scholarly journals Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Zhonghua Du ◽  
Lin Jia ◽  
Yichen Wang ◽  
Cong Wang ◽  
Xue Wen ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals SyntDB: defining orthologues of human long noncoding RNAs across primates

2019 ◽  
Author(s):  
Oleksii Bryzghalov ◽  
Michał Wojciech Szcześniak ◽  
Izabela Makałowska
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Primate Species ◽  
Evolutionary Relationships ◽  
Computational Pipeline ◽  
Rna Seq ◽  
Ongoing Research ◽  
Functional Studies ◽  
Public Resources

Abstract SyntDB (http://syntdb.amu.edu.pl/) is a collection of data on long noncoding RNAs (lncRNAs) and their evolutionary relationships in twelve primate species, including humans. This is the first database dedicated to primate lncRNAs, thousands of which are uniquely stored in SyntDB. The lncRNAs were predicted with our computational pipeline using publicly available RNA-Seq data spanning diverse tissues and organs. Most of the species included in SyntDB still lack lncRNA annotations in public resources. In addition to providing users with unique sets of lncRNAs and their characteristics, SyntDB provides data on orthology relationships between the lncRNAs of humans and other primates, which are not available on this scale elsewhere. Keeping in mind that only a small fraction of currently known human lncRNAs have been functionally characterized and that lncRNA conservation is frequently used to identify the most relevant lncRNAs for functional studies, we believe that SyntDB will contribute to ongoing research aimed at deciphering the biological roles of lncRNAs.

scholarly journals Full-length annotation with multi-strategy RNA-seq uncovers transcriptional regulation of lncRNAs in diploid cotton G. arboreum1

2020 ◽  
Author(s):  
Xiaomin Zheng ◽  
Yanjun Chen ◽  
Yifan Zhou ◽  
Danyang Li ◽  
Keke Shi ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Rna Seq ◽  
Accurate Identification ◽  
Tissue Samples ◽  
Protein Coding ◽  
Diploid Cotton ◽  
Cap Analysis

AbstractLong noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. High-throughput and accurate identification of lncRNAs is still lacking in plants. To build an accurate atlas of lncRNA in cotton, we combined Isoform-sequencing (Iso-seq), strand-specific RNA-seq (ssRNA-seq), cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA (PULL) to integrate multi-omics data. A total of 9240 lncRNAs from 21 tissue samples of the diploid cotton Gossypium arboreum were identified. We revealed that alternative usage of transcription start site (TSS) and transcription end site (TES) of lncRNAs occurs pervasively during plant growth and responses to stress. We identified the lncRNAs which co-expressed or be linked to the protein coding genes (PCGs) or GWAS studied SNPs associated with ovule and fiber development. We also mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing (ChIRP-seq) and validated the trans transcriptional regulation of lnc-Ga13g0352 via virus induced gene suppression (VIGS) assay. These findings provide valuable research resources for plant community and broaden our understandings of biogenesis and regulation function of plant lncRNAs.One sentence summaryThe full-length annotation and transcriptional regulation of long noncoding RNAs in cotton.

scholarly journals RNA-seq analysis of the key long noncoding RNAs and mRNAs related to cognitive impairment after cardiac arrest and cardiopulmonary resuscitation

Aging ◽  
2020 ◽  
Vol 12 (14) ◽  
pp. 14490-14505
Author(s):  
Chan Chen ◽  
Changliang Liu ◽  
Zhendong Niu ◽  
Ming Li ◽  
Yuhan Zhang ◽  
...  
Keyword(s):  
Cardiac Arrest ◽  
Cognitive Impairment ◽  
Cardiopulmonary Resuscitation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq

scholarly journals Transcriptomic and Genome-wide Association Study Reveal Long Noncoding RNAs Responding to Nitrogen Deficiency in Maize

2020 ◽  
Author(s):  
PENG MA ◽  
Xiao Zhang ◽  
Bowen Luo ◽  
Zhen Chen ◽  
Xuan He ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Snp Array ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome

Abstract Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.

scholarly journals Genome-wide discovery and characterization of long noncoding RNAs in African oil palm (Elaeis guineensis Jacq.)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9585
Author(s):  
Wei Xia ◽  
Yajing Dou ◽  
Rui Liu ◽  
Shufang Gong ◽  
Dongyi Huang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Oil Palm ◽  
Target Genes ◽  
De Novo ◽  
Elaeis Guineensis ◽  
Expression Patterns ◽  
Noncoding Rnas ◽  
Snp Markers ◽  
Long Noncoding Rnas ◽  
Rna Seq

Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism.

Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data

2014 ◽  
Vol 113 (4) ◽  
pp. 1269-1281 ◽  
Author(s):  
Qi Liao ◽  
Jia Shen ◽  
Jianfa Liu ◽  
Xi Sun ◽  
Guoguang Zhao ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Functional Annotation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Genome Wide
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