1
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Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1. Nat Commun 2024; 15:6276. [PMID: 39054315 PMCID: PMC11272775 DOI: 10.1038/s41467-024-50538-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: 11/28/2023] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
HP1 proteins are essential for establishing and maintaining transcriptionally silent heterochromatin. They dimerize, forming a binding interface to recruit diverse chromatin-associated factors. Although HP1 proteins are known to rapidly evolve, the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impacts heterochromatin formation, we performed a targeted mutagenesis screen of the S. pombe HP1 homolog, Swi6. Substitutions within an auxiliary surface adjacent to the HP1 dimerization interface produce Swi6 variants with divergent maintenance properties. Remarkably, substitutions at a single amino acid position lead to the persistent gain or loss of epigenetic inheritance. These substitutions increase Swi6 chromatin occupancy in vivo and altered Swi6-protein interactions that reprogram H3K9me maintenance. We show how relatively minor changes in Swi6 amino acid composition in an auxiliary surface can lead to profound changes in epigenetic inheritance providing a redundant mechanism to evolve HP1-effector specificity.
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Affiliation(s)
- Amanda Ames
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Ajay Larkin
- Department of Biology, Brandeis University, Waltham, MA, 02453, USA
| | - Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48104, USA
| | | | - Bokyung Kim
- Department of Biochemistry, Brandeis University, Waltham, MA, 02453, USA
| | - Julie Suzanne Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48104, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48104, USA
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2
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Lin L, Huang Y, McIntyre J, Chang CH, Colmenares S, Lee YCG. Prevalent fast evolution of genes involved in heterochromatin functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583199. [PMID: 38496614 PMCID: PMC10942301 DOI: 10.1101/2024.03.03.583199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements (TEs). Given the importance of these functions, it is expected that the genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes were found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compile an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigate their evolution over short and long evolutionary time scales in Drosophila. Our analyses find that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number change, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and intrinsically disordered regions (IDRs), purifying selection may have maintained the proportions of IDRs of these proteins. Together with the observed negative associations between evolutionary rates of these genes and genomic TE abundance, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique functional roles of heterochromatin, while the rapid evolution of TEs may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.
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3
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Baumgartner L, Ipsaro JJ, Hohmann U, Handler D, Schleiffer A, Duchek P, Brennecke J. Evolutionary adaptation of an HP1-protein chromodomain integrates chromatin and DNA sequence signals. eLife 2024; 13:RP93194. [PMID: 38995818 PMCID: PMC11245307 DOI: 10.7554/elife.93194] [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: 07/14/2024] Open
Abstract
Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin-binding patterns, likely due to interactions with various specificity factors. Previously, we showed that the chromatin-binding pattern of the HP1 protein Rhino, a crucial factor of the Drosophila PIWI-interacting RNA (piRNA) pathway, is largely defined by a DNA sequence-specific C2H2 zinc finger protein named Kipferl (Baumgartner et al., 2022). Here, we elucidate the molecular basis of the interaction between Rhino and its guidance factor Kipferl. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino's chromodomain, G31D, that does not affect H3K9me2/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the rhinoG31D mutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhino's chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.
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Affiliation(s)
- Lisa Baumgartner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Ulrich Hohmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
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4
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Brand CL, Oliver GT, Farkas IZ, Buszczak M, Levine MT. Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol 2024; 41:msae113. [PMID: 38865490 PMCID: PMC11210505 DOI: 10.1093/molbev/msae113] [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: 11/07/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Genevieve T Oliver
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabella Z Farkas
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Buszczak
- Department of Molecular Biology and Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.569027. [PMID: 38077059 PMCID: PMC10705379 DOI: 10.1101/2023.11.28.569027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
HP1 proteins are essential for establishing and maintaining transcriptionally silent heterochromatin. They dimerize, forming a binding interface to recruit diverse chromatin-associated factors. HP1 proteins are specialized and rapidly evolve, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impacts epigenetic inheritance, we performed a targeted mutagenesis screen of the S. pombe HP1 homolog, Swi6. Substitutions within an auxiliary surface adjacent to the HP1 dimerization interface produced Swi6 variants with divergent maintenance properties. Remarkably, substitutions at a single amino acid position led to the persistent gain or loss of epigenetic inheritance. These substitutions increased Swi6 chromatin occupancy in vivo and altered Swi6-protein interactions that reprogram H3K9me maintenance. We show that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance which provides a redundant mechanism to evolve novel effector specificity. .
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6
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Huang Y, Lee YCG. Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics. Proc Biol Sci 2024; 291:20232775. [PMID: 38593848 PMCID: PMC11003778 DOI: 10.1098/rspb.2023.2775] [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: 12/08/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024] Open
Abstract
Transposable elements (TEs) are selfish genetic elements whose antagonistic interactions with hosts represent a common genetic conflict in eukaryotes. To resolve this conflict, hosts have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, this mechanism is imperfect and fails to fully halt TE replication. Furthermore, TE epigenetic silencing can inadvertently spread repressive marks to adjacent functional sequences, a phenomenon considered a 'curse' of this conflict resolution. Here, we used forward simulations to explore how TE epigenetic silencing and its harmful side effects shape the evolutionary dynamics of TEs and their hosts. Our findings reveal that epigenetic silencing allows TEs and their hosts to stably coexist under a wide range of conditions, because the underlying molecular mechanisms give rise to copy-number dependency of the strength of TE silencing. Interestingly, contrary to intuitive expectations that TE epigenetic silencing should evolve to be as strong as possible, we found a selective benefit for modifier alleles that weaken TE silencing under biologically feasible conditions. These results reveal that the dual nature of TE epigenetic silencing, with both positive and negative effects, complicates its evolutionary trajectory and makes it challenging to determine whether TE epigenetic silencing is a 'blessing' or a 'curse'.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
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7
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Grill S, Riley A, Selvaraj M, Lehmann R. HP6/Umbrea is dispensable for viability and fertility, suggesting essentiality of newly evolved genes is rare. Proc Natl Acad Sci U S A 2023; 120:e2309478120. [PMID: 37725638 PMCID: PMC10523450 DOI: 10.1073/pnas.2309478120] [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: 06/05/2023] [Accepted: 07/15/2023] [Indexed: 09/21/2023] Open
Abstract
The newly evolved gene Heterochromatin Protein 6 (HP6), which has been previously classified as essential, challenged the dogma that functions required for viability are only seen in genes with a long evolutionary history. Based on previous RNA-sequencing analysis in Drosophila germ cells, we asked whether HP6 might play a role in germline development. Surprisingly, we found that CRISPR-generated HP6 mutants are viable and fertile. Using previously generated mutants, we identified an independent lethal allele and an RNAi off-target effect that prevented accurate interpretation of HP6 essentiality. By reviewing existing data, we found that the vast majority of young genes that were previously classified as essential were indeed viable when tested with orthologous methods. Together, our data call into question the frequency with which newly evolved genes gain essential functions and suggest that using multiple independent genetic methods is essential when probing the functions of young genes.
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Affiliation(s)
- Sherilyn Grill
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Ashley Riley
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Monica Selvaraj
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Ruth Lehmann
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA02142
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8
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Caro L, Raman P, Steiner FA, Ailion M, Malik HS. Recurrent but Short-Lived Duplications of Centromeric Proteins in Holocentric Caenorhabditis Species. Mol Biol Evol 2022; 39:6731087. [PMID: 36173809 PMCID: PMC9577544 DOI: 10.1093/molbev/msac206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Centromeric histones (CenH3s) are essential for chromosome inheritance during cell division in most eukaryotes. CenH3 genes have rapidly evolved and undergone repeated gene duplications and diversification in many plant and animal species. In Caenorhabditis species, two independent duplications of CenH3 (named hcp-3 for HoloCentric chromosome-binding Protein 3) were previously identified in C. elegans and C. remanei. Using phylogenomic analyses in 32 Caenorhabditis species, we find strict retention of the ancestral hcp-3 gene and 10 independent duplications. Most hcp-3L (hcp-3-like) paralogs are only found in 1-2 species, are expressed in both males and females/hermaphrodites, and encode histone fold domains with 69-100% identity to ancestral hcp-3. We identified novel N-terminal protein motifs, including putative kinetochore protein-interacting motifs and a potential separase cleavage site, which are well conserved across Caenorhabditis HCP-3 proteins. Other N-terminal motifs vary in their retention across paralogs or species, revealing potential subfunctionalization or functional loss following duplication. An N-terminal extension in the hcp-3L gene of C. afra revealed an unprecedented protein fusion, where hcp-3L fused to duplicated segments from hcp-4 (nematode CENP-C). By extending our analyses beyond CenH3, we found gene duplications of six inner and outer kinetochore genes in Caenorhabditis, which appear to have been retained independent of hcp-3 duplications. Our findings suggest that centromeric protein duplications occur frequently in Caenorhabditis nematodes, are selectively retained for short evolutionary periods, then degenerate or are lost entirely. We hypothesize that unique challenges associated with holocentricity in Caenorhabditis may lead to this rapid "revolving door" of kinetochore protein paralogs.
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Affiliation(s)
- Lews Caro
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pravrutha Raman
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Florian A Steiner
- Department of Molecular Biology and Cellular Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Michael Ailion
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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9
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Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022; 11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The ‘success’, or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated local enrichment of repressive marks, or ‘the epigenetic effect of TEs’, in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance. We found that TE-mediated local enrichment of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi-species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point toward the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite. All the instructions required for life are encoded in the set of DNA present in a cell. It therefore seems natural to think that every bit of this genetic information should serve the organism. And yet most species carry parasitic ‘transposable’ sequences, or transposons, whose only purpose is to multiply and insert themselves at other positions in the genome. It is possible for cells to suppress these selfish elements. Chemical marks can be deposited onto the DNA to temporarily ‘silence’ transposons and prevent them from being able to move and replicate. However, this sometimes comes at a cost: the repressive chemical modifications can spread to nearby genes that are essential for the organism and perturb their function. Strangely, the prevalence of transposons varies widely across the tree of life. These sequences form the majority of the genome of certain species – in fact, they represent about half of the human genetic information. But their abundance is much lower in other organisms, forming a measly 6% of the genome of puffer fish for instance. Even amongst fruit fly species, the prevalence of transposable elements can range between 2% and 25%. What explains such differences? Huang et al. set out to examine this question through the lens of transposon silencing, systematically comparing how this process impacts nearby regions in six species of fruit flies. This revealed variations in the strength of the side effects associated with transposon silencing, resulting in different levels of perturbation on neighbouring genes. A stronger impact was associated with the species having fewer transposons in its genome, suggesting that an evolutionary pressure is at work to keep the abundance of transposons at a low level in these species. Further analyses showed that the genes which determine how silencing marks are distributed may also be responsible for the variations in the impact of transposon silencing. They could therefore be the ones driving differences in the abundance of transposons between species. Overall, this work sheds light on the complex mechanisms shaping the evolution of genomes, and it may help to better understand how transposons are linked to processes such as aging and cancer.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Harsh Shukla
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
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10
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Schoelz JM, Riddle NC. Functions of HP1 proteins in transcriptional regulation. Epigenetics Chromatin 2022; 15:14. [PMID: 35526078 PMCID: PMC9078007 DOI: 10.1186/s13072-022-00453-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
In eukaryotes, DNA is packaged into chromatin, which presents significant barriers to transcription. Non-histone chromatin proteins such as the Heterochromatin Protein 1 (HP1) proteins are critical regulators of transcription, contributing to gene regulation through a variety of molecular mechanisms. HP1 proteins are highly conserved, and many eukaryotic genomes contain multiple HP1 genes. Given the presence of multiple HP1 family members within a genome, HP1 proteins can have unique as well as shared functions. Here, we review the mechanisms by which HP1 proteins contribute to the regulation of transcription. Focusing on the Drosophila melanogaster HP1 proteins, we examine the role of these proteins in regulating the transcription of genes, transposable elements, and piRNA clusters. In D. melanogaster, as in other species, HP1 proteins can act as transcriptional repressors and activators. The available data reveal that the precise impact of HP1 proteins on gene expression is highly context dependent, on the specific HP1 protein involved, on its protein partners present, and on the specific chromatin context the interaction occurs in. As a group, HP1 proteins utilize a variety of mechanisms to contribute to transcriptional regulation, including both transcriptional (i.e. chromatin-based) and post-transcriptional (i.e. RNA-based) processes. Despite extensive studies of this important protein family, open questions regarding their functions in gene regulation remain, specifically regarding the role of hetero- versus homodimerization and post-translational modifications of HP1 proteins.
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Affiliation(s)
- John M Schoelz
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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11
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Abstract
Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat-packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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12
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The birth of piRNAs: how mammalian piRNAs are produced, originated, and evolved. Mamm Genome 2021; 33:293-311. [PMID: 34724117 PMCID: PMC9114089 DOI: 10.1007/s00335-021-09927-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs), small noncoding RNAs 24–35 nucleotides long, are essential for animal fertility. They play critical roles in a range of functions, including transposable element suppression, gene expression regulation, imprinting, and viral defense. In mammals, piRNAs are the most abundant small RNAs in adult testes and the only small RNAs that direct epigenetic modification of chromatin in the nucleus. The production of piRNAs is a complex process from transcription to post-transcription, requiring unique machinery often distinct from the biogenesis of other RNAs. In mice, piRNA biogenesis occurs in specialized subcellular locations, involves dynamic developmental regulation, and displays sexual dimorphism. Furthermore, the genomic loci and sequences of piRNAs evolve much more rapidly than most of the genomic regions. Understanding piRNA biogenesis should reveal novel RNA regulations recognizing and processing piRNA precursors and the forces driving the gain and loss of piRNAs during animal evolution. Such findings may provide the basis for the development of engineered piRNAs capable of modulating epigenetic regulation, thereby offering possible single-dose RNA therapy without changing the genomic DNA. In this review, we focus on the biogenesis of piRNAs in mammalian adult testes that are derived from long non-coding RNAs. Although piRNA biogenesis is believed to be evolutionarily conserved from fruit flies to humans, recent studies argue for the existence of diverse, mammalian-specific RNA-processing pathways that convert precursor RNAs into piRNAs, perhaps associated with the unique features of mammalian piRNAs or germ cell development. We end with the discussion of major questions in the field, including substrate recognition and the birth of new piRNAs.
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13
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Gibert JM, Peronnet F. The Paramount Role of Drosophila melanogaster in the Study of Epigenetics: From Simple Phenotypes to Molecular Dissection and Higher-Order Genome Organization. INSECTS 2021; 12:884. [PMID: 34680653 PMCID: PMC8537509 DOI: 10.3390/insects12100884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 01/06/2023]
Abstract
Drosophila melanogaster has played a paramount role in epigenetics, the study of changes in gene function inherited through mitosis or meiosis that are not due to changes in the DNA sequence. By analyzing simple phenotypes, such as the bristle position or cuticle pigmentation, as read-outs of regulatory processes, the identification of mutated genes led to the discovery of major chromatin regulators. These are often conserved in distantly related organisms such as vertebrates or even plants. Many of them deposit, recognize, or erase post-translational modifications on histones (histone marks). Others are members of chromatin remodeling complexes that move, eject, or exchange nucleosomes. We review the role of D. melanogaster research in three epigenetic fields: Heterochromatin formation and maintenance, the repression of transposable elements by piRNAs, and the regulation of gene expression by the antagonistic Polycomb and Trithorax complexes. We then describe how genetic tools available in D. melanogaster allowed to examine the role of histone marks and show that some histone marks are dispensable for gene regulation, whereas others play essential roles. Next, we describe how D. melanogaster has been particularly important in defining chromatin types, higher-order chromatin structures, and their dynamic changes during development. Lastly, we discuss the role of epigenetics in a changing environment.
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Affiliation(s)
- Jean-Michel Gibert
- Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement (LBD), Institut de Biologie Paris Seine (IBPS), Sorbonne Université, 75005 Paris, France
| | - Frédérique Peronnet
- Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement (LBD), Institut de Biologie Paris Seine (IBPS), Sorbonne Université, 75005 Paris, France
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14
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Schoelz JM, Feng JX, Riddle NC. The Drosophila HP1 family is associated with active gene expression across chromatin contexts. Genetics 2021; 219:iyab108. [PMID: 34849911 PMCID: PMC8633139 DOI: 10.1093/genetics/iyab108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/07/2021] [Indexed: 11/13/2022] Open
Abstract
Drosophila Heterochromatin Protein 1a (HP1a) is essential for heterochromatin formation and is involved in transcriptional silencing. However, certain loci require HP1a to be transcribed. One model posits that HP1a acts as a transcriptional silencer within euchromatin while acting as an activator within heterochromatin. However, HP1a has been observed as an activator of a set of euchromatic genes. Therefore, it is not clear whether, or how, chromatin context informs the function of HP1 proteins. To understand the role of HP1 proteins in transcription, we examined the genome-wide binding profile of HP1a as well as two other Drosophila HP1 family members, HP1B and HP1C, to determine whether coordinated binding of these proteins is associated with specific transcriptional outcomes. We found that HP1 proteins share many of their endogenous binding targets. These genes are marked by active histone modifications and are expressed at higher levels than nontarget genes in both heterochromatin and euchromatin. In addition, HP1 binding targets displayed increased RNA polymerase pausing compared with nontarget genes. Specifically, colocalization of HP1B and HP1C was associated with the highest levels of polymerase pausing and gene expression. Analysis of HP1 null mutants suggests these proteins coordinate activity at transcription start sites to regulate transcription. Depletion of HP1B or HP1C alters expression of protein-coding genes bound by HP1 family members. Our data broaden understanding of the mechanism of transcriptional activation by HP1a and highlight the need to consider particular protein-protein interactions, rather than broader chromatin context, to predict impacts of HP1 at transcription start sites.
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Affiliation(s)
- John M Schoelz
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Justina X Feng
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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15
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Yang SY. Germline masculinization by Phf7 in D. melanogaster requires its evolutionarily novel C-terminus and the HP1-family protein HP1D3csd. Sci Rep 2021; 11:6308. [PMID: 33737548 PMCID: PMC7973481 DOI: 10.1038/s41598-021-85560-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/25/2021] [Indexed: 11/09/2022] Open
Abstract
Germ cells in Drosophila melanogaster need intrinsic factors along with somatic signals to activate proper sexual programs. A key factor for male germline sex determination is PHD finger protein 7 (Phf7), a histone reader expressed in the male germline that can trigger sex reversal in female germ cells and is also important for efficient spermatogenesis. Here we find that the evolutionarily novel C-terminus in Phf7 is necessary to turn on the complete male program in the early germline of D. melanogaster, suggesting that this domain may have been uniquely acquired to regulate sexual differentiation. We further looked for genes regulated by Phf7 related to sex determination in the embryonic germline by transcriptome profiling of FACS-purified embryonic gonads. One of the genes positively-regulated by Phf7 in the embryonic germline was an HP1family member, Heterochromatin Protein 1D3 chromoshadow domain (HP1D3csd). We find that this gene is needed for Phf7 to induce male-like development in the female germline, indicating that HP1D3csd is an important factor acting downstream of Phf7 to regulate germline masculinization.
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Affiliation(s)
- Shu Yuan Yang
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan. .,Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan.
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16
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Keenen MM, Brown D, Brennan LD, Renger R, Khoo H, Carlson CR, Huang B, Grill SW, Narlikar GJ, Redding S. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife 2021; 10:e64563. [PMID: 33661100 PMCID: PMC7932698 DOI: 10.7554/elife.64563] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.
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Affiliation(s)
- Madeline M Keenen
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - David Brown
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy D Brennan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Roman Renger
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Harrison Khoo
- Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Christopher R Carlson
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Cluster of Excellence Physics of Life, Technische Universität DresdenDresdenGermany
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Marine Biological LaboratoryWoods HoleUnited States
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17
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Liu J, Ali M, Zhou Q. Establishment and evolution of heterochromatin. Ann N Y Acad Sci 2020; 1476:59-77. [PMID: 32017156 PMCID: PMC7586837 DOI: 10.1111/nyas.14303] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein-coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic "dark matter" in the context of topologically associated domains and phase-separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever-changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Mujahid Ali
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
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18
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Wang L, Barbash DA, Kelleher ES. Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity. PLoS Genet 2020; 16:e1008861. [PMID: 32525870 PMCID: PMC7310878 DOI: 10.1371/journal.pgen.1008861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 06/23/2020] [Accepted: 05/14/2020] [Indexed: 02/05/2023] Open
Abstract
In metazoan germlines, the piRNA pathway acts as a genomic immune system, employing small RNA-mediated silencing to defend host DNA from the harmful effects of transposable elements (TEs). Expression of genomic TEs is proposed to initiate self regulation by increasing the production of repressive piRNAs, thereby “adapting” piRNA-mediated control to the most active TE families. Surprisingly, however, piRNA pathway proteins, which execute piRNA biogenesis and enforce silencing of targeted sequences, evolve rapidly and adaptively in animals. If TE silencing is ensured through piRNA biogenesis, what necessitates changes in piRNA pathway proteins? Here we used interspecific complementation to test for functional differences between Drosophila melanogaster and D. simulans alleles of three adaptively evolving piRNA pathway proteins: Armitage, Aubergine and Spindle-E. In contrast to piRNA-mediated transcriptional regulators examined in previous studies, these three proteins have cytoplasmic functions in piRNA maturation and post-transcriptional silencing. Across all three proteins we observed interspecific divergence in the regulation of only a handful of TE families, which were more robustly silenced by the heterospecific piRNA pathway protein. This unexpected result suggests that unlike transcriptional regulators, positive selection has not acted on cytoplasmic piRNA effector proteins to enhance their function in TE repression. Rather, TEs may evolve to “escape” silencing by host proteins. We further discovered that D. simulans alleles of aub and armi exhibit enhanced off-target effects on host transcripts in a D. melanogaster background, as well as modest reductions in the efficiency of piRNA biogenesis, suggesting that promiscuous binding of D. simulans Aub and Armi proteins to host transcripts reduces their participation in piRNA production. Avoidance of genomic auto-immunity may therefore be a critical target of selection. Our observations suggest that piRNA effector proteins are subject to an evolutionary trade-off between defending the host genome from the harmful effect of TEs while also minimizing collateral damage to host genes. Transposable elements are mobile fragments of selfish DNA that burden host genomes with deleterious mutations and incite genome instability. Host cells employ a specialized small-RNA mediated silencing pathway, the piRNA pathway, to act as a genomic immune system suppressing the mobilization of TEs. Changes in genomic TE content are met with rapid changes in the piRNA pool, thereby maintaining host control over transposition. However, piRNA pathway proteins—which enact piRNA biogenesis and silence target TEs—also evolve adaptively. To isolate forces that underlie this adaptive evolution, we examined functional divergence between two Drosophila species for three adaptively evolving piRNA pathway proteins. To our surprise, we found very few differences in TE regulation, suggesting that evolution has not generally acted to enhance control of TE parasites. Rather, we discovered interspecific differences in the regulation of host mRNAs for two proteins, which suggested that proteins evolve to avoid off-target silencing of host transcripts. We propose that the avoidance of such “genomic autoimmunity” is an important and underappreciated force driving the adaptive evolution of piRNA proteins.
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Affiliation(s)
- Luyang Wang
- Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Daniel A. Barbash
- Dept. Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America
| | - Erin S. Kelleher
- Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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19
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Courret C, Chang CH, Wei KHC, Montchamp-Moreau C, Larracuente AM. Meiotic drive mechanisms: lessons from Drosophila. Proc Biol Sci 2019; 286:20191430. [PMID: 31640520 DOI: 10.1098/rspb.2019.1430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Meiotic drivers are selfish genetic elements that bias their transmission into gametes, often to the detriment of the rest of the genome. The resulting intragenomic conflicts triggered by meiotic drive create evolutionary arms races and shape genome evolution. The phenomenon of meiotic drive is widespread across taxa but is particularly prominent in the Drosophila genus. Recent studies in Drosophila have provided insights into the genetic origins of drivers and their molecular mechanisms. Here, we review the current literature on mechanisms of drive with an emphasis on sperm killers in Drosophila species. In these systems, meiotic drivers often evolve from gene duplications and targets are generally linked to heterochromatin. While dense in repetitive elements and difficult to study using traditional genetic and genomic approaches, recent work in Drosophila has made progress on the heterochromatic compartment of the genome. Although we still understand little about precise drive mechanisms, studies of male drive systems are converging on common themes such as heterochromatin regulation, small RNA pathways, and nuclear transport pathways. Meiotic drive systems are therefore promising models for discovering fundamental features of gametogenesis.
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Affiliation(s)
- Cécile Courret
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette 91190, France
| | - Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California, Berkley, CA, USA
| | - Catherine Montchamp-Moreau
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette 91190, France
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20
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Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. EvoChromo: towards a synthesis of chromatin biology and evolution. Development 2019; 146:146/19/dev178962. [PMID: 31558570 DOI: 10.1242/dev.178962] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past few years, interest in chromatin and its evolution has grown. To further advance these interests, we organized a workshop with the support of The Company of Biologists to debate the current state of knowledge regarding the origin and evolution of chromatin. This workshop led to prospective views on the development of a new field of research that we term 'EvoChromo'. In this short Spotlight article, we define the breadth and expected impact of this new area of scientific inquiry on our understanding of both chromatin and evolution.
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Affiliation(s)
- Ines A Drinnenberg
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique UMR 3664, Paris 75005, France
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Peter R Andersen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Wendy A Bickmore
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Douglas H Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - James M Gahan
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zachary H Harvey
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Henikoff
- Division of Basic Sciences and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joyce Y Kao
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.,Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karolin Luger
- Howard Hughes Medical Institute and Department of Biochemistry, CU Boulder, Boulder, CO 80303, USA
| | - Harmit S Malik
- Division of Basic Sciences and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - José M Martín-Durán
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8092 Zürich, Switzerland
| | - Peter Sarkies
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, IMperial College London, Du Cane Road, London W12 0NN, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna A-1090, Austria
| | - Joseph W Thornton
- Department of Human Genetics, and Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, IMperial College London, Du Cane Road, London W12 0NN, UK
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
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21
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Kopp A, Barmina O, Prigent SR. Phylogenetic position of the Drosophila fima and dentissima lineages, and the status of the D. melanogaster species group. Mol Phylogenet Evol 2019; 139:106543. [PMID: 31247309 DOI: 10.1016/j.ympev.2019.106543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 12/31/2022]
Abstract
The subgenus Sophophora of Drosophila, which includes D. melanogaster, is an important model for the study of molecular evolution, comparative genomics, and evolutionary developmental biology. Numerous phylogenetic studies have examined species relationships in the well-known melanogaster, obscura, willistoni, and saltans species groups, as well as the relationships among these clades. In contrast, other species groups of Sophophora have been relatively neglected and have not been subjected to molecular phylogenetic analysis. Here, we focus on the endemic African Drosophila fima and dentissima lineages. We find that both these clades fall within the broadly defined melanogaster species group, but are otherwise distantly related to each other. The new phylogeny supports pervasive divergent and convergent evolution of male-specific grasping structures (sex combs). We discuss the implications of these results for defining the boundaries of the melanogaster species group, and weigh the relative merits of "splitting" and "lumping" approaches to the taxonomy of this key model system.
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Affiliation(s)
- A Kopp
- Department of Evolution and Ecology, University of California Davis, United States.
| | - O Barmina
- Department of Evolution and Ecology, University of California Davis, United States
| | - S R Prigent
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205, CNRS-MNHN-UPMC-EPHE, PSL University, 45 rue Buffon, 75005 Paris, France
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22
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Parey E, Crombach A. Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. Genome Biol Evol 2019; 11:660-677. [PMID: 30689829 PMCID: PMC6411481 DOI: 10.1093/gbe/evz019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2019] [Indexed: 12/30/2022] Open
Abstract
In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given color names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly Drosophila melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the evolution of the different chromatin types. Our results indicate that for the euchromatic types, YELLOW and RED, young associated proteins are more specialized than old ones; and for genes found in either chromatin type, intron/exon structure is lineage-specific. Next, we provide evidence that a subset of GREEN-associated proteins is involved in a centromere drive in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.
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Affiliation(s)
- Elise Parey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, France.,Inria, Antenne Lyon La Doua, Villeurbanne, France.,Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, Villeurbanne, France
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23
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Helleu Q, Levine MT. Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera. Mol Biol Evol 2019; 35:2375-2389. [PMID: 29924345 PMCID: PMC6188558 DOI: 10.1093/molbev/msy128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that interspecies hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of coevolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter. Here we describe many such candidates encoded by the Heterochromatin Protein 1 (HP1) gene family across Diptera, an insect Order that encompasses dramatic episodes of heterochromatic sequence turnover. Using BLAST, synteny analysis, and phylogenetic tree building across 64 Diptera genomes, we discovered a staggering 121 HP1 duplication events. In contrast, we observed virtually no gene duplication in gene families that share a common “chromodomain” with HP1s, including Polycomb and Su(var)3-9. The remarkably high number of Dipteran HP1 paralogs arises from distant clades undergoing convergent HP1 family amplifications. These independently derived, young HP1s span diverse ages, domain structures, and rates of molecular evolution, including episodes of positive selection. Moreover, independently derived HP1s exhibit convergent expression evolution. While ancient HP1 parent genes are transcribed ubiquitously, young HP1 paralogs are transcribed primarily in male germline tissue, a pattern typical of young genes. Pervasive gene youth, rapid evolution, and germline specialization implicate heterochromatin-encoded selfish elements driving recurrent HP1 gene family expansions. The 121 young genes offer valuable experimental traction for elucidating the germline processes shaped by Diptera’s many dramatic episodes of heterochromatin turnover.
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Affiliation(s)
- Quentin Helleu
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
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24
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Mills BB, Thomas AD, Riddle NC. HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism. PLoS One 2018; 13:e0205867. [PMID: 30346969 PMCID: PMC6197686 DOI: 10.1371/journal.pone.0205867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/02/2018] [Indexed: 11/30/2022] Open
Abstract
Heterochromatin Protein 1 (HP1) proteins are an important family of chromosomal proteins conserved among all major eukaryotic lineages. While HP1 proteins are best known for their role in heterochromatin, many HP1 proteins function in euchromatin as well. As a group, HP1 proteins carry out diverse functions, playing roles in the regulation of gene expression, genome stability, chromatin structure, and DNA repair. While the heterochromatic HP1 proteins are well studied, our knowledge of HP1 proteins with euchromatic distribution is lagging behind. We have created the first mutations in HP1B, a Drosophila HP1 protein with euchromatic function, and the Drosophila homolog most closely related to mammalian HP1α, HP1β, and HP1γ. We find that HP1B is a non-essential protein in Drosophila, with mutations affecting fertility and animal activity levels. In addition, animals lacking HP1B show altered food intake and higher body fat levels. Gene expression analysis of animals lacking HP1B demonstrates that genes with functions in various metabolic processes are affected primarily by HP1B loss. Our findings suggest that there is a link between the chromatin protein HP1B and the regulation of metabolism.
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Affiliation(s)
- Benjamin B. Mills
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andrew D. Thomas
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nicole C. Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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25
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Wiley EA, Horrell S, Yoshino A, Schornak CC, Bagnani C, Chalker DL. Diversification of HP1-like Chromo Domain Proteins in Tetrahymena thermophila. J Eukaryot Microbiol 2017; 65:104-116. [PMID: 28692189 PMCID: PMC5762428 DOI: 10.1111/jeu.12443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 12/18/2022]
Abstract
Proteins that possess a chromo domain are well-known for their roles in heterochromatin assembly and maintenance. The Heterochromatin Protein 1 (HP1) family, with a chromo domain and carboxy-terminal chromo shadow domain, targets heterochromatin through interaction with histone H3 methylated on lysine 9 (H3K9me2/3). The structural and functional diversity of these proteins observed in both fission yeast and metazoans correlate with chromatin specialization. To expand these studies, we examined chromo domain proteins in the ciliate Tetrahymena thermophila, which has functionally diverse and developmentally regulated heterochromatin domains. We identified thirteen proteins similar to HP1. Together they possess only a fraction of the possible chromo domain subtypes and most lack a recognizable chromo shadow domain. Using fluorescence microscopy to track chromatin localization of tagged proteins through the life cycle, we show evidence that in T. thermophila this family has diversified with biological roles in RNAi-directed DNA elimination, germline genome structure, and somatic heterochromatin. Those proteins with H3K27me3 binding sequence characteristics localize to chromatin in mature nuclei, whereas those with H3K9me2/3 binding characteristics localize to developing nuclei undergoing DNA elimination. Findings point to an expanded and diversified family of chromo domain proteins that parallels heterochromatin diversity in ciliates.
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Affiliation(s)
- Emily A Wiley
- W.M. Keck Science Center of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711
| | - Scott Horrell
- Department of Biology, Washington University, St. Louis, Missouri, 63130
| | - Alyssa Yoshino
- W.M. Keck Science Center of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711
| | - Cara C Schornak
- Department of Biology, Washington University, St. Louis, Missouri, 63130
| | - Claire Bagnani
- W.M. Keck Science Center of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California, 91711
| | - Douglas L Chalker
- Department of Biology, Washington University, St. Louis, Missouri, 63130
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Lee YCG, Leek C, Levine MT. Recurrent Innovation at Genes Required for Telomere Integrity in Drosophila. Mol Biol Evol 2017; 34:467-482. [PMID: 27836984 PMCID: PMC6307840 DOI: 10.1093/molbev/msw248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly. Nevertheless, no global analysis of the evolutionary forces that shape these fast-evolving proteins has been performed on any eukaryote. The abundant population and comparative genomic resources of Drosophila melanogaster and its close relatives offer us a unique opportunity to fill this gap. Here we leverage population genetics, molecular evolution, and phylogenomics to define the scope and evolutionary mechanisms driving fast evolution of genes required for telomere integrity. We uncover evidence of pervasive positive selection across multiple evolutionary timescales. We also document prolific expansion, turnover, and expression evolution in gene families founded by telomeric proteins. Motivated by the mutant phenotypes and molecular roles of these fast-evolving genes, we put forward four alternative, but not mutually exclusive, models of intra-genomic conflict that may play out at very termini of eukaryotic chromosomes. Our findings set the stage for investigating both the genetic causes and functional consequences of telomere protein evolution in Drosophila and beyond.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Courtney Leek
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA
| | - Mia T Levine
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Genome-wide identification, evolution of chromobox family genes and their expression in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2016; 203:25-34. [PMID: 27614332 DOI: 10.1016/j.cbpb.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/18/2016] [Accepted: 09/02/2016] [Indexed: 01/30/2023]
Abstract
Chromobox (Cbx) family proteins are transcriptional repressors that involved in epigenetic and developmental processes. In this study, comprehensive analyses of Cbxs were performed using available genome databases from representative animal species. The Cbx family were originated from one Polycomb (Pc) gene like the yeast Pc, which duplicated into two and gave rise to the Pc and the Heterochromatin protein 1 (Hp1) identified in invertebrates from protozoon to lancelet. Rapid expansion of Cbx family members was observed in vertebrates as ~8 (5 Pc and 3 Hp1) were identified in spotted gar, coelacanth and tetrapods. Further expansion of the members to ~14 (9 Pc and 5 Hp1) was observed in teleosts due to the third round genome duplication (3R). Based on transcriptome data from eight adult tilapia tissues, most of the Cbxs were found to be dominantly expressed in the brain, testis, ovary and heart. Analyses of the gonadal transcriptome data from four developmental stages revealed that all Cbxs were expressed in both ovary and testis except Cbx7b, with significant increase of the total and average RPKM from 5 to 90dah (days after hatching). By in situ hybridization, the three most highly and sexual dimorphically expressed Cbx genes in gonads, Cbx1b, Cbx3a and Cbx5, were found to be expressed in phase I and II oocytes of the ovary, and in secondary spermatocytes (Cbx1b and Cbx3a) and spermatids (Cbx5) of the testis. Our results revealed the evolution of Cbx genes and indicated a potential role of Cbxs in epigenetic regulation of gametogenesis.
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Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive. Proc Natl Acad Sci U S A 2016; 113:4110-5. [PMID: 26979956 DOI: 10.1073/pnas.1519332113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sex chromosome meiotic drive, the non-Mendelian transmission of sex chromosomes, is the expression of an intragenomic conflict that can have extreme evolutionary consequences. However, the molecular bases of such conflicts remain poorly understood. Here, we show that a young and rapidly evolving X-linked heterochromatin protein 1 (HP1) gene, HP1D2, plays a key role in the classical Paris sex-ratio (SR) meiotic drive occurring in Drosophila simulans Driver HP1D2 alleles prevent the segregation of the Y chromatids during meiosis II, causing female-biased sex ratio in progeny. HP1D2 accumulates on the heterochromatic Y chromosome in male germ cells, strongly suggesting that it controls the segregation of sister chromatids through heterochromatin modification. We show that Paris SR drive is a consequence of dysfunctional HP1D2 alleles that fail to prepare the Y chromosome for meiosis, thus providing evidence that the rapid evolution of genes controlling the heterochromatin structure can be a significant source of intragenomic conflicts.
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Levine MT, Vander Wende HM, Hsieh E, Baker EP, Malik HS. Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila. Mol Biol Evol 2016; 33:1641-53. [PMID: 26979388 DOI: 10.1093/molbev/msw053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the piwi-interacting-RNA pathway of gene silencing, for example, the female germline-restricted TE silencer, HP1D/Rhino Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker, a young, tandem duplicate gene of HP1D/rhino We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several TE families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker, at least ten additional, structurally diverse, HP1D/rhino-derived daughter and "granddaughter" genes emerged during a short 15-million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification.
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Affiliation(s)
- Mia T Levine
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Emily Hsieh
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - EmilyClare P Baker
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle,
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Fang C, Schmitz L, Ferree PM. An unusually simple HP1 gene set in Hymenopteran insects. Biochem Cell Biol 2015; 93:596-603. [PMID: 26419616 DOI: 10.1139/bcb-2015-0046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The heterochromatin protein 1 (HP1) gene family includes a set of paralogs in higher eukaryotes that serve fundamental roles in heterochromatin structure and maintenance, and other chromatin-related functions. At least 10 full and 16 partial HP1 genes exist among Drosophila species, with multiple gene gains, losses, and sub-functionalizations within this insect group. An important question is whether this diverse set of HP1 genes and their dynamic evolution represent the standard rule in eukaryotic groups. Here we have begun to address this question by bio-informatically identifying the HP1 family genes in representative species of the insect order Hymenoptera, which includes all ants, bees, wasps, and sawflies. Compared to Drosophila species, Hymenopterans have a much simpler set of HP1 genes, including one full and two partial HP1s. All 3 genes appear to have been present in the common ancestor of the Hymenopterans and they derive from a Drosophila HP1B-like gene. In ants, a partial HP1 gene containing only a chromoshadow domain harbors amino acid changes at highly conserved sites within the PxVxL recognition region, suggesting that this gene has undergone sub-functionalization. In the jewel wasp Nasonia vitripennis, the full HP1 and partial chromoshadow-only HP1 are expressed in both germ line and somatic tissues. However, the partial chromodomain-only HP1 is expressed exclusively in the ovary and testis, suggesting that it may have a specialized chromatin role during gametogenesis. Our findings demonstrate that the HP1 gene family is much simpler and evolutionarily less dynamic within the Hymenopterans compared to the much younger Drosophila group, a pattern that may reflect major differences in the range of chromatin-related functions present in these and perhaps other insect groups.
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Affiliation(s)
- C Fang
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - L Schmitz
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - P M Ferree
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
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Zhang B, Zheng J, Peng Y, Liu X, Hoffmann AA, Ma CS. Stress Responses of Small Heat Shock Protein Genes in Lepidoptera Point to Limited Conservation of Function across Phylogeny. PLoS One 2015. [PMID: 26196395 PMCID: PMC4511463 DOI: 10.1371/journal.pone.0132700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The small heat shock protein (sHsp) family is thought to play an important role in protein refolding and signal transduction, and thereby protect organisms from stress. However little is known about sHsp function and conservation across phylogenies. In the current study, we provide a comprehensive assessment of small Hsp genes and their stress responses in the oriental fruit moth (OFM), Grapholita molesta. Fourteen small heat shock proteins of OFM clustered with related Hsps in other Lepidoptera despite a high level of variability among them, and in contrast to the highly conserved Hsp11.1. The only known lepidopteran sHsp ortholog (Hsp21.3) was consistently unaffected under thermal stress in Lepidoptera where it has been characterized. However the phylogenetic position of the sHsps within the Lepidoptera was not associated with conservation of induction patterns under thermal extremes or diapause. These findings suggest that the sHsps have evolved rapidly to develop new functions within the Lepidoptera.
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Affiliation(s)
- Bo Zhang
- Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jincheng Zheng
- Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Peng
- Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology, China Agricultural University, Yuanmingyuan West Road, Beijing, China
| | - Ary A. Hoffmann
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chun-Sen Ma
- Group of Climate Change Biology, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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Levine MT, Vander Wende HM, Malik HS. Mitotic fidelity requires transgenerational action of a testis-restricted HP1. eLife 2015; 4:e07378. [PMID: 26151671 PMCID: PMC4491702 DOI: 10.7554/elife.07378] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/08/2015] [Indexed: 01/02/2023] Open
Abstract
Sperm-packaged DNA must undergo extensive reorganization to ensure its timely participation in embryonic mitosis. Whereas maternal control over this remodeling is well described, paternal contributions are virtually unknown. In this study, we show that Drosophila melanogaster males lacking Heterochromatin Protein 1E (HP1E) sire inviable embryos that undergo catastrophic mitosis. In these embryos, the paternal genome fails to condense and resolve into sister chromatids in synchrony with the maternal genome. This delay leads to a failure of paternal chromosomes, particularly the heterochromatin-rich sex chromosomes, to separate on the first mitotic spindle. Remarkably, HP1E is not inherited on mature sperm chromatin. Instead, HP1E primes paternal chromosomes during spermatogenesis to ensure faithful segregation post-fertilization. This transgenerational effect suggests that maternal control is necessary but not sufficient for transforming sperm DNA into a mitotically competent pronucleus. Instead, paternal action during spermiogenesis exerts post-fertilization control to ensure faithful chromosome segregation in the embryo. DOI:http://dx.doi.org/10.7554/eLife.07378.001 The genetic information of cells is packaged into structures called chromosomes, which are made up of long strands of DNA that are wrapped around proteins to form a structure called chromatin. The cells of most animals contain two copies of every chromosome, but the egg and sperm cells contain only one copy. This means that when an egg fuses with a sperm cell during fertilization, the resulting ‘zygote’ will contain two copies of each chromosome—one inherited from the mother, and one from the father. These chromosomes duplicate and divide many times within the developing embryo in a process known as mitosis. The first division of the zygote is particularly complicated, as the egg and sperm chromosomes must go through extensive—and yet different—chromatin reorganization processes. For instance, paternal DNA is inherited via sperm, where specialized sperm proteins package the DNA more tightly than in the maternal DNA, which is packaged by histone proteins used throughout development. For paternal DNA to participate in mitosis in the embryo, it must first undergo a transition to a histone-packaged state. Despite these differences, both maternal and paternal chromosomes must undergo mitosis at the same time if the zygote is to successfully divide. Although it is known that the egg cell contributes essential proteins that are incorporated into the sperm chromatin to help it reorganize, the importance of paternal proteins in coordinating this process remains poorly understood. Many members of a family of proteins called Heterochromatin Protein 1 (or HP1 for short) have previously been shown to control chromatin organization in plants and animals. In 2012, researchers found that several HP1 proteins are found only in the testes of the fruit fly species Drosophila melanogaster. They predicted that these proteins might help control the reorganization of the paternal chromosomes following fertilization. Levine et al.—including researchers involved in the 2012 study—have now used genetic and cell-based techniques to show that one member of the HP1 family (called HP1E) ensures that the paternal chromosomes are ready for cell division at the same time as the maternal chromosomes. Male flies that are unable to produce this protein do not have any offspring because, while these flies' sperm can fertilize eggs, the resulting zygotes cannot divide as normal. Further experiments revealed that HP1E is not inherited through the chromatin of mature sperm, but instead influences the structure of the chromosomes during the final stages of the development of the sperm cells in the fly testes. This study shows that both maternal and paternal proteins are needed to control how the paternal chromosomes reorganize in fruit fly embryos. Although difficult to discover and decipher, this work re-emphasizes the importance of paternal epigenetic contributions—changes that alter how DNA is read, without changing the DNA sequence itself—for ensuring the viability of resulting offspring. Future work will reveal both the molecular mechanism of this epigenetic transfer of information, as well as why certain Drosophila species are able to naturally overcome the loss of the essential HP1E protein. DOI:http://dx.doi.org/10.7554/eLife.07378.002
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Affiliation(s)
- Mia T Levine
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Helen M Vander Wende
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H. Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genomics 2015; 16:58. [PMID: 25888265 PMCID: PMC4363184 DOI: 10.1186/s12864-015-1244-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. Results A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. Conclusion We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tapan Kumar Mohanta
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Nibedita Mohanta
- Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa, 757003, India.
| | - Pratap Parida
- Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
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Abstract
Sex chromosome drivers are selfish elements that subvert Mendel's first law of segregation and therefore are overrepresented among the products of meiosis. The sex-biased progeny produced then fuels an extended genetic conflict between the driver and the rest of the genome. Many examples of sex chromosome drive are known, but the occurrence of this phenomenon is probably largely underestimated because of the difficulty to detect it. Remarkably, nearly all sex chromosome drivers are found in two clades, Rodentia and Diptera. Although very little is known about the molecular and cellular mechanisms of drive, epigenetic processes such as chromatin regulation could be involved in many instances. Yet, its evolutionary consequences are far-reaching, from the evolution of mating systems and sex determination to the emergence of new species.
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Affiliation(s)
- Quentin Helleu
- Laboratoire Évolution Génomes et Spéciation, CNRS UPR9034, Gif-sur-Yvette, France and Université Paris-Sud, Orsay, France
| | - Pierre R Gérard
- Laboratoire Évolution Génomes et Spéciation, CNRS UPR9034, Gif-sur-Yvette, France and Université Paris-Sud, Orsay, France
| | - Catherine Montchamp-Moreau
- Laboratoire Évolution Génomes et Spéciation, CNRS UPR9034, Gif-sur-Yvette, France and Université Paris-Sud, Orsay, France
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Nishibuchi G, Nakayama JI. Biochemical and structural properties of heterochromatin protein 1: understanding its role in chromatin assembly. J Biochem 2014; 156:11-20. [DOI: 10.1093/jb/mvu032] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Canzio D, Larson A, Narlikar GJ. Mechanisms of functional promiscuity by HP1 proteins. Trends Cell Biol 2014; 24:377-86. [PMID: 24618358 DOI: 10.1016/j.tcb.2014.01.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/19/2014] [Accepted: 01/22/2014] [Indexed: 01/03/2023]
Abstract
Heterochromatin protein 1 (HP1) proteins were originally identified as critical components in heterochromatin-mediated gene silencing and are now recognized to play essential roles in several other processes including gene activation. Several eukaryotes possess more than one HP1 paralog. Despite high sequence conservation, the HP1 paralogs achieve diverse functions. Further, in many cases, the same HP1 paralog is implicated in multiple functions. Recent biochemical studies have revealed interesting paralog-specific biophysical differences and unanticipated conformational versatility in HP1 proteins that may account for this functional promiscuity. Here we review these findings and describe a molecular framework that aims to link the conformational flexibility of HP1 proteins observed in vitro with their functional promiscuity observed in vivo.
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Affiliation(s)
- Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Adam Larson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.
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Eissenberg JC, Elgin SCR. HP1a: a structural chromosomal protein regulating transcription. Trends Genet 2014; 30:103-10. [PMID: 24555990 DOI: 10.1016/j.tig.2014.01.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/17/2014] [Accepted: 01/17/2014] [Indexed: 01/16/2023]
Abstract
Heterochromatin protein 1 (HP1a in Drosophila) is a conserved eukaryotic chromosomal protein that is prominently associated with pericentric heterochromatin and mediates the concomitant gene silencing. Mechanistic studies implicate HP1 family proteins as 'hub proteins,' able to interact with a variety of chromosomal proteins through the chromo-shadow domain (CSD), as well as to recognize key histone modification sites [primarily histone H3 di/trimethyl Lys9 (H3K9me2/3)] through the chromodomain (CD). Consequently, HP1 has many important roles in chromatin architecture and impacts both gene expression and gene silencing, utilizing a variety of mechanisms. Clearly, HP1 function is altered by context, and potentially by post-translational modifications (PTMs). Here, we report on recent ideas as to how this versatile protein accomplishes its diverse functions.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine, Doisy Research Center, 1100 South Grand Boulevard, St Louis, MO 63104, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, Campus Box 1037, One Brookings Drive, St Louis, MO 63130-4899, USA.
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Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AFA, Imhof A, Mellone BG, Malik HS. Stepwise evolution of essential centromere function in a Drosophila neogene. Science 2013; 340:1211-4. [PMID: 23744945 DOI: 10.1126/science.1234393] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Evolutionarily young genes that serve essential functions represent a paradox; they must perform a function that either was not required until after their birth or was redundant with another gene. How young genes rapidly acquire essential function is largely unknown. We traced the evolutionary steps by which the Drosophila gene Umbrea acquired an essential role in chromosome segregation in D. melanogaster since the gene's origin less than 15 million years ago. Umbrea neofunctionalization occurred via loss of an ancestral heterochromatin-localizing domain, followed by alterations that rewired its protein interaction network and led to species-specific centromere localization. Our evolutionary cell biology approach provides temporal and mechanistic detail about how young genes gain essential function. Such innovations may constantly alter the repertoire of centromeric proteins in eukaryotes.
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Affiliation(s)
- Benjamin D Ross
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
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Abstract
Heterochromatin is the enigmatic eukaryotic genome compartment found mostly at telomeres and centromeres. Conventional approaches to sequence assembly and genetic manipulation fail in this highly repetitive, gene-sparse, and recombinationally silent DNA. In contrast, genetic and molecular analyses of euchromatin-encoded proteins that bind, remodel, and propagate heterochromatin have revealed its vital role in numerous cellular and evolutionary processes. Utilizing the 12 sequenced Drosophila genomes, Levine et al1 took a phylogenomic approach to discover new such protein “surrogates” of heterochromatin function and evolution. This paper reported over 20 new members of what was traditionally believed to be a small and static Heterochromatin Protein 1 (HP1) gene family. The newly identified HP1 proteins are structurally diverse, lineage-restricted, and expressed primarily in the male germline. The birth and death of HP1 genes follows a “revolving door” pattern, where new HP1s appear to replace old HP1s. Here, we address alternative evolutionary models that drive this constant innovation.
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Affiliation(s)
- Mia T Levine
- Division of Basic Sciences; Howard Hughes Medical Institute; Fred Hutchinson Cancer Research Center; Seattle, WA USA
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