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MAPCap enables high-resolution detection and differential expression analysis of transcription start sites

ABSTRACT: Promoter architecture, shape and usage play an important role in the regulation of eukaryotic gene expression. Several promoter profiling techniques have been developed to detect transcription start sites and alternative promoter usage between tissues or during development. However promoter profiling has not been utilized in studies that demand quantification of expression changes between developmental stages, tissues and conditions. In this study, we combine promoter profiling and differential expression analysis in a single setup, using a fast and simple protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with a new software “icetea” (https://bioconductor.org/packages/icetea). The use of random molecular barcodes and spike-ins in MAPCap enables accurate quantification of expression from promoters. We detected sex-specific promoter usage in the brains of Drosophila melanogaster larvae. Comparison of male and female mutant flies of the male-less helicase (MLE), a protein known to be essential for the dosage compensation of the male X-chromosome, indicated that the sensitivity of promoters to dosage compensation depends on their genomic location. Our results expand the scope of promoter profiling methods to differential expression analysis and provide quantitative insights into promoter usage during dosage compensation.

ORGANISM(S): Mus musculus Drosophila melanogaster

PROVIDER: GSE125831 | GEO | 2019/06/04

REPOSITORIES: GEO

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A mutually exclusive stem loop arrangement in roX2 RNA is essential for X chromosome regulation in Drosophila

Project description:The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX lncRNAs harbor several redundant domains to interact with the ubiquitin ligase MSL2 and the RNA helicase MLE for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By employing the uvCLAP methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild type and various MLE mutant derivatives including a catalytic inactive MLE derivative MLEGET we show that the minimal roX RNA contains two mutually exclusive stem-loops which exist in a peculiar structural arrangement: when one stem-loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.

2017-10-01 | GSE87792 | GEO

The interaction of MLE with CLAMP zinc finger domains is important for dosage compensation in Drosophila melanogaster

Project description:The Drosophila male-specific lethal (MSL) complex binds to the male X chromosome to activate transcription, and consists of five proteins, MSL1, MSL2, MSL3, MOF, MLE, and two roX RNAs. The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. MSL2 is expressed only in males and interacts with the N-terminal zinc-finger of the transcription factor CLAMP that is important for specific recruitment of the MSL complex on the male X chromosome. Here we found that the unstructured C-terminal region of MLE interacts with 6-7 zinc-finger domains of CLAMP. In vitro 4-5 zinc fingers are critical for specific DNA-binding of CLAMP with GA-repeats, which constitute the core motif at the high affinity binding sites for MSL proteins. Deletion of the Clamp Binding Domain (CBD) in MLE results in decreasing of MSL proteins association with male X chromosome and increasing of male lethality. These results suggest that interactions of unstructured regions in MSL2 and MLE with CLAMP zinc finger domains are important for the specific recruitment of the MSL complex on the male X chromosome.

2024-03-20 | GSE239354 | GEO

Mapping of MLE and MSL2 using iCLIP

Project description:Dosage compensation in Drosophila is an epigenetic phenomenon utilizing proteins and long non-coding RNAs (lncRNAs) for transcriptional up-regulation of the entire X-chromosome. Here, UV cross-linking followed by deep sequencing (iCLIP) show that two enzymes in the Male-Specific Lethal complex, MLE RNA helicase and MSL2 ubiquitin ligase, bind evolutionarily conserved domains containing tandem stem-loops in roX1 and roX2 RNAs in vivo.

2013-07-18 | E-MTAB-1669 | biostudies-arrayexpress

Genome-wide analysis of distribution of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early female embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT)

Project description:Transcription factor CLAMP associates with RNA helicase, Maleless MLE as part of Male-specific MSL complex in males, which regulates dosage compensation in males. Both CLAMP and MLE are maternally deposited proteins (protein expression detectd in 0- Hr embryo, before zygotic genome activation) and MLE is also a conserved component of spliceosome. Moreover, CLAMP too associates with many other RNA binding protein compoments of spliceosomes. Both these proteins are well expressed in females, but apart from that might influence splicing in females, not much is known if they have any female-specific function. Furthermore, whether they regulate each other's function in females is not known as well, especially before zygotic genome activation starts, in a pre-MZT embryo (0-2 Hr Embryo). Therefore, we performed CutnRun assay to detrmine MLE binding sites on chromatin in female embryos before (0-2 Hr) and after MZT (2-4 Hr). And then identify, in absence of maternal CLAMP, whether there is change is distribution of control MLE female peaks. We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZT and 2-4 Hr post-MZT embryonic stages in females. CLAMP unlike to males do not affect MLE distribution on chromatin in females.

2023-12-31 | GSE220981 | GEO

Sex-dependent and -independent X-chromosome histone modifications in Drosophila melanogaster

Project description:Drosophila X chromosomes are subject to dosage compensation in males and are known to have a specialized chromatin structure in the male soma. We are interested in how specific chromatin structure change contributes to X chromosome hyperactivity and dosage compensation. We have conducted a global analysis of localize two dosage compensation complex dependent histone marks H4AcK16 and H3PS10 and one dosage compensation complex independent histone mark H3diMeK4 in the genome, especially on X chromosome by ChIP-chip approach in both male and female adult flies. We also probed general genomewide chromatin structure by deep DNA sequencing of sheared ChIP input DNA from male and female adult flies.

2010-01-11 | GSE15593 | GEO

The activation potential of MOF is constrained for dosage compensation

Project description:The H4K16 acetyltransferase MOF plays a crucial role in dosage compensation in Drosophila, but has additional, global functions. We compared the molecular context and effect of MOF in male and female flies combining chromosome-wide mapping and transcriptome studies with analyses of defined reporter loci in transgenic flies. MOF distributes dynamically between two complexes, the Dosage Compensation Complex and a complex containing MBD-R2, a global facilitator of transcription. These different targeting principles define the distribution of MOF between the X chromosome and autosomes and at transcription units with 5’ or 3’ enrichment. The male X chromosome differs from all other chromosomes in that H4K16 acetylation levels do not correlate with transcription output. The reconstitution of this phenomenon at a model locus revealed that the activation potential of MOF is constraint in male cells in the context of the DCC to arrive at the two-fold activation of transcription characteristic of dosage compensation. ChIP-chip profiling of MBD-R2, MOF and MSL1 in adult male and female flies, and SL2 cells, incl. at least 3 biological replicates

2010-06-26 | E-GEOD-20695 | biostudies-arrayexpress

Sex-biased gene expression in 18 day embryonic chicken heart, brain, and gonad

Project description:The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes. In many organisms dosage compensation has thus evolved to equalize sex-linked gene expression in males and females1,2, in mammals achieved by X chromosome inactivation and in flies and worms by up- or down-regulation of X-linked expression, respectively. Another form of dosage compensation ensures that expression levels on the X chromosome and on autosomes are balanced3,4. While otherwise widespread in systems with heteromorphic sex chromosomes, the case of dosage compensation in birds (males ZZ, females ZW) remains an unsolved enigma5,6. Here we use a microarray approach to show that male day 18 chicken embryos generally express higher levels of Z-linked genes than female birds, both in soma and in gonads. The distribution of male-to-female fold-change values for Z chromosome genes is wide and has a mean of 1.4-1.6, which is consistent with absence of dosage compensation and sex-specific feedback regulation of gene expression at individual loci2. Intriguingly, without global dosage compensation, female chicken has significantly lower expression levels of Z-linked compared to autosomal genes, which is not the case in male birds. The pronounced sex difference in gene expression is likely to contribute to sexual dimorphism among birds, and potentially has implication to avian sex determination. Keywords: dosage compensation, sex-biased gene expression, soma and gonad

2007-08-07 | GSE8693 | GEO

Mechanism of selective incorporation of lncRNA into a chromatin modifier

Project description:The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we designed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-rich sequences and tandem stem-loop structures. In vitro, the helicase binds and remodels many RNAs beyond its main target, roX2. Unwinding of roX2 by the helicase triggers their selective association with the DCC, via the MSL2 subunit. Whereas the core DCC alone does not show intrinsic RNA binding specificity, the presentation of remodeled roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of MSL2. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.

2020-05-27 | GSE143455 | GEO

The sex-specific factor SOA establishes X chromosome dosage compensation in Anopheles mosquitos

Project description:The Anopheles mosquito is one of thousands of species in which sex differences play a central role in their biology, as only females need a blood meal in order to produce eggs. Sex differentiation is regulated by sex chromosomes, but their presence creates a dosage imbalance between males (XY) and females (XX). Dosage compensation (DC) can re-equilibrate the expression of sex-chromosomal genes, but because the molecular mechanisms providing DC have only been studied in a few model organisms, key questions about its evolutionary diversity and functional necessity remain unresolved. Here, we reveal the DC pathway in the malaria mosquito Anopheles gambiae. We identified SOA, a previously uncharacterized gene, whose expression is sufficient to induce a global upregulation of X-linked genes. Sex-specific alternative splicing prevents the production of a functional SOA protein in females. The male SOA isoform encodes a DNA-binding protein that recognizes the promoters of X chromosomal genes through a CA repeat sequence. Male mosquitos lacking SOA exhibit a chromosome-wide downregulation of the X, which is compatible with viability, but causes a developmental delay. Thus, our molecular analysis of the first DC master regulator in a non-model organism elucidates the evolutionary steps leading to the establishment of a chromosome-specific fine-tuning mechanism.

2023-07-13 | PXD042353 | Pride

Chromatin proteins linked to dosage compensation in Drosophila captured by ChIP-mass spectrometry

Project description:We report the usage of ChIP-mass spectrometry in identifying proteins and histone modifications involved in Drosophila dosage compensation. We identified a chromatin targeting factor, CG4747, that is involved in recognition of H3K36me3 and robust recruitment of the Drosophila MSL complex to its correct targets on the male X chromosome.

2012-11-06 | GSE42025 | GEO

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