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Rieder, L. E.

Publications and source records attributed to Rieder, L. E..

11 recordsLinked to original sources

The Drosophila maternal-effect gene abnormal oocyte (ao) does not repress histone gene expression

The abnormal oocyte (ao) gene of Drosophila melanogaster is a maternal-effect lethal gene previously identified as encoding a transcriptional regulator of core histones. However, background genetic mutations in existing ao mutant strains could compromise their utility in manipulating histone levels. To distinguish the true ao phenotype from background effects, we created two new ao reagents: a CRISPR/Cas9-mediated knockout of the ao allele for genetic and molecular analyses and an epitope-tagged ao allele for cytological experiments. Using these reagents, we confirm previous findings that loss of ao causes maternal-effect lethality, which can be rescued by either a decrease in the histone gene copy number or by Y chromosome heterochromatin. Our data indicate that ao genetically interacts with the heterochromatin, as previously suggested. However, contrary to a prior study, we find neither Ao localization to histone genes nor ao repression of core histone transcript levels. Thus, the molecular basis for ao-associated maternal-effect lethality remains unknown. Article SummaryA series of foundational papers established that abnormal oocyte (ao), a euchromatic maternal-effect lethal gene, interacts with heterochromatin and the histone multigene cluster to dictate embryonic viability in D. melanogaster. An earlier report argued that ao encodes a protein that localizes to and represses histone gene expression, thereby connecting histone gene overexpression with ao mutant maternal-effect lethality. Using new reagents for genetics and cytology, we recapitulate findings that ao encodes a maternal-effect lethal gene, whose loss is ameliorated by excess heterochromatin or loss of histone genes. However, we find that ao does not affect histone gene expression. Thus, how ao loss causes maternal-effect lethality remains unknown.

genetics↗

Cis element length variability does not confer differential transcription factor occupancy at the D. melanogaster histone locus

Histone genes require precise regulation to maintain histone homeostasis and ensure nucleosome stoichiometry. Animal histone genes often have unique clustered genomic organization. However, there is variability of histone gene number and organization as well as differential regulation of the histone genes across species. The Drosophila melanogaster histone locus has unique organizational characteristics as it exists as a series of [~]100 highly regular, tandemly repeated arrays of the 5 replication-dependent histone genes at a single locus. Yet D. melanogaster are viable with only 12 transgenic histone gene arrays. We hypothesized that the histone genes across the locus are differentially regulated. We discovered that the GA-repeat within the H3/H4 promoter is the only variable sequence across the histone gene arrays. The H3/H4 promoter GA-repeat is targeted by CLAMP to promote histone gene expression. We also show two additional GA-binding transcription factors, GAGA Factor and Pipsqueak, target the GA-repeat. When we further examined CLAMP and GAF targeting, we determined that neither CLAMP nor GAF show bias for any GA-repeat lengths. Furthermore, we found that the distribution of GA-repeats targeted by both CLAMP and GAF do not change throughout early development. Together our results suggest that the transcription factors targeting the H3/H4 GA-repeat do not impact differential regulation of the histone genes, but indicate that future studies should interrogate additional cis elements or factors that impact histone gene regulation.

genetics↗

Zelda is dispensable for Drosophila melanogaster histone gene regulation

To ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The pioneer factors Zelda and CLAMP collaborate at a subset of genes to regulate zygotic genome activation in Drosophila melanogaster and target early activated genes to induce transcription. CLAMP also regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis. The relationship between Zelda and CLAMP led us to hypothesize that Zelda helps identify histone genes for early embryonic expression. We found that Zelda targets the histone locus early during embryogenesis, prior to histone gene expression. However, depletion of zelda in the early embryo does not affect histone mRNA levels or histone locus body formation. While surprising, these results concur with other investigations into Zeldas role in the early embryo, suggesting the earliest factors responsible for specifying the zygotic histone genes remain undiscovered.

genetics↗

Sequence reliance of a Drosophila context-dependent transcription factor

Despite binding similar cis elements in multiple locations, a single transcription factor often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent transcription factor CLAMP targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, loci-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.

genetics↗

A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes

ObjectivesInvestigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF. ResultsWe developed a hybrid RNA FISH and IF protocol for use on Drosophila melanogaster polytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi-sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level in Drosophila melanogaster polytene chromosomes.

genetics↗

A bioinformatics screen reveals Hox and chromatin remodeling factors at the Drosophila histone locus

Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.

molecular biology↗

MSL2 targets histone genes in Drosophila virilis

Histone genes are amongst the most evolutionary conserved in eukaryotic genomes, yet cis-regulatory mechanisms of histone gene regulation differ considerably amongst species. In Drosophila melanogaster, an interaction between GA-rich cis elements in the H3/H4 promoter and the GA-binding transcription factor CLAMP is important for promoting histone gene regulation and factor recruitment to the locus. CLAMP also participates in male dosage compensation by recruiting the Male Specific Lethal Complex (MSLc) to the X-chromosome. We discovered that the male-specific protein of MSLc, MSL2, is recruited to the autosomal major histone locus in D. virilis but not to the minor locus or to the single histone locus in other species. While the histone coding sequences are well conserved between species, the critical GA-rich cis elements in the H3/H4 promoter are poorly conserved between D. melanogaster and D. virilis. We show that CLAMP still targets the two D. virilis histone loci in vivo. Further, CLAMP interacts with the D. virilis H3/H4 promoter in vitro, even when the poorly-conserved GA-rich cis elements are deleted, indicating that the protein interacts differently with the D. virilis promoter than it does with the D. melanogaster promoter. Since CLAMP and MSL2 directly interact in D. melanogaster, we propose that D. virilis CLAMP recruits MSL2 to an ectopic autosomal site through interaction with X-like cis elements. Further, localization of MSL2 to one of the D. virilis histone loci suggests that the loci are regulated differently and that males and females have different requirements for histone gene regulation.

genetics↗

A cost-free CURE: Using bioinformatics to identify DNA-binding factors at a specific genomic locus

Research experiences provide diverse benefits for undergraduates. Many academic institutions have adopted course-based undergraduate research experiences (CUREs) to improve student access to research opportunities. However, potential instructors of a CURE might still face financial or practical hurdles that prevent implementation. Bioinformatics research offers an alternative that is free, safe, compatible with remote learning, and may be more accessible for students with disabilities. Here, we describe a bioinformatics CURE that leverages publicly available datasets to discover novel proteins that target an instructor-determined genomic locus of interest. We use the free, user-friendly bioinformatics platform Galaxy to map ChIP-seq datasets to a genome, which removes the computing burden from students. Both faculty and students directly benefit from this CURE, as faculty can perform candidate screens and publish CURE results. Students gain not only basic bioinformatics knowledge, but also transferable skills, including scientific communication, database navigation, and primary literature experience. The CURE is flexible and can be expanded to analyze different types of high-throughput data or to investigate different genomic loci in any species.

scientific communication and education↗

Max is likely not at the Drosophila histone locus

The histone locus body (HLB) is a conserved nuclear body that regulates histone mRNA production in metazoans. While some HLB components are known, there are likely uncharacterized factors that target the histone locus. We identified the Drosophila melanogaster protein Max, which interacts with known HLB member Myc, as an HLB candidate. We mapped Max ChIP-seq and ChIP-nexus datasets, which revealed encouraging signal over the histone gene array. However, we discovered that Max does not colocalize with HLB components on polytene chromosomes. Therefore, we conclude that Max is likely not at the D. melanogaster histone locus.

genetics↗

Drosophila Histone Locus Body assembly and function involves multiple interactions

The histone locus body (HLB) assembles at replication-dependent (RD) histone loci and concentrates factors required for RD histone mRNA biosynthesis. The D. melanogaster genome has a single locus comprised of [~]100 copies of a tandemly arrayed repeat unit containing one copy of each of the 5 RD histone genes. To determine sequence elements required for D. melanogaster HLB formation and histone gene expression, we used transgenic gene arrays containing 12 copies of the histone repeat unit that functionally complement loss of the [~]200 endogenous RD histone genes. A 12x histone gene array in which all H3-H4 promoters were replaced with H2a-H2b promoters does not form an HLB or express high levels of RD histone mRNA in the presence of the endogenous histone genes. In contrast, this same transgenic array is active in HLB assembly and RD histone gene expression in the absence of the endogenous RD histone genes and rescues the lethality caused by homozygous deletion of the RD histone locus. The HLB formed in the absence of endogenous RD histone genes on the mutant 12x array contains all known factors present in the wild type HLB including CLAMP, which normally binds to GAGA repeats in the H3-H4 promoter. These data suggest that multiple protein-protein and/or protein-DNA interactions contribute to HLB formation, and that the large number of endogenous RD histone gene copies sequester available factor(s) from attenuated transgenic arrays, thereby preventing HLB formation and gene expression.

cell biology↗

Targeting of the dosage-compensated male X-chromosome during early Drosophila development

The essential process of dosage compensation, which corrects for the imbalance in X-linked gene expression between XX females and XY males, represents a key model for how genes are targeted for coordinated regulation. However, the mechanism by which dosage compensation complexes identify the X-chromosome during early development remained unknown because of the difficulty of sexing embryos prior to zygotic transcription. We used meiotic drive to sex Drosophila embryos prior to zygotic transcription and ChIP-seq to measure dynamics of dosage compensation factor targeting. The Drosophila Male-Specific Lethal dosage compensation complex (MSLc) requires the ubiquitous zinc-finger protein Chromatin-Linked Adaptor for MSL Proteins (CLAMP) to identify the X-chromosome. We observe a multi-stage process in which MSLc first identifies CLAMP binding sites throughout the genome followed by concentration at the strongest X-linked MSLc sites. We provide insight into the dynamic mechanism by which a large transcription complex identifies its binding sites during early development.

developmental biology↗