Identification and analysis of mouse non-coding RNA using transcriptome data

Zhao, Yuhui; Liu, Wanfei; Zeng, Jingyao; Liu, Shoucheng; Tan, Xinyu; Aljohi, Hasanawad; Hu, Songnian

doi:10.1007/s11427-015-4929-x

Cited by 9 publications

(6 citation statements)

References 66 publications

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“…The expression of mouse lncRNAs has been investigated in several tissues like brain, liver, heart, and testes, and the expression profiles could be retrieved from NONCODE database and the work of Zhao et al [33, 34]. Comparative analysis revealed that a total of 122 lincRNAs (13%), transcribed from 112 potential gene loci, were only found in mouse retinas.…”

Section: Resultsmentioning

confidence: 99%

“…The lincRNAs were then picked out by comparing the genomic location to known genes by cuffcompare (Cufflinks package, v2.2.1) [32]. Cuffcompare was also used to compare the locations and structures of lincRNAs identified in this work to previous annotation [21, 33, 34]. Notably, for lncRNAs deposited in NONCODE, their expression in particular tissues were accepted only when the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) > 0.01.…”

Section: Methodsmentioning

confidence: 99%

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Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing

et al. 2019

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Background A great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, the biological roles of lncRNAs in the mouse retina remains largely unknown due to the lack of a comprehensive annotation of lncRNAs expressed in the retina. Results In this study, we applied the long-reads sequencing strategy to unravel the transcriptomes of developing mouse retinas and identified a total of 940 intergenic lncRNAs (lincRNAs) in embryonic and neonatal retinas, including about 13% of them were transcribed from unannotated gene loci. Subsequent analysis revealed that function of lincRNAs expressed in mouse retinas were closely related to the physiological roles of this tissue, including 90 lincRNAs that were differentially expressed after the functional loss of key regulators of retinal ganglion cell (RGC) differentiation. In situ hybridization results demonstrated the enrichment of three class IV POU-homeobox genes adjacent lincRNAs ( linc-3a , linc-3b and linc-3c ) in ganglion cell layer and indicated they were potentially RGC-specific. Conclusions In summary, this study systematically annotated the lincRNAs expressed in embryonic and neonatal mouse retinas and implied their crucial regulatory roles in retinal development such as RGC differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5903-y) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing

et al. 2019

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“…RNA‐Seq has been used extensively in biological analyses (Fu et al, ; Gershoni & Pietrokovski, ; Moore et al, ; Ren et al, ; Schumacher et al, ; Zhao et al, ). In this study, we used RNA‐Seq to analyse changes in the testes of roosters exposed to different photoperiods at the transcriptional level.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, RNA sequencing (RNA‐Seq) has been used to study the transcriptional regulation mechanisms in many species, such as human, pig, cow, goat, mouse and rat (Fu et al, ; Gershoni & Pietrokovski, ; Moore, McCabe, Green, Newsom, & Lucy, ; Ren et al, ; Schumacher, Gotze, Kordes, Benes, & Haussinger, ; Zhao et al, ). This approach has identified genes involved in differential regulation.…”

Section: Introductionmentioning

confidence: 99%

Photoperiodic effect on the testicular transcriptome in broiler roosters

Sun

Wang

et al. 2020

Animal Physiology Nutrition

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Information about the effects of photoperiod on the testicular transcriptome of broiler roosters is limited. The aim of the present study was to explore the effect of different photoperiodic regimes on gene expression in the testes of broiler breeder roosters. One hundred and twenty Arbor Acres broiler breeder roosters aged 20 weeks were assigned to one of three groups (n = 40) and subjected to different photoperiodic regimes: control (CTR; 12.5 L:11.5 D), short day (SD; 8 L:16 D) and long day (LD; 16 L:8 D). After 4 weeks, the testes of 10 randomly selected birds from each group were dissected, sliced and haematoxylin-eosin stained. The testicular transcriptome of roosters from the SD and LD groups was determined by RNA sequencing (RNA-Seq), and the results were confirmed using quantitative real-time PCR. The seminiferous tubule area and sperm count increased significantly with the prolongation of photoperiod (p < .01). Additionally, the RNA-Seq results indicated that 387 genes were upregulated and 1,052 genes were downregulated in the LD group compared with those in the SD group. Several crucial genes involved in rooster testicular development and reproduction were also screened, including heat shock proteins 90, extracellular regulated protein kinases 1, phosphatidylinositol 3-kinase, adenosine 5'-monophosphate -activated protein kinase, BCL-6 and Smad3. The differentially expressed genes were enriched in the mammalian targets of rapamycin (mTOR), forkhead box (FoxO), transforming growth factor beta (TGF-β) and insulin signalling pathway. In conclusion, a 16 hr photoperiod for 4 weeks increased the seminiferous tubule duct area and promoted spermatogenesis in the rooster's testicles, and the mTOR, FoxO, TGF-β and insulin signalling pathways may be involved. K E Y W O R D S photoperiod, RNA-seq, rooster, testicular development S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Sun L, Guo L, Wang J, et al. Photoperiodic effect on the testicular transcriptome in broiler roosters.

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“…Dramatic changes in the expression of coding genes, ncRNAs, pseudogenes, and splice isoforms are seen during the transition from pluripotent stem cells to early differentiating neurons and several lncRNAs undergo dramatic expression changes suggesting important roles for ncRNAs in neurogenesis (Hjelm et al 2013;Lin et al 2011). Distinct ncRNA expression signatures are retrieved from different cell types indicating that ncRNA signatures can represent and resolve a particular phenotype (Godoy et al 2018;Isakova et al 2020;Zhao et al 2016). However, cell specific ncRNA signatures are still in their infancy and temporal developmental dependencies of cell-type specific markers derived from single cell and bulk RNA sequencing studies are under-investigated or even missing for ncRNA species other than miRNAs.…”

Section: Introductionmentioning

confidence: 99%

NOCICEPTRA2.0 - a comprehensive ncRNA atlas of human native and iPSC-derived sensory neurons

Zeidler

Tavares‐Ferreira

Brougher

et al. 2023

Preprint

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Non-coding RNAs (ncRNAs) play a critical role in regulating gene expression during development and in the pathogenesis of diseases. In particular, microRNAs have been extensively studied in the context of neurogenesis, the differentiation of pain sensing nociceptive neurons and the pathogenesis of pain disorder, however, little is known about the developmental signatures of other ncRNA species throughout sensory neuron differentiation. Moreover, there is currently no information available about the general expression signatures of ncRNAs in human dorsal root ganglia (DRGs) harboring the cell bodies of primary afferent nociceptors. To bridge this knowledge gap, we developed a comprehensive atlas of small ncRNA species signatures during the differentiation of human induced pluripotent stem cell (iPSC)-derived nociceptive neurons. By employing a combination of iPSC-derived sensory neuron and human DRG long and short RNA co-sequencing, we identified specific signatures that describe the developmental processes and the sig-natures of all currently known small ncRNA species in detail. Our analysis revealed that different ncRNA species, including tRNAs, snoRNAs, lncRNAs, and piRNAs, are associated with different stages of sensory neuron differentiation and maturation. We retrieved pro-nounced similarities in ncRNA expression between human DRG and late-stage iPSC-derived sensory neurons, which further supports the use of iPSC-derived sensory neurons to uncover functional and regulatory changes in ncRNAs and their suitability as a as a human model system to bridge the transla-tional gap between preclinical findings mostly from rodent models and our understanding of human disorders for the development of mechanism-based treatments. In summary, our findings provide important insights into the role of ncRNA species other than microRNAs in human nociceptors. The updated NOCICEPTRA2.0 Tool will be the first fully comprehensive searchable ncRNA database for human sensory neurons enabling researchers to investigate important hub ncRNA regulators in nociceptors in full detail.

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Identification and analysis of mouse non-coding RNA using transcriptome data

Cited by 9 publications

References 66 publications

Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing

Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing

Photoperiodic effect on the testicular transcriptome in broiler roosters

NOCICEPTRA2.0 - a comprehensive ncRNA atlas of human native and iPSC-derived sensory neurons

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