Pleiotropic Fitness Effects of the LncRNA Uhg4 in Drosophila Melanogaster

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2022 Nov 30

PMID 36451091

Authors

Rebecca A MacPherson

Vijay Shankar

Lakshmi T Sunkara

Rachel C Hannah

Marion R Campbell 3rd

Robert R H Anholt

Trudy F C Mackay

Affiliations

Soon will be listed here.

Abstract

Background: 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 development, stress response, and cancer. However, the functions of many lncRNAs remain 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 tissues, with maximal expression in ovaries; however, it has no annotated function(s).

Results: We used CRISPR-Cas9 germline gene editing to generate multiple deletions spanning the promoter region and first exon of Uhg4. Females showed arrested egg development and both males and females were sterile. In addition, Uhg4 deletion mutants 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 co-regulated genes and genetic interaction networks associated with Uhg4. Gene ontology analyses highlighted a broad spectrum of biological processes, including regulation of transcription and translation, morphogenesis, and stress response.

Conclusion: Uhg4 is a lncRNA essential for reproduction with pleiotropic effects on multiple fitness traits.

References

Cichewicz K, Hirsh J . ShinyR-DAM: a program analyzing Drosophila activity, sleep and circadian rhythms. Commun Biol. 2018; 1:25. PMC: 6002956. DOI: 10.1038/s42003-018-0031-9. View

Kufel J, Grzechnik P . Small Nucleolar RNAs Tell a Different Tale. Trends Genet. 2018; 35(2):104-117. DOI: 10.1016/j.tig.2018.11.005. View

Rom A, Melamed L, Gil N, Goldrich M, Kadir R, Golan M . Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability. Nat Commun. 2019; 10(1):5092. PMC: 6841665. DOI: 10.1038/s41467-019-13075-8. View

Goudarzi M, Berg K, Pieper L, Schier A . Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility. Elife. 2019; 8. PMC: 6347452. DOI: 10.7554/eLife.40815. View

Li C, Shen C, Shang X, Tang L, Xiong W, Ge H . Two novel testis-specific long noncoding RNAs produced by are dispensable for male fertility in mice. J Reprod Dev. 2019; 66(1):57-65. PMC: 7040208. DOI: 10.1262/jrd.2019-104. View

Galindo M, Pueyo J, Fouix S, Bishop S, Couso J . Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol. 2007; 5(5):e106. PMC: 1852585. DOI: 10.1371/journal.pbio.0050106. View

Prensner J, Chinnaiyan A . The emergence of lncRNAs in cancer biology. Cancer Discov. 2011; 1(5):391-407. PMC: 3215093. DOI: 10.1158/2159-8290.CD-11-0209. View

Bratkovic T, Bozic J, Rogelj B . Functional diversity of small nucleolar RNAs. Nucleic Acids Res. 2019; 48(4):1627-1651. PMC: 7038934. DOI: 10.1093/nar/gkz1140. View

Jenny A, Hachet O, Zavorszky P, Cyrklaff A, Weston M, St Johnston D . A translation-independent role of oskar RNA in early Drosophila oogenesis. Development. 2006; 133(15):2827-33. DOI: 10.1242/dev.02456. View

10.

Yap K, Mukhina S, Zhang G, Tan J, Ong H, Makeyev E . A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival. Mol Cell. 2018; 72(3):525-540.e13. PMC: 6224606. DOI: 10.1016/j.molcel.2018.08.041. View

11.

Everett L, Huang W, Zhou S, Carbone M, Lyman R, Arya G . Gene expression networks in the Genetic Reference Panel. Genome Res. 2020; 30(3):485-496. PMC: 7111517. DOI: 10.1101/gr.257592.119. View

12.

Clemson C, Hutchinson J, Sara S, Ensminger A, Fox A, Chess A . An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell. 2009; 33(6):717-26. PMC: 2696186. DOI: 10.1016/j.molcel.2009.01.026. View

13.

Maeda R, Sitnik J, Frei Y, Prince E, Gligorov D, Wolfner M . The lncRNA male-specific abdominal plays a critical role in Drosophila accessory gland development and male fertility. PLoS Genet. 2018; 14(7):e1007519. PMC: 6067764. DOI: 10.1371/journal.pgen.1007519. View

14.

Smid M, Coebergh van den Braak R, van de Werken H, van Riet J, van Galen A, de Weerd V . Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons. BMC Bioinformatics. 2018; 19(1):236. PMC: 6013957. DOI: 10.1186/s12859-018-2246-7. View

15.

Soshnev A, Ishimoto H, McAllister B, Li X, Wehling M, Kitamoto T . A conserved long noncoding RNA affects sleep behavior in Drosophila. Genetics. 2011; 189(2):455-68. PMC: 3189806. DOI: 10.1534/genetics.111.131706. View

16.

Zeni P, Mraz M . LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol. 2020; 18(5):619-632. PMC: 8078528. DOI: 10.1080/15476286.2020.1838783. View

17.

Pritykin Y, Brito T, Schupbach T, Singh M, Pane A . Integrative analysis unveils new functions for the Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA. 2017; 23(7):1097-1109. PMC: 5473144. DOI: 10.1261/rna.058594.116. View

18.

Hartford C, Lal A . When Long Noncoding Becomes Protein Coding. Mol Cell Biol. 2020; 40(6). PMC: 7048269. DOI: 10.1128/MCB.00528-19. View

19.

Lykke-Andersen S, Chen Y, Ardal B, Lilje B, Waage J, Sandelin A . Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes. Genes Dev. 2014; 28(22):2498-517. PMC: 4233243. DOI: 10.1101/gad.246538.114. View

20.

Engreitz J, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C . The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013; 341(6147):1237973. PMC: 3778663. DOI: 10.1126/science.1237973. View