A long non-coding RNA promotes full activation of adult gene expression in the chicken α-globin domain

Arriaga-Canon, Cristian; Fonseca-Guzmán, Yael; Valdes-Quezada, Christian; Arzate-Mejía, Rodrigo G.; Guerrero, Georgina; Recillas‐Targa, Félix

doi:10.4161/epi.27030

Cited by 32 publications

(19 citation statements)

References 34 publications

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“…Once considered the noise in transcription, lncRNAs have been shown to play important roles in a wide range of biological processes (reviewed in Batista and Chang, 2013;Fatica and Bozzoni, 2014). Although there has been tremendous effort to identify lncRNAs in chicken development and diseases (Liu et al, 2018(Liu et al, , 2017Li et al, , 2016Li et al, , 2012Ren et al, 2018;Wu et al, 2018;Wang et al, 2017b;Zhang et al, 2017;Lin et al, 2016), there are very few reports to functionally annotate them (Roeszler et al, 2012;Arriaga-Canon et al, 2014;Cai et al, 2017;Fan et al, 2017). The nomenclature of the chicken lncRNAs has not reached a consensus and the current databases are still under constant improvement.…”

Section: Discussionmentioning

confidence: 99%

Long noncoding RNAs regulate Wnt signaling during feather regeneration

et al. 2018

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Long non-coding RNAs (lncRNAs) are non-protein coding transcripts that are involved in a broad range of biological processes. Here, we examine the functional role of lncRNAs in feather regeneration. RNAseq profiling of the regenerating feather blastema revealed that Wnt signaling is among the most active pathways during feather regeneration, with Wnt ligands and their inhibitors showing distinct expression patterns. Co-expression analysis identified hundreds of lncRNAs with similar expression patterns to either the Wnt ligands (the Lwnt group) or their downstream target genes (the Twnt group). Among these, we randomly picked two lncRNAs in the Lwnt group and three lncRNAs in the Twnt group to validate their expression and function. Members in the Twnt group regulated feather regeneration and axis formation, whereas members in the Lwnt group showed no obvious phenotype. Further analysis confirmed that the three Twnt group members inhibit Wnt signal transduction and, at the same time, are downstream target genes of this pathway. Our results suggest that the feather regeneration model can be utilized to systematically annotate the functions of lncRNAs in the chicken genome.

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Section: Discussionmentioning

confidence: 99%

Long noncoding RNAs regulate Wnt signaling during feather regeneration

et al. 2018

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“…Arriaga‐Canon et al . () identified and studied the nuclear α ‐globin transcript lncRNA (lncRNA‐ α GT), which is responsible for the stage‐specific activation of the adult alpha D‐globin gene in chicken. The lncRNA‐ α GT is transcribed in sense with the globin genes.…”

Section: Identification Of Lncrnas In Domesticated Animal Speciesmentioning

confidence: 99%

Mining long noncoding RNA in livestock

2016

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Genome-wide association studies in livestock based on high-resolution genotyping and sequencing have revealed that the majority of signals associated with complex phenotypic traits are located outside of annotated protein-coding regions in the genome. The approaches of next-generation sequencing applied to whole transcriptome and chromatin profiles have provided information about existing genome-wide transcriptional activity and have revealed that the genomes are templates for thousands of long noncoding transcripts (lncRNAs). Despite their lack of coding capacity, many lncRNAs have been found to play functional roles in a variety of biological processes, which is adding a novel regulatory network to the complex structural organization and function of the genome. Here, we summarize main features of lncRNAs, provide an overview about computational tools and pipelines used for identification of lncRNAs from whole transcriptome datasets and review the current state of knowledge about lncRNAs in livestock species. Although lncRNAs are increasingly emerging as an integral component of the regulatory information encoded in the genome, the complexity of the transcriptomes in domesticated animals is inadequately characterized in comparison to human and mouse. Progress in elucidating whole transcriptomes of livestock species, including identification, functional annotation and characterization of lncRNAs, will be essential for a better understanding of basic biological processes associated with developmental, metabolic and immunological regulation and adaptation and phenotypic variation of complex traits in domesticated animals.

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“…The loss of lncRNA MHM expression in hens can cause asymmetric development of the ovary, and the loss of lncRNA MHM expression in males may result in decreased expression of the DMRT1 gene in testis [10]. Similarly, the lncRNA alphaGT controls the expression of the α-globin gene from the embryo to adult and plays a key role in chicken development [12]. However, there is almost no research on the combination of lncRNAs and shell gland development.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis in the shell gland of laying hens affecting eggshell qualities

Yang¹,

Zhao²,

Han³

et al. 2020

Preprint

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Background Eggshell plays an important role in protecting against physical damage and microorganic invasion. It is subject to quality loss with increasing hen age, and fragile eggshells result in huge economic losses to the poultry industry. Therefore, improving eggshell quality is particularly important. However, little is known about the potential molecular mechanisms regulating eggshell quality in chickens. Methods In this study, we aimed to compare differential expression of long non-coding RNAs (lncRNAs) and mRNAs between old and young laying hens to identify related candidate genes for chicken shell gland development by the method of high-throughput RNA sequencing (RNA-seq). Results In total, we detected 176 and 383 differentially expressed (DE) lncRNAs and mRNAs, respectively. Moreover, functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases revealed that DE-lncRNAs and DE-mRNAs were significantly enriched in “phosphate-containing compound metabolic process”, “mitochondrial proton-transporting ATP synthase complex”, “inorganic anion transport”, and other terms related to eggshell calcification and cuticularization. Through integrated analysis, we found that some important genes such as FGF14, COL25A1, GPX8, and GRXCR1 and their corresponding lncRNAs were expressed differentially between two groups, and the results of quantitative real-time polymerase chain reaction (qPCR) among these genes were also in excellent agreement with the sequencing data. In addition, our research indicates that FGF14, COL25A1, GPX8, and the members of the SLC family may be key genes that affect eggshell quality in hens. Conclusions This study provides a catalog of lncRNAs and mRNAs of the laying hen eggshell gland and will contribute to a fuller understanding of the molecular mechanisms of the function of the shell gland in poultry. Our findings will provide a valuable reference for the development of breeding programs aimed at breeding excellent poultry with high eggshell quality or regulating dietary nutrient levels to improve eggshell quality.

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A long non-coding RNA promotes full activation of adult gene expression in the chicken α-globin domain

Cited by 32 publications

References 34 publications

Long noncoding RNAs regulate Wnt signaling during feather regeneration

Long noncoding RNAs regulate Wnt signaling during feather regeneration

Mining long noncoding RNA in livestock

Transcriptome analysis in the shell gland of laying hens affecting eggshell qualities

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