Critical roles of long noncoding RNAs in <i>Drosophila</i> spermatogenesis

Wen, Kejia; Yang, Lijuan; Xiong, Tuanlin; Di, Chao; Ma, Danhui; Wu, Menghua; Xue, Zhaoyu; Zhang, Xuedi; Long, Li; Zhang, Weimin; Zhang, Jiaying; Bi, Xiaolin; Dai, Junbiao; Zhang, Qiangfeng; Lu, Zhi John; Gao, Guanjun

doi:10.1101/gr.199547.115

Cited by 152 publications

(171 citation statements)

References 65 publications

(89 reference statements)

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“…LncRNAs required for spermatogenesis and fertility have been identified in Drosophila 19 . Also, regulatory elements such as enhancers and regulatory non-coding RNAs that are spermatozoa-specific in mammalian species have been identified 20–23 , supporting the possibility that lncRNAs may impact DF in egg-laying hens.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens

Adetula

Nwafor

et al. 2018

Sci Rep

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Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg-laying birds with long- and short-DF (n = 7); and sought to uncover key lncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 lncRNAs including 2576 novel lncRNAs. Differential expression (DE) analysis of lncRNA identified 223 lncRNAs differentially expressed between the two groups. DE-lncRNA target genes prediction uncovered over 200 lncRNA target genes and functional enrichment tests predict a potential function of DE-lncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-lncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of lncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key lncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of lncRNAs regulating DF.

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Section: Introductionmentioning

confidence: 99%

Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens

Adetula

Nwafor

et al. 2018

Sci Rep

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“…However, the length distribution of the ant lncRNAs was similar to that of proteincoding genes (Fig. S8C), which was a departure from what observed in mammals, Drosophila, and C. elegans 23,29,55,56 . As expected, virtually none of the lncRNAs had annotated PFAM domains, in contrast to protein-coding genes ( Fig.…”

Section: Annotation Of Long Non-coding Rnas In Harpegnathos and Campomentioning

confidence: 63%

High-quality genome assemblies uncover caste-specific long non-coding RNAs in ants

Shields

Bonasio

2017

Preprint

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Ants are an emerging model system for neuroepigenetics, as embryos with virtually identical genomes develop into different adult castes that display strikingly different physiology, morphology, and behavior. Although a number of ant genomes have been sequenced to date, their draft quality is an obstacle to sophisticated analyses of epigenetic gene regulation. Using long reads generated with Pacific Biosystem single molecule real time sequencing, we have reassembled de novo high-quality genomes for two ant species: Camponotus floridanus and Harpegnathos saltator. The long reads allowed us to span large repetitive regions and join sequences previously found in separate scaffolds, leading to comprehensive and accurate protein-coding annotations that facilitated the identification of a Gp-9-like gene as differentially expressed in Harpegnathos castes. The new assemblies also enabled us to annotate long noncoding RNAs for the first time in ants, revealing several that were specifically expressed during Harpegnathos development and in the brains of different castes. These upgraded genomes, along with the new coding and non-coding annotations, will aid future efforts to identify epigenetic mechanisms of phenotypic and behavioral plasticity in ants.

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“…It is clear from such studies that the transcriptome levels of lncRNAs are greater than those of mRNAs during spermatogenesis and that the expression of lncRNAs is also dynamically regulated. Mechanistic details of lncRNA function during spermatogenesis have been provided by only a few studies, including our report of the role of mrhl RNA in regulation of Wnt signaling through p68 RNA helicase (27,(44)(45)(46). The present report describes a new dimension in the context of spermatogenesis, with lncRNA regulating the expression of an important transcription factor and such regulation being crucial for meiotic entry or spermatogonial differentiation.…”

Section: Discussionmentioning

confidence: 94%

Mrhl Long Noncoding RNA Mediates Meiotic Commitment of Mouse Spermatogonial Cells by Regulating Sox8 Expression

Kataruka

Akhade

Kayyar

et al. 2017

Molecular and Cellular Biology

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Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, including spermatogenesis. Our previous studies have revealed the regulatory loop of mrhl RNA and Wnt signaling, where mrhl RNA negatively regulates Wnt signaling and gets downregulated upon Wnt signaling activation. This downregulation of mrhl RNA is important for the meiotic progression of spermatogonial cells. In our present study, we identified the transcription factor Sox8 as the regulatory link between mrhl RNA expression, Wnt signaling activation, and meiotic progression. In contrast to reports from other groups, we report the expression of Sox8 in germ cells and describe the molecular mechanism of Sox8 regulation by mrhl RNA during differentiation of spermatogonial cells. Binding of mrhl RNA to the Sox8 promoter is accompanied by the assembly of other regulatory factors involving Myc-Max-Mad transcription factors, corepressor Sin3a, and coactivator Pcaf. In the context of Wnt signaling, Sox8 directly regulates the expression of premeiotic and meiotic markers. Prolonged Wnt signaling activation in spermatogonial cells leads to changes in global chromatin architecture and a decrease in levels of stem cell markers.KEYWORDS Myc-Mad-Max, Sin3A, Sox8, Wnt signaling, mrhl RNA T he complexity of the eukaryotic genome has been attributed to its multifaceted regulatory networks. Over recent years, significant advancements in high-throughput analyses of the transcriptome have demonstrated the abundance of transcripts that do not code for proteins (noncoding RNAs [ncRNAs]). These ncRNAs are broadly classified as small and long noncoding RNAs. The small ncRNAs, such as microRNA (miRNA) and small interfering RNA (siRNA), play important roles in transcriptional and posttranscriptional gene regulation, while Piwi-associated RNAs (piRNAs) are involved in transposon regulation (1, 2). Another class is that of the long noncoding RNAs (lncRNAs), which are of various sizes between 200 bp and several kilobases (3). The role of lncRNAs in a plethora of functions, for example, dosage compensation (Xist and roX) (4, 5), genomic imprinting (Air and Kcnq1ot1) (6, 7), pluripotency (Evx1as and Hoxb5/6as) (8), cell differentiation and development (Fendrr, Bvht, Miat, Hotair, etc.) (9), nuclear architecture (NEAT1) (10), chromosome segregation (Concr) (11), immune response (lincRNA-EPS, EGOT) (12, 13), etc., have been characterized. lncRNAs bring about such copious functions by employment of diverse mechanisms such as translational inhibition (lincRNA-p21) (14), mRNA degradation (1/2-sbs RNAs) (15), RNA decoys (Gas5) (16)

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Critical roles of long noncoding RNAs in Drosophila spermatogenesis

Cited by 152 publications

References 65 publications

Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens

Transcriptome sequencing reveals key potential long non-coding RNAs related to duration of fertility trait in the uterovaginal junction of egg-laying hens

High-quality genome assemblies uncover caste-specific long non-coding RNAs in ants

Mrhl Long Noncoding RNA Mediates Meiotic Commitment of Mouse Spermatogonial Cells by Regulating Sox8 Expression

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