Identification of 170 New Long Noncoding RNAs in Schistosoma mansoni

Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes such as organism development or cancer progression. Little, however, is known about their effects in helminths parasites, such as Schistosoma mansoni. Here, we present a computational pipeline to identify and characterize lncRNAs from RNA-seq data with high confidence from S. mansoni adult worms. Through the utilization of different criteria such as genome localization, exon number, gene length, and stability, we identified 170 new putative lncRNAs. All novel S. mansoni lncRNAs have no conserved synteny including human and mouse. These closest protein coding genes were enriched in 10 significant Gene Ontology terms related to metabolism, transport, and biosynthesis. Fifteen putative lncRNAs showed differential expression, and three displayed sex-specific differential expressions in praziquantel sensitive and resistant adult worm couples. Together, our method can predict a set of novel lncRNAs from the RNA-seq data. Some lncRNAs are shown to be differentially expressed suggesting that those novel lncRNAs can be given high priority in further functional studies focused on praziquantel resistance.

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PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

Nucleic Acids Research ◽

10.1093/nar/gkaa910 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D1489-D1495 ◽

Cited By ~ 1

Author(s):

Jingjing Jin ◽

Peng Lu ◽

Yalong Xu ◽

Zefeng Li ◽

Shizhou Yu ◽

...

Keyword(s):

Noncoding Rna ◽

Regulatory Networks ◽

Expression Patterns ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Data Driven ◽

Rna Seq ◽

Protein Coding ◽

User Friendly ◽

Coding Potential

Abstract Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.

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Long Noncoding RNAs in Plants

Annual Review of Plant Biology ◽

10.1146/annurev-arplant-093020-035446 ◽

2021 ◽

Vol 72 (1) ◽

Author(s):

Andrzej T. Wierzbicki ◽

Todd Blevins ◽

Szymon Swiezewski

Keyword(s):

Gene Expression ◽

Nuclear Dna ◽

Noncoding Rnas ◽

Chromatin Accessibility ◽

Long Noncoding Rnas ◽

Annual Review ◽

Publication Date ◽

Protein Coding ◽

Ribonucleic Acids ◽

Coding Potential

Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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When Long Noncoding Becomes Protein Coding

Molecular and Cellular Biology ◽

10.1128/mcb.00528-19 ◽

2020 ◽

Vol 40 (6) ◽

Cited By ~ 14

Author(s):

Corrine Corrina R. Hartford ◽

Ashish Lal

Keyword(s):

Cell Division ◽

Cell Signaling ◽

Transcription Regulation ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Open Reading Frames ◽

Protein Coding ◽

Small Proteins ◽

Coding Potential ◽

Reading Frames

ABSTRACT Recent advancements in genetic and proteomic technologies have revealed that more of the genome encodes proteins than originally thought possible. Specifically, some putative long noncoding RNAs (lncRNAs) have been misannotated as noncoding. Numerous lncRNAs have been found to contain short open reading frames (sORFs) which have been overlooked because of their small size. Many of these sORFs encode small proteins or micropeptides with fundamental biological importance. These micropeptides can aid in diverse processes, including cell division, transcription regulation, and cell signaling. Here we discuss strategies for establishing the coding potential of putative lncRNAs and describe various functions of known micropeptides.

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SyntDB: defining orthologues of human long noncoding RNAs across primates

Nucleic Acids Research ◽

10.1093/nar/gkz941 ◽

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.

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

10.1101/2020.07.21.214502 ◽

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.

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Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

Molecular and Cellular Biology ◽

10.1128/mcb.00955-15 ◽

2015 ◽

Vol 36 (5) ◽

pp. 809-819 ◽

Cited By ~ 51

Author(s):

Gireesh K. Bogu ◽

Pedro Vizán ◽

Lawrence W. Stanton ◽

Miguel Beato ◽

Luciano Di Croce ◽

...

Keyword(s):

Cell Line ◽

Cell Lines ◽

De Novo ◽

Noncoding Rnas ◽

Mouse Cell ◽

Long Noncoding Rnas ◽

Chromatin State ◽

Rna Seq ◽

Gene Encoding ◽

Protein Coding

Discovering and classifying long noncoding RNAs (lncRNAs) across all mammalian tissues and cell lines remains a major challenge. Previously, mouse lncRNAs were identified using transcriptome sequencing (RNA-seq) data from a limited number of tissues or cell lines. Additionally, associating a few hundred lncRNA promoters with chromatin states in a single mouse cell line has identified two classes of chromatin-associated lncRNA. However, the discovery and classification of lncRNAs is still pending in many other tissues in mouse. To address this, we built a comprehensive catalog of lncRNAs by combining known lncRNAs with high-confidence novel lncRNAs identified by mapping andde novoassembling billions of RNA-seq reads from eight tissues and a primary cell line in mouse. Next, we integrated this catalog of lncRNAs with multiple genome-wide chromatin state maps and found two different classes of chromatin state-associated lncRNAs, including promoter-associated (plncRNAs) and enhancer-associated (elncRNAs) lncRNAs, across various tissues. Experimental knockdown of an elncRNA resulted in the downregulation of the neighboring protein-codingKdm8gene, encoding a histone demethylase. Our findings provide 2,803 novel lncRNAs and a comprehensive catalog of chromatin-associated lncRNAs across different tissues in mouse.

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Application of Long Noncoding RNAs in Osteosarcoma: Biomarkers and Therapeutic Targets

Cellular Physiology and Biochemistry ◽

10.1159/000479205 ◽

2017 ◽

Vol 42 (4) ◽

pp. 1407-1419 ◽

Cited By ~ 72

Author(s):

Zhihong Li ◽

Pengcheng Dou ◽

Tang Liu ◽

Shasha He

Keyword(s):

Prognostic Biomarker ◽

Noncoding Rnas ◽

Therapeutic Targets ◽

Therapeutic Strategies ◽

Long Noncoding Rnas ◽

Protein Coding ◽

Rna Molecules ◽

Primary Bone ◽

Coding Potential ◽

Potential Biomarkers

Osteosarcoma is the most common primary bone malignancy in children and adolescents. Although improvements in therapeutic strategies were achieved, the outcome remains poor for most patients with metastatic or recurrent osteosarcoma. Therefore, it is imperative to identify novel and effective prognostic biomarker and therapeutic targets for the disease. Long noncoding RNAs (lncRNAs) are a novel class of RNA molecules defined as transcripts >200 nucleotides that lack protein coding potential. Many lncRNAs are deregulated in cancer and are important regulators for malignancies. Nine lncRNAs (91H, BCAR4, FGFR3-AS1, HIF2PUT, HOTTIP, HULC, MALAT-1, TUG1, UCA1) are upregulated and considered oncogenic for osteosarcoma. Loc285194 and MEG3 are two lncRNAs downregulated and as tumor suppressor for the disease. Moreover, the expressions of LINC00161 and ODRUL are associated with chemo-resistance of osteosarcoma. The mechanisms for these lncRNAs in regulating development of osteosarcoma are diverse, e.g. ceRNA, Wnt/β-catenin pathway, etc. The lncRNAs identified may serve as potential biomarkers or therapeutic targets for osteosarcoma.

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Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development

International Journal of Molecular Sciences ◽

10.3390/ijms22105087 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5087

Author(s):

Sebastian Gasparis ◽

Mateusz Przyborowski ◽

Anna Nadolska-Orczyk

Keyword(s):

Target Genes ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Shoot Apices ◽

Protein Coding ◽

Cis Acting ◽

Rna Molecules ◽

Functional Studies ◽

Potential Target ◽

Genome Wide

Long noncoding RNAs (lncRNAs) are a class of RNA molecules with gene regulatory functions in plant development and the stress response. Although the number of lncRNAs identified in plants is rapidly increasing, very little is known about their role in barley development. In this study, we performed global identification of barley lncRNAs based on 53 RNAseq libraries derived from nine different barley tissues and organs. In total, 17,250 lncRNAs derived from 10,883 loci were identified, including 8954 novel lncRNAs. Differential expression of lncRNAs was observed in the developing shoot apices and grains, the two organs that have a direct influence on the final yield. The regulatory interaction of differentially expressed lncRNAs with the potential target genes was evaluated. We identified 176 cis-acting lncRNAs in shoot apices and 424 in grains, while the number of trans-acting lncRNAs in these organs was 1736 and 540, respectively. The potential target protein-coding genes were identified, and their biological function was annotated using MapMan ontology. This is the first insight into the roles of lncRNAs in barley development on the genome-wide scale, and our results provide a solid background for future functional studies.

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Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network

BioMed Research International ◽

10.1155/2015/839590 ◽

2015 ◽

Vol 2015 ◽

pp. 1-14 ◽

Cited By ~ 11

Author(s):

Yun Xiao ◽

Yanling Lv ◽

Hongying Zhao ◽

Yonghui Gong ◽

Jing Hu ◽

...

Keyword(s):

Bayesian Network ◽

Regulatory Network ◽

Noncoding Rnas ◽

Nervous System Development ◽

Long Noncoding Rnas ◽

Functional Enrichment ◽

Biological Processes ◽

Rna Seq ◽

Protein Coding ◽

Protein Coding Genes

Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes. However, functions of most lncRNAs are poorly characterized. Here, we represent a framework to predict functions of lncRNAs through construction of a regulatory network between lncRNAs and protein-coding genes. Using RNA-seq data, the transcript profiles of lncRNAs and protein-coding genes are constructed. Using the Bayesian network method, a regulatory network, which implies dependency relations between lncRNAs and protein-coding genes, was built. In combining protein interaction network, highly connected coding genes linked by a given lncRNA were subsequently used to predict functions of the lncRNA through functional enrichment. Application of our method to prostate RNA-seq data showed that 762 lncRNAs in the constructed regulatory network were assigned functions. We found that lncRNAs are involved in diverse biological processes, such as tissue development or embryo development (e.g., nervous system development and mesoderm development). By comparison with functions inferred using the neighboring gene-based method and functions determined using lncRNA knockdown experiments, our method can provide comparable predicted functions of lncRNAs. Overall, our method can be applied to emerging RNA-seq data, which will help researchers identify complex relations between lncRNAs and coding genes and reveal important functions of lncRNAs.

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Long noncoding RNAs in biology and hematopoiesis

Blood ◽

10.1182/blood-2013-03-456111 ◽

2013 ◽

Vol 121 (24) ◽

pp. 4842-4846 ◽

Cited By ~ 28

Author(s):

Vikram R. Paralkar ◽

Mitchell J. Weiss

Keyword(s):

Gene Expression ◽

Transcriptome Sequencing ◽

Protein Localization ◽

Noncoding Rnas ◽

Cell Types ◽

Long Noncoding Rnas ◽

Protein Coding ◽

Regulate Gene Expression ◽

Multiple Processes ◽

Coding Potential

Abstract Genome and transcriptome sequencing have revealed a rich assortment of noncoding RNAs in eukaryote cells, including long noncoding RNAs (lncRNAs), which regulate gene expression independent of protein coding potential. LncRNAs modulate protein coding gene expression in many cell types by regulating multiple processes, including epigenetic control of transcription, mRNA stability, and protein localization. Although little is known about lncRNAs in hematopoiesis, they are likely to exert widespread roles in this process.

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