A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster

Marsano, Renè Massimiliano; Giordano, Elena; Messina, Giovanni; Dimitri, Patrizio

doi:10.1016/j.tig.2019.06.002

Cited by 50 publications

(56 citation statements)

References 110 publications

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“…TEs turned out to be an important source of promoters also in the heterochromatin. Heterochromatic genes are regularly transcribed in Drosophila [86] and their promoters have peculiar structural and functional features compared to euchromatic gene promoters [87]. As proposed by Yasuhara et al [87] "an attractive possibility is an acquisition of TE-derived promoters given the predominance of TE-like sequences in heterochromatin and the finding that some TE promoters are transcribed in heterochromatin".…”

Section: Tes As Promoter Suppliersmentioning

confidence: 99%

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Moschetti

Palazzo

Lorusso

et al. 2020

Biology

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Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.

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Section: Tes As Promoter Suppliersmentioning

confidence: 99%

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Moschetti

Palazzo

Lorusso

et al. 2020

Biology

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“…For the activating modifications, we find H3K27ac near the TSS, H3K4me3 near the TSS, and H3K36me3 along the gene body. Both repressive modifications show less localized enrichment patterns, which may be because we are examining genes, and not pericentric and repetitive regions which are typically heterochromatic (reviewed in 59). We do find that H3K9me3 has pronounced depletion at the TSS of some genes at the 1-day time point, which is unique compared to other stages examined here.…”

Section: Resultsmentioning

confidence: 99%

Analysis of cell-type-specific chromatin modifications and gene expression inDrosophilaneurons that direct reproductive behavior

Palmateer

Moseley

Ray

et al. 2020

Preprint

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Examining the role of chromatin modifications and gene expression in neurons is critical for understanding how the potential for behaviors are established and maintained. We investigate this question by examining Drosophila melanogaster fru P1 neurons that underlie reproductive behaviors in both sexes. We developed a method to purify cell-type-specific chromatin (Chromatag), using a tagged histone H2B variant that is expressed using the versatile Gal4/UAS gene expression system. Here, we use Chromatag to evaluate five chromatin modifications, at three life stages in both sexes. We find substantial changes in chromatin modification profiles across development and fewer differences between males and females. We generated cell-type-specific RNA-seq data sets, using translating ribosome affinity purification (TRAP), and identify actively translated genes in fru P1 neurons, revealing novel stage- and sex-differences in gene expression. We compare chromatin modifications to the gene expression data and find patterns of chromatin modifications associated with gene expression. An examination of the genic features where chromatin modifications resides shows certain chromatin modifications are maintained in the same genes across development, whereas others are more dynamic, which may point to modifications important for cell fate determination in neurons. Using a computational analysis to identify super-enhancer-containing genes we discovered differences across development, and between the sexes that are cell-type-specific. A set of super-enhancer-containing genes that overlapped with those determined to be expressed with the TRAP approach were validated as expressed in fru P1 neurons.Author SummaryDifferences in male and female reproductive behaviors are pervasive in nature and important for species propagation. Studies of sex differences in the fruit fly, Drosophila melanogaster, have been ongoing since the early 1900s, with many of the critical molecular and neural circuit determinates that create sexually dimorphic behavior identified. This system is a powerful model to understand fundamental principles about the underpinnings of complex behavior at high resolution. In this study, we examine the gene expression and chromatin modification differences specifically in a set of neurons that direct male and female reproductive behaviors in Drosophila. We describe differences across development and between the sexes with the goal of understanding how the potential for behavior is created and maintained.

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“…Furthermore, some essential genes are located in heterochromatin and are transcribed [ 71 ]. It thus appears that heterochromatin constitute only a distinct chromatin compartment in which some proteins remain, whereas the others either do not enter it or are not retained.…”

Section: 3d Genomementioning

confidence: 99%

Divide and Rule: Phase Separation in Eukaryotic Genome Functioning

Razin

Ulianov

2020

Cells

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The functioning of a cell at various organizational levels is determined by the interactions between macromolecules that promote cellular organelle formation and orchestrate metabolic pathways via the control of enzymatic activities. Although highly specific and relatively stable protein-protein, protein-DNA, and protein-RNA interactions are traditionally suggested as the drivers for cellular function realization, recent advances in the discovery of weak multivalent interactions have uncovered the role of so-called macromolecule condensates. These structures, which are highly divergent in size, composition, function, and cellular localization are predominantly formed by liquid-liquid phase separation (LLPS): a physical-chemical process where an initially homogenous solution turns into two distinct phases, one of which contains the major portion of the dissolved macromolecules and the other one containing the solvent. In a living cell, LLPS drives the formation of membrane-less organelles such as the nucleolus, nuclear bodies, and viral replication factories and facilitates the assembly of complex macromolecule aggregates possessing regulatory, structural, and enzymatic functions. Here, we discuss the role of LLPS in the spatial organization of eukaryotic chromatin and regulation of gene expression in normal and pathological conditions.

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A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster

Cited by 50 publications

References 110 publications

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Analysis of cell-type-specific chromatin modifications and gene expression inDrosophilaneurons that direct reproductive behavior

Divide and Rule: Phase Separation in Eukaryotic Genome Functioning

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