scholarly journals Identification of lncRNAs Differentially Expressed during Natural and Induced Estrus in Sheep

2021 ◽  
Author(s):  
Bujun Mei ◽  
Rong Liu
Keyword(s):  
Mirna Precursor ◽  
Rna Seq ◽  
Tissue Samples ◽  
Reproduction Mode ◽  
Sheep Industry ◽  
Physiological Processes ◽  
Regulation Mechanisms ◽  
Non Coding Rnas ◽  
Mongolian Sheep ◽  
Plat Form

Background: The manipulation of the estrous cycle or induction of estrus is a commonly used technique in sheep industry. The goal of this study was to identify and characterize differences of non-coding RNAs (lincRNAs) expression between induced estrus and natural estrus using the BGISEQ-500 plat form in 7 Mongolian sheep, which will provide insights into the regulation mechanisms of lncRNAs in different reproduction mode of sheep. Methods: During the late spring, ovarian, pituitary, hypothalamic, pineal and uterine tissue samples were collected from four artificially induced estrus and three naturally estrus Mongolian sheep. Total RNA was extracted from the five tissues using TRIzol reagent (Invitrogen) and treated with DNase I following the manufacturer’s instructions. A total of 35 sheep samples were sequenced using the BGISEQ-500 plat form. Bioinformatics methods were used to analysis expression difference analysis between groups, SNP and InDel, alternative splicing, lncRNA’s miRNA precursor prediction, lncRNA target gene and family prediction. Result: 211 novel lncRNAs were systematically identified using RNA-Seq technology. Meanwhile, we found that there are diversifications of lncRNAs in induced estrus vs. nature estrus of ewes. Therefore, we predict that, under the action of exogenous hormones, many physiological processes of ewes may be affected to varying degrees through the change of LncRNA to a variety of pathways.

scholarly journals CircRNAs as Potential Blood Biomarkers and Key Elements in Regulatory Networks in Gastric Cancer

2022 ◽  
Vol 23 (2) ◽  
pp. 650
Author(s):  
Laís Reis-das-Mercês ◽  
Tatiana Vinasco-Sandoval ◽  
Rafael Pompeu ◽  
Aline Cruz Ramos ◽  
Ana K. M. Anaissi ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Minimally Invasive ◽  
Regulatory Networks ◽  
Expression Profiles ◽  
Functional Enrichment ◽  
Circular Rnas ◽  
Rna Seq ◽  
Tissue Samples ◽  
Molecular Alterations ◽  
Non Coding Rnas

Gastric cancer (GC) is the fifth most common type of cancer and the third leading cause of cancer death in the world. It is a disease that encompasses a variety of molecular alterations, including in non-coding RNAs such as circular RNAs (circRNAs). In the present study, we investigated hsa_circ_0000211, hsa_circ_0000284, hsa_circ_0000524, hsa_circ_0001136 and hsa_circ_0004771 expression profiles using RT-qPCR in 71 gastric tissue samples from GC patients (tumor and tumor-adjacent samples) and volunteers without cancer. In order to investigate the suitability of circRNAs as minimally invasive biomarkers, we also evaluated their expression profile through RT-qPCR in peripheral blood samples from patients with and without GC (n = 41). We also investigated the predicted interactions between circRNA-miRNA-mRNA and circRNA-RBP using the KEGG and Reactome databases. Overall, our results showed that hsa_circ_0000211, hsa_circ_0000284 and hsa_circ_0004771 presented equivalent expression profiles when analyzed by different methods (RNA-Seq and RT-qPCR) and different types of samples (tissue and blood). Further, functional enrichment results identified important signaling pathways related to GC. Thus, our data support the consideration of circRNAs as new, minimally invasive biomarkers capable of aiding in the diagnosis of GC and with great potential to be applied in clinical practice.

Regulation mechanisms of positive cold tolerance in Mongolian sheep

2020 ◽  
Vol 70 (1) ◽  
pp. 27-37
Author(s):  
Yu Cao ◽  
Jing Pan ◽  
Yanru Zhang ◽  
Huanmin Zhou
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Molecular Evidence ◽  
Rna Seq ◽  
Cold Response ◽  
Kegg Pathways ◽  
Adaptive Thermogenesis ◽  
Regulation Mechanisms ◽  
Mongolian Sheep

Abstract Mongolian sheep survive well on the Mongolian plateau during tremendously cold winters, but their cold response mechanisms are not well understood. By comparing with Dorper sheep originating from South Africa, we expected to reveal the cold tolerance mechanisms of Mongolian sheep on the basis of transcriptome data, further providing molecular evidence for the targeted breeding of sheep. Based on the mRNA data of RNA-seq, we selected candidate genes among the differentially expressed genes; 7 from adipose tissue, 33 from skeletal muscle, and 10 from the liver. According to enriched KEGG pathways and previous research results, the effects of the above candidate genes mainly involved weakening the synthesis of long-chain fatty acids, raising the adaptive thermogenesis and browning adipogenesis in fat, reducing glucose 6-phosphate, stimulating citrulline generation and enhancing lipid metabolism in skeletal muscle, and postponing cell senescence in the liver. The findings also demonstrate the regulation mechanisms of cold tolerance in different tissues of Mongolian sheep.

scholarly journals Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1268
Author(s):  
Shengchao Zhang ◽  
Sibtain Ahmad ◽  
Yuxia Zhang ◽  
Guohua Hua ◽  
Jianming Yi
Keyword(s):  
Mammary Gland ◽  
Crude Protein ◽  
Regulatory Mechanism ◽  
Differentially Expressed ◽  
Milk Replacer ◽  
Rna Seq ◽  
Fat Pad ◽  
Mammary Fat Pad ◽  
Non Coding Rnas ◽  
Gland Development

Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs’ quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.

scholarly journals Differential Expression of BARD1 Isoforms in Melanoma

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 320
Author(s):  
Lorissa I. McDougall ◽  
Ryan M. Powell ◽  
Magdalena Ratajska ◽  
Chi F. Lynch-Sutherland ◽  
Sultana Mehbuba Hossain ◽  
...  
Keyword(s):  
Long Range ◽  
Patient Outcomes ◽  
Splice Variants ◽  
Significant Proportion ◽  
Nanopore Sequencing ◽  
Rna Seq ◽  
Splice Isoforms ◽  
Tissue Samples ◽  
Multiple Transcripts ◽  
Mrna Variants

Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.

scholarly journals The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1160
Author(s):  
Athina N. Markou ◽  
Stavroula Smilkou ◽  
Emilia Tsaroucha ◽  
Evi Lianidou
Keyword(s):  
False Positive ◽  
Tissue Samples ◽  
Dna Contamination ◽  
Dnase Treatment ◽  
Circular Dnas ◽  
Non Coding Rnas ◽  
Nsclc Patients ◽  
Treatment Step ◽  
Primary Tissue ◽  
Positive Results

The presence of contaminating gDNA in RNA preparations is a frequent cause of false positives in RT-PCR-based analysis. However, in some cases, this cannot be avoided, especially when there are no exons–intron junctions in the lncRNA sequences. Due to the lack of exons in few of long noncoding RNAs (lncRNAs) and the lack of DNAse treatment step in most studies reported so far, serious questions are raised about the specificity of lncRNA detection and the potential of reporting false-positive results. We hypothesized that minute amounts of gDNA usually co-extracted with RNA could give false-positive signals since primers would specifically bind to gDNA due to the lack of junction. In the current study, we evaluated the effect of gDNA and other forms of DNA like extrachromosomal circular DNAs (eccDNAs) contamination and the importance of including a DNAse treatment step on lncRNAsexpression.As a model, we have chosen as one of the most widely studied lncRNAs in cancer namely MALAT1, which lacks exons. When we tested this hypothesis in plasma and primary tissue samples from NSCLC patients, our findings clearly indicated that results on MALAT1 expression are highly affected by the presence of DNA contamination and that the DNAse treatment step is absolutely necessary to avoid false positive results.

scholarly journals Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 630
Author(s):  
Yongqing Lan ◽  
Meng Li ◽  
Shuangli Mi
Keyword(s):  
Transcription Factor ◽  
Cell Model ◽  
Myeloid Differentiation ◽  
Rna Seq ◽  
Hematopoietic Differentiation ◽  
Granulocytic Differentiation ◽  
Expression Of Genes ◽  
Non Coding Rnas

Hematopoietic differentiation is a well-orchestrated process by many regulators such as transcription factor and long non-coding RNAs (lncRNAs). However, due to the large number of lncRNAs and the difficulty in determining their roles, the study of lncRNAs is a considerable challenge in hematopoietic differentiation. Here, through gene co-expression network analysis over RNA-seq data generated from representative types of mouse myeloid cells, we obtained a catalog of potential key lncRNAs in the context of mouse myeloid differentiation. Then, employing a widely used in vitro cell model, we screened a novel lncRNA, named Gdal1 (Granulocytic differentiation associated lncRNA 1), from this list and demonstrated that Gdal1 was required for granulocytic differentiation. Furthermore, knockdown of Cebpe, a principal transcription factor of granulocytic differentiation regulation, led to down-regulation of Gdal1, but not vice versa. In addition, expression of genes involved in myeloid differentiation and its regulation, such as Cebpa, were influenced in Gdal1 knockdown cells with differentiation blockage. We thus systematically identified myeloid differentiation associated lncRNAs and substantiated the identification by investigation of one of these lncRNAs on cellular phenotype and gene regulation levels. This study promotes our understanding of the regulation of myeloid differentiation and the characterization of roles of lncRNAs in hematopoietic system.

scholarly journals Transcriptomic and ChIP-seq Integrative Analysis Reveals Important Roles of Epigenetically Regulated lncRNAs in Placental Development in Meishan Pigs

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 397
Author(s):  
Dadong Deng ◽  
Xihong Tan ◽  
Kun Han ◽  
Ruimin Ren ◽  
Jianhua Cao ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Rna Seq ◽  
Sequencing Data ◽  
Placental Development ◽  
Cytoskeleton Organization ◽  
New Class ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Non Coding Rnas ◽  
Two Stages ◽  
Regulatory Functions

The development of the placental fold, which increases the maternal–fetal interacting surface area, is of primary importance for the growth of the fetus throughout the whole pregnancy. However, the mechanisms involved remain to be fully elucidated. Increasing evidence has revealed that long non-coding RNAs (lncRNAs) are a new class of RNAs with regulatory functions and could be epigenetically regulated by histone modifications. In this study, 141 lncRNAs (including 73 up-regulated and 68 down-regulated lncRNAs) were identified to be differentially expressed in the placentas of pigs during the establishment and expanding stages of placental fold development. The differentially expressed lncRNAs and genes (DElncRNA-DEgene) co-expression network analysis revealed that these differentially expressed lncRNAs (DElncRNAs) were mainly enriched in pathways of cell adhesion, cytoskeleton organization, epithelial cell differentiation and angiogenesis, indicating that the DElncRNAs are related to the major events that occur during placental fold development. In addition, we integrated the RNA-seq (RNA sequencing) data with the ChIP-seq (chromatin immunoprecipitation sequencing) data of H3K4me3/H3K27ac produced from the placental samples of pigs from the two stages (gestational days 50 and 95). The analysis revealed that the changes in H3K4me3 and/or H3K27ac levels were significantly associated with the changes in the expression levels of 37 DElncRNAs. Furthermore, several H3K4me3/H3K27ac-lncRNAs were characterized to be significantly correlated with genes functionally related to placental development. Thus, this study provides new insights into understanding the mechanisms for the placental development of pigs.

scholarly journals Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jinyu Zhang ◽  
Huanqing Xu ◽  
Yuming Yang ◽  
Xiangqian Zhang ◽  
Zhongwen Huang ◽  
...  
Keyword(s):  
Growth And Yield ◽  
Biological Processes ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
P Deficiency ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes ◽  
Non Coding Rnas ◽  
Sensitive Genotype

Abstract Background Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear. Results In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress. Conclusions These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.

Abstract 286: Long Noncoding RNAs Are Differentially Expressed in Heart Failure

2012 ◽  
Vol 111 (suppl_1) ◽  
Author(s):  
Emma L Robinson ◽  
Syed Haider ◽  
Hillary Hei ◽  
Richard T Lee ◽  
Roger S Foo
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Significant Proportion ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Control Of Gene Expression ◽  
Failing Heart ◽  
Novel Transcripts ◽  
Non Coding Rnas

Heart failure comprises of clinically distinct inciting causes but a consistent pattern of change in myocardial gene expression supports the hypothesis that unifying biochemical mechanisms underlie disease progression. The recent RNA-seq revolution has enabled whole transcriptome profiling, using deep-sequencing technologies. Up to 70% of the genome is now known to be transcribed into RNA, a significant proportion of which is long non-coding RNAs (lncRNAs), defined as polyribonucleotides of ≥200 nucleotides. This project aims to discover whether the myocardium expression of lncRNAs changes in the failing heart. Paired end RNA-seq from a 300-400bp library of ‘stretched’ mouse myocyte total RNA was carried out to generate 76-mer sequence reads. Mechanically stretching myocytes with equibiaxial stretch apparatus mimics pathological hypertrophy in the heart. Transcripts were assembled and aligned to reference genome mm9 (UCSC), abundance determined and differential expression of novel transcripts and alternative splice variants were compared with that of control (non-stretched) mouse myocytes. Five novel transcripts have been identified in our RNA-seq that are differentially expressed in stretched myocytes compared with non-stretched. These are regions of the genome that are currently unannotated and potentially are transcribed into non-coding RNAs. Roles of known lncRNAs include control of gene expression, either by direct interaction with complementary regions of the genome or association with chromatin remodelling complexes which act on the epigenome.Changes in expression of genes which contribute to the deterioration of the failing heart could be due to the actions of these novel lncRNAs, immediately suggesting a target for new pharmaceuticals. Changes in the expression of these novel transcripts will be validated in a larger sample size of stretched myocytes vs non-stretched myocytes as well as in the hearts of transverse aortic constriction (TAC) mice vs Sham (surgical procedure without the aortic banding). In vivo investigations will then be carried out, using siLNA antisense technology to silence novel lncRNAs in mice.

scholarly journals Reference transcriptome assembly and annotation for perennial ryegrass

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1086-1088 ◽  
Author(s):  
Hiroshi Shinozuka ◽  
Noel O.I. Cogan ◽  
German C. Spangenberg ◽  
John W. Forster
Keyword(s):  
Perennial Ryegrass ◽  
Transcriptome Assembly ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Grass Species ◽  
Rna Seq ◽  
Pasture Grass ◽  
Tissue Samples ◽  
Genome Sequence Assembly ◽  
Transcriptome Resource

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931 547 255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48 713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling, and identification of candidate genes for multiple biological functions.

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