Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation

AbstractCarrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We discovered and annotated 8484 new genes, including 2095 new protein-coding and 6373 non-coding transcripts. Moreover, we identified 639 differentially expressed lncRNAs between the phenotypically contrasted genotypes, including certain only detected in a particular tissue. We then established correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.

Download Full-text

Identification and functional prediction of anthocyanin biosynthesis regulatory long non-coding RNAs (lncRNAs) in carrot

10.1101/2020.10.27.356964 ◽

2020 ◽

Author(s):

Constanza Chialva ◽

Thomas Blein ◽

Martin Crespi ◽

Diego Lijavetzky

Keyword(s):

Anthocyanin Biosynthesis ◽

Expression Profiles ◽

Biological Processes ◽

Rna Seq ◽

Functional Prediction ◽

Human Diet ◽

Storage Organs ◽

Non Coding Rnas ◽

Anthocyanin Production ◽

Molecular Framework

ABSTRACTCarrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We identified 639 differentially expressed lncRNAs between genotypes, and certain were specifically associated with a particular tissue. We then established regulatory correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript (NAT) linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.

Download Full-text

Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries

10.1101/2021.03.01.433483 ◽

2021 ◽

Author(s):

Calla L. Telzrow ◽

Paul J. Zwack ◽

Shannon Esher Righi ◽

Fred S. Dietrich ◽

Cliburn Chan ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Rna Sequencing ◽

Rnase H ◽

Rrna Genes ◽

Rna Seq ◽

Protein Coding ◽

Expression Levels ◽

Non Coding Rna ◽

Long Non Coding Rna ◽

Enrichment Methods

ABSTRACTRibosomal RNA (rRNA) is the major RNA constituent of cells, therefore most RNA sequencing (RNA-Seq) experiments involve removal of rRNA. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing would need to be performed to balance the sequencing reads wasted on rRNA. The ideal RNA enrichment method would remove all rRNA without affecting other RNA in the sample. We have tested the performance of three RNA enrichment methods on RNA isolated from Cryptococcus neoformans, a fungal pathogen of humans. We show that the RNase H depletion method unambiguously outperforms the commonly used Poly(A) isolation method: the RNase H method more efficiently depletes rRNA while more accurately recapitulating the expression levels of other RNA observed in an unenriched “gold standard”. The RNase H depletion method is also superior to the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding gene expression levels, while the Ribo-Zero depletion method performs moderately better in preserving non-coding RNA (ncRNA). Finally, we have leveraged this dataset to identify novel long non-coding RNA (lncRNA) genes and to accurately map the C. neoformans mitochondrial rRNA genes.ARTICLE SUMMARYWe compare the efficacy of three different RNA enrichment methods for RNA-Seq in Cryptococcus neoformans: RNase H depletion, Ribo-Zero depletion, and Poly(A) isolation. We show that the RNase H depletion method, which is evaluated in C. neoformans samples for the first time here, is highly efficient and specific in removing rRNA. Additionally, using data generated through these analyses, we identify novel long non-coding RNA genes in C. neoformans. We conclude that RNase H depletion is an effective and reliable method for preparation of C. neoformans RNA-Seq libraries.

Download Full-text

Pituitary Transcriptomic Study Reveals the Differential Regulation of lncRNAs and mRNAs Related to Prolificacy in Different FecB Genotyping Sheep

Genes ◽

10.3390/genes10020157 ◽

2019 ◽

Vol 10 (2) ◽

pp. 157 ◽

Cited By ~ 9

Author(s):

Jian Zheng ◽

Zhibo Wang ◽

Hua Yang ◽

Xiaolei Yao ◽

Pengcheng Yang ◽

...

Keyword(s):

Litter Size ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Pituitary Cells ◽

Rna Seq ◽

Non Coding Rna ◽

Long Non Coding Rna ◽

Hu Sheep

Long non-coding RNA (LncRNA) have been identified as important regulators in the hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, their expression pattern and potential roles in the pituitary are yet unclear. To explore the potential mRNAs and lncRNAs that regulate the expression of the genes involved in sheep prolificacy, we used stranded specific RNA-seq to profile the pituitary transcriptome (lncRNA and mRNA) in high prolificacy (genotype FecB BB, litter size = 3; H) and low prolificacy sheep (genotype FecB B+; litter size = 1; L). Our results showed that 57 differentially expressed (DE) lncRNAs and 298 DE mRNAs were found in the pituitary between the two groups. The qRT-PCR results correlated well with the RNA-seq results. Moreover, functional annotation analysis showed that the target genes of the DE lncRNAs were significantly enriched in pituitary function, hormone-related pathways as well as response to stimulus and some other terms related to reproduction. Furthermore, a co-expression network of lncRNAs and target genes was constructed and reproduction related genes such as SMAD2, NMB and EFNB3 were included. Lastly, the interaction of candidate lncRNA MSTRG.259847.2 and its target gene SMAD2 were validated in vitro of sheep pituitary cells. These differential mRNA and lncRNA expression profiles provide a valuable resource for understanding the molecular mechanisms underlying Hu sheep prolificacy.

Download Full-text

Differential Expression of Long Non-Coding RNA (lncRNA) in Mediterranean Mussel (Mytilus galloprovincialis) Hemocytes under Immune Stimuli

Genes ◽

10.3390/genes12091393 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1393

Author(s):

Patricia Pereiro ◽

Rebeca Moreira ◽

Beatriz Novoa ◽

Antonio Figueras

Keyword(s):

Regulation Of Gene Expression ◽

Poly I:C ◽

Rna Seq ◽

Protein Coding ◽

Non Coding Rna ◽

Discrete Response ◽

Mediterranean Mussel ◽

Long Non Coding Rna ◽

Mollusk Species

The Mediterranean mussel is one of the most economically relevant bivalve mollusk species in Europe and China. The absence of massive mortalities and their resistance to pathogens affecting other cultured bivalves has been under study in recent years. The transcriptome response of this species to different immune stimuli has been extensively studied, and even the complexity of its genome, which has recently been sequenced, has been suggested as one of the factors contributing to this resistance. However, studies concerning the non-coding RNA profiles remain practically unexplored—especially those corresponding to the lncRNAs. To the best of our knowledge, this is the second characterization and study of lncRNAs in this bivalve species. In this work, we identified the potential repertoire of lncRNAs expressed in mussel hemocytes, and using RNA-Seq we analyzed the lncRNA profile of mussel hemocytes stimulated in vitro with three different immune stimuli: LPS, poly I:C, and β-glucans. Compared to unstimulated hemocytes, LPS induced the highest modulation of lncRNAs, whereas poly I:C and β-glucans induced a similar discrete response. Based on the potential cis-regulatory activity of the lncRNAs, we identified the neighboring protein-coding genes of the regulated lncRNAs to estimate—at least partially—the processes in which they are implicated. After applying correlation analyses, it seems that—especially for LPS—the lncRNAs could participate in the regulation of gene expression, and substantially contribute to the immune response.

Download Full-text

Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione

Antioxidants ◽

10.3390/antiox9050402 ◽

2020 ◽

Vol 9 (5) ◽

pp. 402

Author(s):

Qinqin Guo ◽

Lixin Cui ◽

Weijun Sun ◽

Feng Li ◽

Haisheng Hao ◽

...

Keyword(s):

Early Stage ◽

Expression Profiles ◽

Glutathione Metabolism ◽

Bovine Embryos ◽

Protein Coding ◽

Citrate Cycle ◽

Non Coding Rna ◽

Long Non Coding Rna ◽

Go Terms

We measured differential expression profiles of genes and long non-coding RNA (lncRNA) using RNA sequencing in bovine embryos with or without glutathione (GSH) treatment. Bovine embryos fertilized in vitro were treated with GSH to blastocyst. Embryos at the 8-16-cell and morula stages were collected, with embryos without GSH treatment as the control. RNA was isolated, amplified, and sequenced. Differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) were identified and bioinformatic analyses carried out. Transcript levels were confirmed using quantitative RT-PCR. A total of 4100 DEGs were identified, of which 3952 were in GSH-treated morulae and 884 in untreated morulae. More gene ontology (GO) terms were associated with GSH treatment than with control conditions. KEGG analysis showed that glutathione metabolism, citrate cycle, and metabolic pathways involving glycine, serine, and threonine were observed only in GSH-treated embryos. Among 4273 DElncRNAs identified, 59 were potentially important in GSH-treated embryo development, including 14 involved in glutathione metabolism. The 59 DElncRNAs co-expressed with protein-coding mRNAs involved similar GO terms and pathways as the DEGs. This appears to be the first comprehensive profiling of DEGs and DElncRNAs in bovine embryos fertilized in vitro with or without GSH, and the first systematic screen of potential lncRNAs in bovine embryos.

Download Full-text

Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

10.21203/rs.3.rs-37391/v2 ◽

2020 ◽

Author(s):

Chunyan Li ◽

Xiaoyun He ◽

Zijun Zhang ◽

Chunhuan Ren ◽

Mingxing Chu

Keyword(s):

Pineal Gland ◽

Target Genes ◽

Expression Profiles ◽

Enrichment Analysis ◽

Rna Seq ◽

Non Coding Rna ◽

Important Regulator ◽

Gsh Metabolism ◽

Transcriptome Expression ◽

Long Non Coding Rna

Abstract Background: long non-coding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, there is little report about lncRNA in pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified.Results: Overall, 135 DE lncRNAs and 1,360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, like XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included.Conclusion: All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

Download Full-text

Long non-coding RNA expression profiles in human parathyroid tumors

Endocrine Abstracts ◽

10.1530/endoabs.49.gp130 ◽

2017 ◽

Author(s):

Annamaria Morotti ◽

Irene Forno ◽

Valentina Andre ◽

Andrea Terrasi ◽

Chiara Verdelli ◽

...

Keyword(s):

Expression Profiles ◽

Rna Expression ◽

Parathyroid Tumors ◽

Non Coding Rna ◽

Long Non Coding Rna

Download Full-text

Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

BMC Plant Biology ◽

10.1186/s12870-021-02835-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Guoning Wang ◽

Xingfen Wang ◽

Yan Zhang ◽

Jun Yang ◽

Zhikun Li ◽

...

Keyword(s):

Disease Resistance ◽

Verticillium Wilt ◽

Dynamic Characteristics ◽

Target Genes ◽

Acid Metabolism ◽

Expression Profiles ◽

Enrichment Analysis ◽

Alpha Linolenic Acid ◽

Non Coding Rna ◽

Long Non Coding Rna

Abstract Background Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear. Results Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA. Conclusion This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

Download Full-text

Long non-coding RNA LINC00665 promotes gemcitabine resistance of Cholangiocarcinoma cells via regulating EMT and stemness properties through miR-424-5p/BCL9L axis

Cell Death and Disease ◽

10.1038/s41419-020-03346-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Min Lu ◽

Xinglei Qin ◽

Yajun Zhou ◽

Gang Li ◽

Zhaoyang Liu ◽

...

Keyword(s):

Acquired Resistance ◽

Transcriptional Regulators ◽

First Line ◽

Protein Coding ◽

Gemcitabine Resistance ◽

Non Coding Rna ◽

Sphere Formation ◽

Long Non Coding Rna ◽

Line Chemotherapy

AbstractGemcitabine is the first-line chemotherapy drug for cholangiocarcinoma (CCA), but acquired resistance has been frequently observed in CCA patients. To search for potential long noncoding RNAs (lncRNAs) involved in gemcitabine resistance, two gemcitabine resistant CCA cell lines were established and dysregulated lncRNAs were identified by lncRNA microarray. Long intergenic non-protein coding RNA 665 (LINC00665) were found to rank the top 10 upregulated lncRNAs in our study, and high LINC00665 expression was closely associated with poor prognosis and chemoresistance of CCA patients. Silencing LINC00665 in gemcitabine resistant CCA cells impaired gemcitabine tolerance, while enforced LINC00665 expression increased gemcitabine resistance of sensitive CCA cells. The gemcitabine resistant CCA cells showed increased EMT and stemness properties, and silencing LINC00665 suppressed sphere formation, migration, invasion and expression of EMT and stemness markers. In addition, Wnt/β-Catenin signaling was activated in gemcitabine resistant CCA cells, but LINC00665 knockdown suppressed Wnt/β-Catenin activation. B-cell CLL/lymphoma 9-like (BCL9L), the nucleus transcriptional regulators of Wnt/β-Catenin signaling, plays a key role in the nucleus translocation of β-Catenin and promotes β-Catenin-dependent transcription. In our study, we found that LINC00665 regulated BCL9L expression by acting as a molecular sponge for miR-424-5p. Moreover, silencing BCL9L or miR-424-5p overexpression suppressed gemcitabine resistance, EMT, stemness and Wnt/β-Catenin activation in resistant CCA cells. In conclusion, our results disclosed the important role of LINC00665 in gemcitabine resistance of CCA cells, and provided a new biomarker or therapeutic target for CCA treament.

Download Full-text

Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽

10.3390/ani11072006 ◽

2021 ◽

Vol 11 (7) ◽

pp. 2006

Author(s):

Hongyu Liu ◽

Ibrar Muhammad Khan ◽

Huiqun Yin ◽

Xinqi Zhou ◽

Muhammad Rizwan ◽

...

Keyword(s):

Target Genes ◽

Expression Profiles ◽

Age Groups ◽

Adherens Junction ◽

Integrated Analysis ◽

Sequencing Data ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Rna Interaction ◽

Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

Download Full-text