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Pleiotropic Fitness Effects of the lncRNA Uhg4 in Drosophila melanogaster

ABSTRACT: Long noncoding RNAs (lncRNAs) are a diverse class of RNAs that are critical for gene regulation, DNA repair and splicing, and have been implicated in cancer, stress response, and development. However, the function of many lncRNAs remains unknown. In Drosophila melanogaster, U snoRNA host gene 4 (Uhg4) encodes an antisense long noncoding RNA that is host to seven small nucleolar RNAs (snoRNAs). Uhg4 is expressed ubiquitously during development and in all adult fly tissues with maximal expression in ovaries; however, it has no annotated function(s). Here, we used CRISPR-Cas9 germline gene editing to generate multiple deletions spanning the promoter region and first exon of Uhg4. Mutant flies were sterile, showed delayed development and decreased viability, and changes in sleep and responses to stress. Whole genome RNA sequencing of Uhg4 deletion flies and their controls identified coregulated genes and genetic interaction networks. Gene ontology analyses highlighted a broad spectrum of biological processes, including morphogenesis, stress response, and regulation of transcription and translation. Thus, Uhg4 is a lncRNA essential for reproduction with pleiotropic effects on multiple fitness traits.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE199865 | GEO | 2022/04/26

REPOSITORIES: GEO

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Project description:Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct flow-sorted B-cell subsets, comprising pre-B1, pre-B2, immature, naive, memory, and plasma cells from bone marrow biopsies (n=7), and naive, centroblast, centrocyte, memory, and plasmablast cells from tonsil tissue samples (n=6), respectively. A remapping strategy was used to assign the array probes to 37630 gene-level probe sets, reflecting the most recent updates in genomic and transcriptomic databases, which enabled expression profiling of 19579 long noncoding RNAs, comprising 3947 antisense RNAs, 5277 lincRNAs, 7625 pseudogenes, and 2730 additional lncRNAs. As a first step towards inferring the functions of the identified lncRNAs in developing B-cells, we analysed their co-expression with well-characterized protein-coding genes, a method known as â??guilt by associationâ??. By using weighted gene co-expression network analysis, we identified 272 lincRNAs, 471 antisense RNAs, 376 pseudogene RNAs, and 64 lncRNAs within seven sub-networks associated with distinct stages of B-cell development, such as early B-cell development, B-cell proliferation, affinity maturation of antibody, and terminal differentiation. These data provide an important resource for future studies on the functions of lncRNAs in development of the adaptive immune response, and the pathogenesis of B-cell malignancies that originate from distinct B-cell subpopulations. Tonsils were collected from six patients (homo sapiens) during routine tonsillectomy. Mononuclear cells were isolated from tonsils and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of naive, centroblasts, centrocytes, menory and plasmablast cells were isolated and a total of 30 gene expression profiles were generated using the HuEx-1_0-st-v2-micro array chip from Affymetrix.

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Pleiotropic Fitness Effects of the lncRNA Uhg4 in Drosophila melanogaster

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