The comprehensive detection of miRNA, lncRNA, and circRNA in regulation of mouse melanocyte and skin development

Zhu, Zhiwei; Ma, Yan; Li, Yuan; Li, Pengfei; Cheng, Zhi-xue; Li, Huifeng; Zhang, Lihuan; Tang, Zhongwei

doi:10.1186/s40659-020-0272-1

Cited by 26 publications

(18 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to protein-coding genes, lncRNAs may also be involved in the skin color variation 32 , 42 . We investigated lncRNA expression across four color skins (Supplementary Table S13 and Fig.…”

Section: Discussionmentioning

confidence: 99%

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Gan

Chung-Davidson

Chen

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.

show abstract

Section: Discussionmentioning

confidence: 99%

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Gan

Chung-Davidson

Chen

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The functional interaction between lncRNA and miRNAs is fundamental during embryonic development in mammals [ 76 , 77 , 78 , 79 ]. The ability of HOTAIR to function as a competitive endogenous RNAs (ceRNA) to regulate gene expression competing with microRNA binding sites is often the basis of the processes related to cell differentiation and development.…”

Section: Hotair and Mirnas Interaction In Embryonic Development Anmentioning

confidence: 99%

Functional Interaction among lncRNA HOTAIR and MicroRNAs in Cancer and Other Human Diseases

Cantile

Bonito

Tracey

et al. 2021

Cancers

View full text Add to dashboard Cite

LncRNAs are a class of non-coding RNAs mostly involved in regulation of cancer initiation, metastatic progression, and drug resistance, through participation in post-transcription regulatory processes by interacting with different miRNAs. LncRNAs are able to compete with endogenous RNAs by binding and sequestering miRNAs and thereby regulating the expression of their target genes, often represented by oncogenes. The lncRNA HOX transcript antisense RNA (HOTAIR) represents a diagnostic, prognostic, and predictive biomarker in many human cancers, and its functional interaction with miRNAs has been described as crucial in the modulation of different cellular processes during cancer development. The aim of this review is to highlight the relation between lncRNA HOTAIR and different microRNAs in human diseases, discussing the contribution of these functional interactions, especially in cancer development and progression.

show abstract

“…The transcriptome was assembled using StringTie (version 1.3.1) based on the reference genome. LncRNAs were identified as described in reference [49]. The expression of lncRNA was calculated based on FPKMs by using StringTie (version 1.3.1).…”

Section: Bioinformatics Data Analysismentioning

confidence: 99%

Exosomal long non-coding RNA MSTRG.292666.16 is associated with osimertinib (AZD9291) resistance in non-small cell lung cancer

Deng

Fang

Xie

et al. 2020

Aging

View full text Add to dashboard Cite

Acquired resistance of osimertinib is encountered in clinic treatment of non-small cell lung cancer (NSCLC). However, the molecular mechanisms of osimertinib resistance are not fully revealed. This study aimed to investigate the roles of exosomes in delivering osimertinib resistance in NSCLC. Exosomes were successfully isolated. LncRNA sequencing identified a total of 123 differentially expressed lncRNAs, including 45 upregulated lncRNAs and 78 downregulated lncRNAs. The relative expression level of lncRNA MSTRG.292666.16 was significantly upregulated in osimertinibresistant plasma, osimertinib-resistant H1975R cells and their derived exosomes, compared with those in osimertinib-sensitive plasma, H1975 cells and exosomes (P < 0.05). Besides, osimertinib-resistant exosomes could regulate gene expressions induced by osimertinib, including miRNA-21, miRNA-125b, TGFβ, ARF6 and c-Kit. Osimertinib-resistant exosomes could be taken up by osimertinib-sensitive H1975 cells and resulting in osimertinibresistance in vivo. Knockdown of lncRNA MSTRG.292666.16 decreased osimertinib resistance of H1975R cells. Our results suggest that exosomal lncRNA MSTRG.292666.16 might be associated with osimertinib resistance in NSCLC.

show abstract

The comprehensive detection of miRNA, lncRNA, and circRNA in regulation of mouse melanocyte and skin development

Cited by 26 publications

References 53 publications

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Functional Interaction among lncRNA HOTAIR and MicroRNAs in Cancer and Other Human Diseases

Exosomal long non-coding RNA MSTRG.292666.16 is associated with osimertinib (AZD9291) resistance in non-small cell lung cancer

Contact Info

Product

Resources

About