FlyBase at 25: looking to the future

Gramates, L. Sian; Marygold, Steven J; Santos, Gilberto dos; Urbano, Jose-Maria; Antonazzo, Giulia; Matthews, Beverley; Rey, Alix J.; Tabone, Christopher J.; Crosby, Madeline A.; Emmert, David B.; Falls, Kathleen; Goodman, Joshua L.; Hu, Yanhui; Ponting, Laura; Schroeder, Andrew J.; Strelets, Victor B.; Thurmond, Jim; Zhou, Pinglei

doi:10.1093/nar/gkw1016

Cited by 556 publications

(593 citation statements)

References 38 publications

(36 reference statements)

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“…Drosophila HP1a protein amino acid sequence was obtained from FlyBase 33 . Disorder was predicted using Predictor of Natural Disorder Regions (PONDR) version VL-XT 34 .…”

Section: Methodsmentioning

confidence: 99%

Phase separation drives heterochromatin domain formation

Strom

Emelyanov

Mir

et al. 2017

Nature

1,525

1,431

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Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability1, and silencing of transposon and gene expression2. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA3. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments4. We show that Drosophila HP1a protein undergoes liquid–liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

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“…Drosophila HP1a protein amino acid sequence was obtained from FlyBase 33 . Disorder was predicted using Predictor of Natural Disorder Regions (PONDR) version VL-XT 34 .…”

Section: Methodsmentioning

confidence: 99%

Phase separation drives heterochromatin domain formation

Strom

Emelyanov

Mir

et al. 2017

Nature

1,525

1,431

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“…Potential SoxN binding sites were identified by entering target gene sequences from FlyBase (Gramates et al, 2017) into Find Individual Motif Occurrences (FIMO) (Grant et al, 2011). The SoxN motif was downloaded from the TRANSFAC database, generated from HT-SELEX data (Nitta et al, 2015).…”

Section: Binding Site Predictionmentioning

confidence: 99%

SoxNeuro and shavenbaby act cooperatively to shape denticles in the embryonic epidermis of Drosophila

Rizzo

Bejsovec

2017

Development

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During development, extracellular signals are integrated by cells to induce the transcriptional circuitry that controls morphogenesis. In the fly epidermis, Wingless (Wg)/Wnt signaling directs cells to produce either a distinctly shaped denticle or no denticle, resulting in a segmental pattern of denticle belts separated by smooth, or 'naked', cuticle. Naked cuticle results from Wg repression of shavenbaby (svb), which encodes a transcription factor required for denticle construction. We have discovered that although the svb promoter responds differentially to altered Wg levels, Svb alone cannot produce the morphological diversity of denticles found in wild-type belts. Instead, a second Wg-responsive transcription factor, SoxNeuro (SoxN), cooperates with Svb to shape the denticles. Coexpressing ectopic SoxN with svb rescued diverse denticle morphologies. Conversely, removing SoxN activity eliminated the residual denticles found in svb mutant embryos. Furthermore, several known Svb target genes are also activated by SoxN, and we have discovered two novel target genes of SoxN that are expressed in denticle-producing cells and that are regulated independently of Svb. We conclude that proper denticle morphogenesis requires transcriptional regulation by both SoxN and Svb.

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“…RNA Seq data indicates that its transcript is limited to males, and begins at the early pupal stages [24], consistent with the timing of sperm production [25]. ClustalW alignment shows that Vrs is evolutionarily conserved between Drosophila species and some other Diptera (Figure 3), thus the protein evolved before the divergence of Drosophila from other Diptera.…”

Section: Vrs Is a Spermatid Protein Important For Embryonic Chromosommentioning

confidence: 67%

Versager is expressed at the histone-to-protamine transition during spermiogenesis and is required for embryonic chromosome transmission in Drosophila melanogaster

Binder¹,

Wakimoto²,

Davis³

et al. 2017

Res J Dev Biol

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Background: Chromatin remodeling is one of the most intriguing features of spermiogenesis, during which nuclei undergo drastic morphological changes leading to extensive chromatin compaction. Genetic and cytological accessibility make Drosophila melanogaster a powerful model to study this process. In fruit flies, paternal histones are largely replaced with sperm specific nuclear basic proteins in a highly coordinated manner. This remodeling is essential not only for sperm function but also for proper behavior of paternal chromosomes in the embryo. Our understanding of the changes associated with sperm chromatin and their role in embryonic chromosome behavior is incomplete, and will depend on the identification and characterization of additional components. One such newly identified gene, versager (vrs), is described here. Methods: Chromosome transmission was genetically monitored from vrs Z2566 males using chromosomespecific visible mutations. Recombination and deletion mapping was used to localize the mutation, and DNA sequencing was used to identify the causative lesion. Both in vivo RNAi expression knockdown and rescue by transgene expression of EGFP-tagged protein were used to verify the gene identity. The developmental expression pattern of Vrs was defined based on the EGFP signal in testis relative to RFP-tagged H2Av expression. Behavior of DAPI-stained chromosomes in early embryos from vrs Z2566 males was examined using confocal microscopy. Results: Genetic observations indicated that vrsZ2566 is required in males for high fidelity transmission of paternally derived chromosomes. DNA sequencing revealed that the vrs Z2566 mutation is a missense mutation in Celera predicted gene CG5538 and results in a D2V amino acid substitution. This residue was found to be conserved in Drosophila species and related Diptera. RNAi knockdown of vrs resulted in paternal-effect chromosome loss, and a vrs + -EGFP transgene fully rescued the mutant phenotype. Confocal microscopy of testis revealed nuclear localization of Vrs-EGFP specifically at the canoe stage of spermiogenesis, overlapping with the time of removal of H2Av-RFP at the histone-to-protamine transition. Examination of early stage embryos revealed micronuclei, isolated chromosomes and bridges indicative of chromosome loss events during the first three divisions. Approximately a quarter of later stage embryos arrested with an abnormal number of metaphase and fragmented nuclei. Conclusions: A novel sperm-specific paternal-effect gene, vrs, was identified that is expressed at the histone-to-protamine transition and is important for embryonic chromosome behavior and development. The histone-to-protamine transition may be a developmental period sensitive to perturbations that may lead to embryonic mitotic errors, aneuploidy and developmental arrest.

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FlyBase at 25: looking to the future

Cited by 556 publications

References 38 publications

Phase separation drives heterochromatin domain formation

Phase separation drives heterochromatin domain formation

SoxNeuro and shavenbaby act cooperatively to shape denticles in the embryonic epidermis of Drosophila

Versager is expressed at the histone-to-protamine transition during spermiogenesis and is required for embryonic chromosome transmission in Drosophila melanogaster

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