scholarly journals Differential Expression and Functional Analysis of High-throughput Sequencing about Long Noncoding RNAs in Corneal Transplantation

2020 ◽  
Author(s):  
Jing Wen ◽  
Jing Wu ◽  
Huiwen Tian ◽  
Xiaoli Lu ◽  
Shumei Lin ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Differential Expression ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Corneal Transplantation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas

scholarly journals Differences in small noncoding RNAs profile between bull X and Y sperm

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9822
Author(s):  
Hao Zhou ◽  
Jiajia Liu ◽  
Wei Sun ◽  
Rui Ding ◽  
Xihe Li ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Sex Differences ◽  
Embryonic Development ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Mature Oocyte ◽  
Small Noncoding Rnas ◽  
Nucleosomal Dna ◽  
Nucleosome Binding

The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development.

scholarly journals Transcriptome Sequencing to Detect the Potential Role of Long Noncoding RNAs in Salt-Sensitive Hypertensive Rats

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Hao Wu ◽  
Sibo Zhu ◽  
Rui Yuan ◽  
Yang Yi ◽  
Hanqing Wang ◽  
...  
Keyword(s):  
Blood Pressure ◽  
High Throughput ◽  
Serum Sodium ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
High Salt ◽  
Long Noncoding Rnas ◽  
Hypertensive Rats ◽  
Salt Sensitive Hypertension ◽  
Sensitive Group

Backgrounds. Long noncoding RNAs (lncRNAs) play an important role in various biological processes. However, their functions in salt-sensitive hypertension are largely unknown. In this study, the lncRNA-seq technique was employed to compare the expression profiles of lncRNAs and mRNAs in salt-sensitive hypertensive rats. Methods. Blood pressure, serum sodium, and urinary creatinine were texted in salt-sensitive and salt-insensitive rats fed with different salt concentrations. High-throughput sequencing was used to detect the expression of lncRNAs and mRNA in the renal medulla of the two groups. Results. Blood pressure and urinary sodium/creatinine of high-salt diets of the sensitive group were significantly higher than that in the control group. Serum sodium has no significant difference between the two groups in high-salt diets. NONRATG007131.2 and NONRATG012674.2 were the most different lncRNAs in the high salt-sensitive group. Correlation analysis reveals that Matn1, Serpinb12, Anxa8, and Hspa5 may play an important role in salt-sensitive hypertension. Conclusion. This study analyzed the difference in lncRNA and mRNA between salt-sensitive and salt-insensitive rats with different salt diets by high-throughput sequencing. Salt sensitivity and salt concentration were two key factors for the induction of hypertension. We found some potential genes that play an important role in salt-sensitive hypertension.

scholarly journals The small peptide world in long noncoding RNAs

2019 ◽  
Vol 20 (5) ◽  
pp. 1853-1864 ◽  
Author(s):  
Seo-Won Choi ◽  
Hyun-Woo Kim ◽  
Jin-Wu Nam
Keyword(s):  
High Throughput ◽  
Functional Significance ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Small Peptides ◽  
Small Peptide ◽  
Plant Genomes ◽  
The Past ◽  
Sequencing Technologies ◽  
Coding Potential

Abstract Long noncoding RNAs (lncRNAs) are a group of transcripts that are longer than 200 nucleotides (nt) without coding potential. Over the past decade, tens of thousands of novel lncRNAs have been annotated in animal and plant genomes because of advanced high-throughput RNA sequencing technologies and with the aid of coding transcript classifiers. Further, a considerable number of reports have revealed the existence of stable, functional small peptides (also known as micropeptides), translated from lncRNAs. In this review, we discuss the methods of lncRNA classification, the investigations regarding their coding potential and the functional significance of the peptides they encode.

scholarly journals Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yaqiong Wu ◽  
Jing Guo ◽  
Tongli Wang ◽  
Fuliang Cao ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Leaf Color ◽  
Wide Range ◽  
Color Mutation

Abstract Background Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood. Results In this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks. Conclusions This study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.

A preliminary study on the differential expression of long noncoding RNAs and messenger RNAs in obese and control mice

2019 ◽  
Vol 121 (2) ◽  
pp. 1126-1143 ◽  
Author(s):  
Ping Li ◽  
Xiaoyu Chen ◽  
Xuelian Chang ◽  
Tiantian Tang ◽  
Kemin Qi
Keyword(s):  
Differential Expression ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Messenger Rnas ◽  
Preliminary Study ◽  
And Control
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