Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

Despite being the most widely studied mood stabilizer, researchers have not confirmed a mechanism for lithium’s therapeutic efficacy in Bipolar Disorder (BD). Pharmacogenomic applications may be clinically useful in the future for identifying lithium-responsive patients and facilitating personalized treatment. Six genome-wide association studies (GWAS) reviewed here present evidence of genetic variations related to lithium responsivity and side effect expression. Variants were found on genes regulating the glutamate system, including GAD-like gene 1 (GADL1) and GRIA2 gene, a mutually-regulated target of lithium. In addition, single nucleotide polymorphisms (SNPs) discovered on SESTD1 may account for lithium’s exceptional ability to permeate cell membranes and mediate autoimmune and renal effects. Studies also corroborated the importance of epigenetics and stress regulation on lithium response, finding variants on long, non-coding RNA genes and associations between response and genetic loading for psychiatric comorbidities. Overall, the precision medicine model of stratifying patients based on phenotype seems to derive genotypic support of a separate clinical subtype of lithium-responsive BD. Results have yet to be expounded upon and should therefore be interpreted with caution.

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Functional genomics of autoimmune diseases

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2019-216794 ◽

2021 ◽

pp. annrheumdis-2019-216794

Author(s):

Akari Suzuki ◽

Matteo Maurizio Guerrini ◽

Kazuhiko Yamamoto

Keyword(s):

Autoimmune Diseases ◽

Association Studies ◽

Linkage Disequilibrium Block ◽

Causal Variant ◽

Genome Wide Association Studies ◽

Coding Region ◽

Risk Variants ◽

Non Coding Rna ◽

Genome Wide ◽

Long Non Coding Rna

For more than a decade, genome-wide association studies have been applied to autoimmune diseases and have expanded our understanding on the pathogeneses. Genetic risk factors associated with diseases and traits are essentially causative. However, elucidation of the biological mechanism of disease from genetic factors is challenging. In fact, it is difficult to identify the causal variant among multiple variants located on the same haplotype or linkage disequilibrium block and thus the responsible biological genes remain elusive. Recently, multiple studies have revealed that the majority of risk variants locate in the non-coding region of the genome and they are the most likely to regulate gene expression such as quantitative trait loci. Enhancer, promoter and long non-coding RNA appear to be the main target mechanisms of the risk variants. In this review, we discuss functional genetics to challenge these puzzles.

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Genome-wide analysis of long non-coding RNA expression profiles in keratinocytes from psoriasis skin

10.26226/morressier.61081ff8bc981037240fe454 ◽

2021 ◽

Author(s):

Longlong Luo ◽

Nupur khera ◽

Andor Pivarcsi ◽

Ankit Srivastava ◽

Lorenzo Pasquali ◽

...

Keyword(s):

Expression Profiles ◽

Rna Expression ◽

Genome Wide Analysis ◽

Non Coding Rna ◽

Genome Wide ◽

Long Non Coding Rna

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Peer Review #3 of "Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing (v0.2)"

10.7287/peerj.6577v0.2/reviews/3 ◽

2019 ◽

Author(s):

C Bin

Keyword(s):

Epithelial Cell ◽

Cell Line ◽

Rna Sequencing ◽

Porcine Circovirus ◽

Epithelial Cell Line ◽

Rna Expression ◽

Genome Wide Analysis ◽

Non Coding Rna ◽

Genome Wide ◽

Long Non Coding Rna

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Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Genes ◽

10.3390/genes9090459 ◽

2018 ◽

Vol 9 (9) ◽

pp. 459 ◽

Cited By ~ 5

Author(s):

Priyanka Borah ◽

Antara Das ◽

Matthew Milner ◽

Arif Ali ◽

Alison Bentley ◽

...

Keyword(s):

Gene Regulation ◽

Next Generation Sequencing ◽

Non Coding Rna ◽

Genome Wide ◽

Non Coding Rnas ◽

Endogenous Target ◽

Long Non Coding Rna ◽

Nutrient Homeostasis ◽

Generation Sequencing

Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.

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The long non-coding RNA CASC20 is a susceptibility locus for heterotopic ossification: results of a genome-wide association study

Osteoarthritis and Cartilage ◽

10.1016/j.joca.2018.02.337 ◽

2018 ◽

Vol 26 ◽

pp. S156

Author(s):

K. Hatzikotoulas ◽

M.J. Clark ◽

S.J. Macinnes ◽

E. Zeggini ◽

M.J. Wilkinson

Keyword(s):

Association Study ◽

Heterotopic Ossification ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Susceptibility Locus ◽

Non Coding Rna ◽

Genome Wide ◽

A Genome ◽

Long Non Coding Rna

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Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella

Scientific Reports ◽

10.1038/s41598-017-16057-2 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 10

Author(s):

Feiling Liu ◽

Dianhao Guo ◽

Zhuting Yuan ◽

Chen Chen ◽

Huamei Xiao

Keyword(s):

Insecticide Resistance ◽

Plutella Xylostella ◽

Diamondback Moth ◽

Non Coding Rna ◽

Genome Wide ◽

Long Non Coding Rna ◽

Rna Genes

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Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion

10.1101/2021.01.06.425556 ◽

2021 ◽

Author(s):

Audrey Jacq ◽

Denis Becquet ◽

Maria-Montserrat Bello-Goutierrez ◽

Bénédicte Boyer ◽

Séverine Guillen ◽

...

Keyword(s):

Biological Processes ◽

Circadian Expression ◽

Non Coding Rna ◽

Genome Wide ◽

Independent Functions ◽

Rat Pituitary ◽

Genetic Deletion ◽

The Impact ◽

Long Non Coding Rna ◽

Abundant Transcript

AbstractThe functions of the long non-coding RNA, Nuclear enriched abundant transcript 1 (Neat1), are poorly understood. Neat1 is required for the formation of paraspeckles, but its respective paraspeckle-dependent or independent functions are unknown. Several studies including ours reported that Neat1 is involved in the regulation of circadian rhythms. We characterized the impact of Neat1 genetic deletion in a rat pituitary cell line. The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to cells in which Neat1 was deleted by CRISPR/Cas9. The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1, interacting or independently of the circadian system, could play crucial roles in key physiological functions through diverse mechanisms.

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