic development of P. xylostella, using CRISPR/Cas9 technology, provides a basis for screening new genetic control targets of P. xylostella.
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46
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Bateman JR, Johnson JE. Altering enhancer-promoter linear distance impacts promoter competition in cis and in trans. Genetics 2022; 222:6617354. [PMID: 35748724 PMCID: PMC9434180 DOI: 10.1093/genetics/iyac098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
In Drosophila, pairing of maternal and paternal homologs can permit trans-interactions between enhancers on one homolog and promoters on another, an example of a phenomenon called transvection. When chromosomes are paired, promoters in cis and in trans to an enhancer can compete for the enhancer's activity, but the parameters that govern this competition are as yet poorly understood. To assess how the linear spacing between an enhancer and promoter can influence promoter competition in Drosophila, we employed transgenic constructs wherein the eye-specific enhancer GMR is placed at varying distances from a heterologous hsp70 promoter driving a fluorescent reporter. While GMR activates the reporter to a high degree when the enhancer and promoter are spaced by a few hundred base pairs, activation is strongly attenuated when the enhancer is moved 3 kilobases away. By examining transcription of endogenous genes near the point of transgene insertion, we show that linear spacing of 3 kb between GMR and the hsp70 promoter results in elevated transcription of neighboring promoters, suggesting a loss of specificity between the enhancer and its intended transgenic target promoter. Furthermore, increasing spacing between GMR and hsp70 by just 100 bp can enhance transvection, resulting in increased activation of a promoter on a paired homolog at the expense of a promoter in cis to the enhancer. Finally, cis-/trans-promoter competition assays in which one promoter carries mutations to key core promoter elements show that GMR will skew its activity toward a wild type promoter, suggesting that an enhancer is in a balanced competition between its potential target promoters in cis and in trans.
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Affiliation(s)
- Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
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47
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Osuntoki IG, Harrison A, Dai H, Bao Y, Zabet NR. ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. Bioinformatics 2022; 38:3523-3531. [PMID: 35678507 PMCID: PMC9272800 DOI: 10.1093/bioinformatics/btac387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Motivation Several computational and statistical methods have been developed to analyze data generated through the 3C-based methods, especially the Hi-C. Most of the existing methods do not account for dependency in Hi-C data. Results Here, we present ZipHiC, a novel statistical method to explore Hi-C data focusing on the detection of enriched contacts. ZipHiC implements a Bayesian method based on a hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC) to detect interactions in two-dimensional space based on a Hi-C contact frequency matrix. ZipHiC uses data on the sources of biases related to the contact frequency matrix, allows borrowing information from neighbours using the Potts model and improves computation speed using the ABC model. In addition to outperforming existing tools on both simulated and real data, our model also provides insights into different sources of biases that affects Hi-C data. We show that some datasets display higher biases from DNA accessibility or Transposable Elements content. Furthermore, our analysis in Drosophila melanogaster showed that approximately half of the detected significant interactions connect promoters with other parts of the genome indicating a functional biological role. Finally, we found that the micro-C datasets display higher biases from DNA accessibility compared to a similar Hi-C experiment, but this can be corrected by ZipHiC. Availability and implementation The R scripts are available at https://github.com/igosungithub/HMRFHiC.git. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Itunu G Osuntoki
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom.,Statistics, Modelling and Economics Department, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Hongsheng Dai
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Yanchun Bao
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, United Kingdom
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48
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Svoboda M, Frost HR, Bosco G. Internal oligo(dT) priming introduces systematic bias in bulk and single-cell RNA sequencing count data. NAR Genom Bioinform 2022; 4:lqac035. [PMID: 35651651 PMCID: PMC9142200 DOI: 10.1093/nargab/lqac035] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/28/2022] Open
Abstract
Significant advances in RNA sequencing have been recently made possible by using oligo(dT) primers for simultaneous mRNA enrichment and reverse transcription priming. The associated increase in efficiency has enabled more economical bulk RNA sequencing methods and the advent of high-throughput single-cell RNA sequencing, already one of the most widely adopted methods in transcriptomics. However, the effects of off-target oligo(dT) priming on gene expression quantification have not been appreciated. In the present study, we describe the extent, the possible causes, and the consequences of internal oligo(dT) priming across multiple public datasets obtained from various bulk and single-cell RNA sequencing platforms. To explore and address this issue, we developed a computational algorithm for RNA counting methods, which identifies the sequencing read alignments that likely resulted from internal oligo(dT) priming and removes them from the data. Directly comparing filtered datasets to those obtained by an alternative method reveals significant improvements in gene expression measurement. Finally, we infer a list of human genes whose expression quantification is most likely to be affected by internal oligo(dT) priming and predict that when measured using these methods, the expression of most genes may be inflated by at least 10% whereby some genes are affected more than others.
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Affiliation(s)
| | - H Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Giovanni Bosco
- Correspondence may also be addressed to Giovanni Bosco. Tel: +1 603 650 1210; Fax: +1 603 650 1188;
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49
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Adashev VE, Bazylev SS, Potashnikova DM, Godneeva BK, Shatskikh AS, Olenkina OM, Olenina LV, Kotov AA. Comparative transcriptional analysis uncovers molecular processes in early and mature somatic cyst cells of Drosophila testes. Eur J Cell Biol 2022; 101:151246. [PMID: 35667338 DOI: 10.1016/j.ejcb.2022.151246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 04/29/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
The tight interaction between somatic and germline cells is conserved in animal spermatogenesis. The testes of Drosophila melanogaster are the model of choice to identify processes responsible for mature gamete production. However, processes of differentiation and soma-germline interactions occurring in somatic cyst cells are currently understudied. Here we focused on the comparison of transcriptome expression patterns of early and mature somatic cyst cells to find out the developmental changes taking place in them. We employed a FACS-based approach for the isolation of early and mature somatic cyst cells from fly testes, subsequent preparation of RNA-Seq libraries, and analysis of gene differential expression in the sorted cells. We found increased expression of genes involved in cell cycle-related processes in early cyst cells, which is necessary for the proliferation and self-renewal of a crucial population of early cyst cells, cyst stem cells. Genes proposedly required for lamellipodium-like projection organization for proper cyst formation were also detected among the upregulated ones in early cyst cells. Gene Ontology and interactome analyses of upregulated genes in mature cyst cells revealed a striking over-representation of gene categories responsible for metabolic and catabolic cellular processes, as well as genes supporting the energetic state of the cells provided by oxidative phosphorylation that is carried out in mitochondria. Our comparative analyses of differentially expressed genes revealed major peculiarities in early and mature cyst cells and provide novel insight into their regulation, which is important for male fertility.
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Affiliation(s)
- Vladimir E Adashev
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
| | - Sergei S Bazylev
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
| | - Daria M Potashnikova
- Lomonosov Moscow State University, School of Biology, Department of Cell Biology and Histology, Moscow 119234, Russia.
| | - Baira K Godneeva
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
| | - Aleksei S Shatskikh
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
| | - Oxana M Olenkina
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
| | - Ludmila V Olenina
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", 2 Kurchatov Sq., Moscow 123182, Russia.
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50
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Potapova NA. Nonsense Mutations in Eukaryotes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:400-412. [PMID: 35790376 DOI: 10.1134/s0006297922050029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.
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Affiliation(s)
- Nadezhda A Potapova
- Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Moscow, 127051, Russia.
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