scholarly journals Association of single nucleotide polymorphism at long non-coding RNA 8138.1 with duration of fertility in egg-laying hens

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7282
Author(s):  
Adeyinka Abiola Adetula ◽  
Syed Ali Azmal ◽  
Chenghao Sun ◽  
Abdelmotaleb Elokil ◽  
Shijun Li
Keyword(s):  
Laying Hens ◽  
Genetic Relationships ◽  
Laying Hen ◽  
Egg Laying ◽  
Transcriptional Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Non Coding Rna ◽  
Potential Biomarker ◽  
Long Non Coding Rna

A previous genome-wide transcriptional analysis identified long non-coding RNA 8138.1 (lncRNA8138.1) as a candidate gene related to hen duration of the fertility (DF) trait.LncRNA8138.1gene response to growth factor and reproductive system development suggests it has a vital role in reproduction. In this study, we investigated thelncRNA8138.1gene sequence in a population of egg-laying hens. The sequence analysis of thelncRNA8138.1gene containing about 1.6 k nucleotides (nt) was observed with four single nucleotide polymorphisms (SNPs) and 7 nt indel including r.4937159A > G; r.4937219T > C; r.4937258G > C; r.4937318C > G and g.4937319_4937325delinsTGTGTGG. Next, the genomic DNAs from laying hen populations were subjected to polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) to detect a region of 457 bp carryinglncRNA8138.1r.4937159A > G substitution. Further inspection of the region containing r.4937159A > G mutation revealed three genotypes viz., AA, AG, and GG were observed with respective frequencies of 0.106, 0.607, and 0.287 in laying hen population 1 (P1) (n = 1, 042) and respective frequencies of 0.176, 0.708, and 0.116 in laying hen population 2 (P2) (n = 826). Moreover, to further examining the frequencies of r.4937159A > G genotypes in P1 and P2, and their additive and dominance effects; r.4937159A > G locus was significantly associated with DF-trait in both P1 and P2 (EN: the number of eggs, FN: the number of fertile eggs after a single AI), and DN (the number of days post-insemination until last fertile egg). In testing for additive and dominance effects, additive effect was significant (P < 0.05) in both P1 and P2 for DF-trait, and the dominance effect was significant (P < 0.05) for EN and FN traits, suggesting that r.4937159A > G polymorphism is a potential biomarker for DF-trait. However, the identified novel r.4937159A > G mutation and others require further investigation to confirm phenotypic causality and potential genetic relationships with reproductive traits. Overall, our findings suggest the significance of genetic variation in long non-coding RNAs may assist in future breeding programs to improve selection for prolonged DF-trait.

scholarly journals Identification and activity of the functional complex between hnRNPL and the pseudoexfoliation syndrome-associated lncRNA, LOXL1-AS1

2020 ◽  
Vol 29 (12) ◽  
pp. 1986-1995 ◽  
Author(s):  
Heather M Schmitt ◽  
William M Johnson ◽  
Inas F Aboobakar ◽  
Shelby Strickland ◽  
María Gomez-Caraballo ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Open Angle Glaucoma ◽  
Global Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Non Coding Rna ◽  
Functional Complex ◽  
Nuclear Ribonucleoprotein ◽  
Outflow Pathway ◽  
Long Non Coding Rna

Abstract Individuals with pseudoexfoliation (PEX) syndrome exhibit various connective tissue pathologies associated with dysregulated extracellular matrix homeostasis. PEX glaucoma is a common, aggressive form of open-angle glaucoma resulting from the deposition of fibrillary material in the conventional outflow pathway. However, the molecular mechanisms that drive pathogenesis and genetic risk remain poorly understood. PEX glaucoma-associated single-nucleotide polymorphisms are located in and affect activity of the promoter of LOXL1-AS1, a long non-coding RNA (lncRNA). Nuclear and non-nuclear lncRNAs regulate a host of biological processes, and when dysregulated, contribute to disease. Here we report that LOXL1-AS1 localizes to the nucleus where it selectively binds to the mRNA processing protein, heterogeneous nuclear ribonucleoprotein-L (hnRNPL). Both components of this complex are critical for the regulation of global gene expression in ocular cells, making LOXL1-AS1 a prime target for investigation in PEX syndrome and glaucoma.

scholarly journals Genetic impacts on thermostability of onco-lncRNA HOTAIR during the development and progression of endometriosis

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248168
Author(s):  
Cherry Yin-Yi Chang ◽  
Chung-Chen Tseng ◽  
Ming-Tsung Lai ◽  
An-Jen Chiang ◽  
Lun-Chien Lo ◽  
...  
Keyword(s):  
Statistical Significance ◽  
Net Energy ◽  
Nucleotide Polymorphisms ◽  
Rna Structures ◽  
Single Nucleotide ◽  
Non Coding Rna ◽  
And Migration ◽  
Long Non Coding Rna ◽  
Lncrna Hotair

HOTAIR is a well-known long non-coding RNA (lncRNA) involved in various cellular signaling, whereas its functional impacts on endometriosis development are still largely unknown. To this end, six potential functional single nucleotide polymorphisms (SNPs) in HOTAIR, with minor allele frequencies more than 10% in Han population and altered net energy of RNA structures larger than 0.5 kcal/mol, were selected for genotyping study. The study included 207 endometriosis patients and 200 healthy women. Genetic substitutions at rs1838169 and rs17720428 were frequently found in endometriosis patients, and rs1838169 showed statistical significance (p = 0.0174). The G-G (rs1838169-rs17720428) haplotype showed the most significant association with endometriosis (p < 0.0001) with enhanced HOTAIR stability, and patients who harbor such haplotype tended to show higher CA125. Data mining further revealed higher mRNA HOTAIR levels in the endometria of patients with severe endometriosis which consistently showed reduced HOXD10 and HOXA5 levels. HOTAIR knockdown with specific shRNAs down-regulated cell proliferation and migration with the induction of HOXD10 and HOXA5 expression in human ovarian clear cancer cells. Our study therefore provided evidence to indicate a prominent role of HOTAIR in promoting endometriosis, which could be used as a potential target for clinical applications.

scholarly journals Association between long non-coding RNA polymorphisms and cancer risk: a meta-analysis

2018 ◽  
Vol 38 (4) ◽  
Author(s):  
Xin Huang ◽  
Weiyue Zhang ◽  
Zengwu Shao
Keyword(s):  
Cancer Risk ◽  
Meta Analysis ◽  
Predictive Biomarkers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Lncrna Gene ◽  
Non Coding Rna ◽  
Risk Of Cancer ◽  
Long Non Coding Rna ◽  
Larger Sample

Several studies have suggested that long non-coding RNA (lncRNA) gene polymorphisms are associated with cancer risk. In the present study, we conducted a meta-analysis related to studies on the association between lncRNA single-nucleotide polymorphisms (SNPs) and the overall risk of cancer. A total of 12 SNPs in five common lncRNA genes were finally included in the meta-analysis. In the lncRNA antisense non-coding RNA (ncRNA) in the INK4 locus (ANRIL), the rs1333048 A/C, rs4977574 A/G, and rs10757278 A/G polymorphisms, but not rs1333045 C/T, were correlated with overall cancer risk. Our study also demonstrated that other SNPs were correlated with overall cancer risk, namely, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1, rs619586 A/G), HOXA distal transcript antisense RNA (HOTTIP, rs1859168 A/C), and highly up-regulated in liver cancer (HULC, rs7763881 A/C). Moreover, four prostate cancer-associated ncRNA 1 (PRNCR1, rs16901946 G/A, rs13252298 G/A, rs1016343 T/C, and rs1456315 G/A) SNPs were in association with cancer risk. No association was found between the PRNCR1 (rs7007694 C/T) SNP and the risk of cancer. In conclusion, our results suggest that several studied lncRNA SNPs are associated with overall cancer risk. Therefore, they might be potential predictive biomarkers for the risk of cancer. More studies based on larger sample sizes and more lncRNA SNPs are warranted to confirm these findings.

scholarly journals Pharmacogenomics of Lithium Response in Bipolar Disorder

2021 ◽  
Vol 14 (4) ◽  
pp. 287
Author(s):  
Courtney M. Vecera ◽  
Gabriel R. Fries ◽  
Lokesh R. Shahani ◽  
Jair C. Soares ◽  
Rodrigo Machado-Vieira
Keyword(s):  
Bipolar Disorder ◽  
Association Studies ◽  
Mood Stabilizer ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Lithium Response ◽  
Genetic Loading ◽  
Long Non Coding Rna

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.

scholarly journals Mitigation Effects of Bentonite and Yeast Cell Wall Binders on AFB1, DON, and OTA Induced Changes in Laying Hen Performance, Egg Quality, and Health

Toxins ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 156
Author(s):  
Ling Zhao ◽  
Yue Feng ◽  
Jing-Tao Wei ◽  
Meng-Xiang Zhu ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Laying Hens ◽  
Egg Quality ◽  
Dietary Supplementation ◽  
Basal Diet ◽  
Liver Weight ◽  
Laying Hen ◽  
Egg Laying ◽  
Villus Height ◽  
Crypt Depth ◽  
Induced Changes

The objective of this study was to evaluate the efficacy of mycotoxin binders in reducing the adverse effects of co-occurring dietary aflatoxin B1 (AFB1), deoxynivalenol (DON) and ochratoxin A (OTA) on laying hens. Three hundred and sixty 26-week-old Roman laying hens were randomly allocated into four experimental groups with 10 replicates of nine birds each. The four groups received either a basal diet (BD; Control), a BD supplemented with 0.15 mg/kg AFB1 + 1.5 mg/kg DON + 0.12 mg/kg OTA (Toxins), a BD + Toxins with Toxo-HP binder (Toxins + HP), or a BD + Toxins with TOXO XL binder (Toxins + XL) for 12 weeks. Compared to the control, dietary supplementation of mycotoxins decreased (P < 0.10) total feed intake, total egg weight, and egg-laying rate, but increased feed/egg ratio by 2.5–6.1% and mortality during various experimental periods. These alterations induced by mycotoxins were alleviated by supplementation with both TOXO HP and XL binders (P < 0.10). Furthermore, dietary mycotoxins reduced (P < 0.05) eggshell strength by 12.3% and caused an accumulation of 249 μg/kg of DON in eggs at week 12, while dietary supplementation with TOXO HP or XL mitigated DON-induced changes on eggshell strength and prevented accumulation of DON in eggs (P < 0.05). Moreover, dietary mycotoxins increased relative liver weight, but decreased spleen and proventriculus relative weights by 11.6–22.4% (P < 0.05). Mycotoxin exposure also increased alanine aminotransferase activity and reduced immunoglobulin (Ig) A, IgM, and IgG concentrations in serum by 9.2–26.1% (P < 0.05). Additionally, mycotoxin exposure induced histopathological damage and reduced villus height, villus height/crypt depth, and crypt depth in duodenum, jejunum and (or) ileum (P < 0.05). Notably, most of these histological changes were mitigated by supplementation with both TOXO HP and XL (P < 0.05). In conclusion, the present study demonstrated that the mycotoxin binders TOXO HP and XL can help to mitigate the combined effects of AFB1, DON, and OTA on laying hen performance, egg quality, and health.

scholarly journals Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 702
Author(s):  
Simon Jansen ◽  
Ulrich Baulain ◽  
Christin Habig ◽  
Faisal Ramzan ◽  
Jens Schauer ◽  
...  
Keyword(s):  
Random Forests ◽  
Metabolic Pathways ◽  
Genetic Architecture ◽  
Laying Hens ◽  
Enrichment Analysis ◽  
Nucleotide Polymorphisms ◽  
Mineral Density ◽  
Single Nucleotide ◽  
Economic Problems ◽  
Close Proximity

Skeletal disorders, including fractures and osteoporosis, in laying hens cause major welfare and economic problems. Although genetics have been shown to play a key role in bone integrity, little is yet known about the underlying genetic architecture of the traits. This study aimed to identify genes associated with bone breaking strength and bone mineral density of the tibiotarsus and the humerus in laying hens. Potentially informative single nucleotide polymorphisms (SNP) were identified using Random Forests classification. We then searched for genes known to be related to bone stability in close proximity to the SNPs and identified 16 potential candidates. Some of them had human orthologues. Based on our findings, we can support the assumption that multiple genes determine bone strength, with each of them having a rather small effect, as illustrated by our SNP effect estimates. Furthermore, the enrichment analysis showed that some of these candidates are involved in metabolic pathways critical for bone integrity. In conclusion, the identified candidates represent genes that may play a role in the bone integrity of chickens. Although further studies are needed to determine causality, the genes reported here are promising in terms of alleviating bone disorders in laying hens.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

Abstract 375: The Intergenic Long Non-Coding RNA RP11-472n13.3 Modulates Interferon-Gamma Signaling and M1 Macrophage Activation

2017 ◽  
Vol 37 (suppl_1) ◽  
Author(s):  
Ying Wang ◽  
Chenyi Xue ◽  
Muredach Reilly ◽  
Hanrui Zhang
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
Induced Pluripotent Stem Cell ◽  
Myeloid Cell ◽  
Human Monocyte ◽  
Human Macrophage ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
M1 Macrophage ◽  
Long Non Coding Rna

We aim to interrogate the functions of a subset of human macrophage intergenic long non-coding RNA (lincRNAs) which harbor cardiometabolic trait-associated single nucleotide polymorphisms (SNPs). We have found that one lincRNA RP11-472N13.3 overlaps rs7081678, a SNP significantly associated with central obesity (WHRadjBMI; P =5.57x10 -6 ). RP11-472N13.3 expression is enriched in macrophages relative to other obesity relevant tissues. Thus, RP11-472N13.3 SNPs for obesity may act via its myeloid cell modulation in adipose. In human monocyte-derived macrophage (HMDM), human induced pluripotent stem cell-derived macrophages (IPSDM) and THP1-derived macrophages (THP-1Φ), at RNAseq and Q-PCR, RP11-472N13.3 is abundant in M0 and M2(IL-4) macrophages but markedly suppressed in the M1 state (LPS/IFNγ). RP11-472N13.3 localizes almost exclusively to the cytoplasmic fraction of M0-HMDM. Consistent with GENCODE, our HMDM RNAseq data suggest a single 2-exon isoform. ChIP-seq reveals PU.1 and C/EBP-β binding at RP11-472N13.3 transcription start site. In our HMDM RNAseq (n=30 subjects) data, RP11-472N13.3 expression was inversely correlated with IFNγ-JAK-STAT signaling genes (e.g., IRF4, IL-12A, IL-23, STAT1, SOCS1, SOCS3 ), but not LPS/TLR4 activated genes (e.g., TNFA, CXCL9, CXCL10, IL1B ). Furthermore, KD of RP11-472N13.3 using siRNA or LNA-ASO in THP-1Φ, amplified expression of IFNγ target genes but not LPS/TLR4 targets during M1 activation (LPS/IFNγ). These data suggest its potential role in modulating IFNγ signaling. Mechanistic studies are needed to examine the molecular mechanisms.

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