LncExpDB: an expression database of human long non-coding RNAs

Abstract Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

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Long non-coding RNA discovery in Anopheles gambiae using deep RNA sequencing

10.1101/007484 ◽

2014 ◽

Cited By ~ 1

Author(s):

Adam M Jenkins ◽

Robert M Waterhouse ◽

Alan S Kopin ◽

Marc A.T. Muskavitch

Keyword(s):

Anopheles Gambiae ◽

Rna Sequencing ◽

Transcriptional Repression ◽

Expression Profiles ◽

Sequence Evolution ◽

Life Stages ◽

Protein Coding ◽

Malaria Burden ◽

Protein Coding Genes ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs) are mRNA-like transcripts longer than 200 bp that have no protein-coding potential. lncRNAs have recently been implicated in epigenetic regulation, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified over 600 novel lncRNAs and more than 200 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. Those lncRNAs that are antisense to known protein-coding genes or are contained within intronic regions of protein-coding genes may mediate transcriptional repression or stabilization of associated mRNAs. lncRNAs exhibit faster rates of sequence evolution across anophelines compared to previously known and newly identified protein-coding genes. This initial description of lncRNAs in An. gambiae offers the first genome-wide insights into long non-coding RNAs in this vector mosquito and defines a novel set of potential targets for the development of vector-based interventions that may curb the human malaria burden in disease-endemic countries.

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Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Life ◽

10.3390/life10110300 ◽

2020 ◽

Vol 10 (11) ◽

pp. 300

Author(s):

Leyland Fraser ◽

Łukasz Paukszto ◽

Anna Mańkowska ◽

Paweł Brym ◽

Przemysław Gilun ◽

...

Keyword(s):

Target Genes ◽

De Novo ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Differentially Expressed ◽

Biological Processes ◽

Protein Coding ◽

Protein Coding Genes ◽

Potential Target ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

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The conservation and signatures of lincRNAs in Marek’s disease of chicken

Scientific Reports ◽

10.1038/srep15184 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 27

Author(s):

Yanghua He ◽

Yi Ding ◽

Fei Zhan ◽

Huanmin Zhang ◽

Bo Han ◽

...

Keyword(s):

T Cell ◽

Marek's Disease ◽

Marek’S Disease ◽

Protein Coding ◽

Functional Studies ◽

Wide Range ◽

Genetic Mechanisms ◽

Non Coding Rnas ◽

Computational Analyses ◽

Chicken Model

Abstract Long intergenic non-coding RNAs (lincRNAs) associated with a number of cancers and other diseases have been identified in mammals, but they are still formidable to be comprehensively identified and characterized. Marek’s disease (MD) is a T cell lymphoma of chickens induced by Marek’s disease virus (MDV). Here, we used a MD chicken model to develop a precise pipeline for identifying lincRNAs and to determine the roles of lincRNAs in T cell tumorigenesis. More than 1,000 lincRNA loci were identified in chicken bursa. Computational analyses demonstrated that lincRNAs are conserved among different species such as human, mouse and chicken. The putative lincRNAs were found to be associated with a wide range of biological functions including immune responses. Interestingly, we observed distinct lincRNA expression signatures in bursa between MD resistant and susceptible lines of chickens. One of the candidate lincRNAs, termed linc-satb1, was found to play a crucial role in MD immune response by regulating a nearby protein-coding gene SATB1. Thus, our results manifested that lincRNAs may exert considerable influence on MDV-induced T cell tumorigenesis and provide a rich resource for hypothesis-driven functional studies to reveal genetic mechanisms underlying susceptibility to tumorigenesis.

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Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsii

Phytopathology ◽

10.1094/phyto-07-12-0151-r ◽

2013 ◽

Vol 103 (5) ◽

pp. 479-487 ◽

Cited By ~ 6

Author(s):

Efrén Remesal ◽

Blanca B. Landa ◽

María del Mar Jiménez-Gasco ◽

Juan A. Navas-Cortés

Keyword(s):

Rna Polymerase Ii ◽

Sequence Variation ◽

Geographic Origin ◽

Sclerotium Rolfsii ◽

Nuclear Ribosomal Dna ◽

Causal Organism ◽

Protein Coding ◽

Protein Coding Genes ◽

Wide Range ◽

Mycelial Compatibility

Populations of Sclerotium rolfsii, the causal organism of Sclerotium root-rot on a wide range of hosts, can be placed into mycelial compatibility groups (MCGs). In this study, we evaluated three different molecular approaches to unequivocally identify each of 12 previously identified MCGs. These included restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and sequence analysis of two protein-coding genes: translation elongation factor 1α (EF1α) and RNA polymerase II subunit two (RPB2). A collection of 238 single-sclerotial isolates representing 12 MCGs of S. rolfsii were obtained from diseased sugar beet plants from Chile, Italy, Portugal, and Spain. ITS-RFLP analysis using four restriction enzymes (AluI, HpaII, RsaI, and MboI) displayed a low degree of variability among MCGs. Only three different restriction profiles were identified among S. rolfsii isolates, with no correlation to MCG or to geographic origin. Based on nucleotide polymorphisms, the RPB2 gene was more variable among MCGs compared with the EF1α gene. Thus, 10 of 12 MCGs could be characterized utilizing the RPB2 region only, while the EF1α region resolved 7 MCGs. However, the analysis of combined partial sequences of EF1α and RPB2 genes allowed discrimination among each of the 12 MCGs. All isolates belonging to the same MCG showed identical nucleotide sequences that differed by at least in one nucleotide from a different MCG. The consistency of our results to identify the MCG of a given S. rolfsii isolate using the combined sequences of EF1α and RPB2 genes was confirmed using blind trials. Our study demonstrates that sequence variation in the protein-coding genes EF1α and RPB2 may be exploited as a diagnostic tool for MCG typing in S. rolfsii as well as to identify previously undescribed MCGs.

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Coordinate regulation of long non-coding RNAs and protein-coding genes in germ-free mice

BMC Genomics ◽

10.1186/s12864-018-5235-3 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 15

Author(s):

Joseph Dempsey ◽

Angela Zhang ◽

Julia Yue Cui

Keyword(s):

Protein Coding ◽

Coordinate Regulation ◽

Germ Free ◽

Protein Coding Genes ◽

Non Coding Rnas

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Co‐regulation of long non‐coding RNAs and protein‐coding genes during cell quiescence

The FASEB Journal ◽

10.1096/fasebj.2021.35.s1.03263 ◽

2021 ◽

Vol 35 (S1) ◽

Author(s):

Hilary Coller ◽

Huiling Huang ◽

Mithun Mitra ◽

Kaiser Atai ◽

Kirthana Sarathy

Keyword(s):

Protein Coding ◽

Protein Coding Genes ◽

Cell Quiescence ◽

Non Coding Rnas

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DNA methylation patterns of protein-coding genes and long non-coding RNAs in males with schizophrenia

Molecular Medicine Reports ◽

10.3892/mmr.2015.4249 ◽

2015 ◽

Vol 12 (5) ◽

pp. 6568-6576 ◽

Cited By ~ 6

Author(s):

QI LIAO ◽

YUNLIANG WANG ◽

JIA CHENG ◽

DONGJUN DAI ◽

XINGYU ZHOU ◽

...

Keyword(s):

Dna Methylation ◽

Protein Coding ◽

Protein Coding Genes ◽

Non Coding Rnas ◽

Methylation Patterns

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Overlapping protein-coding genes in human genome and their coincidental expression in tissues

Scientific Reports ◽

10.1038/s41598-019-49802-w ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Chao-Hsin Chen ◽

Chao-Yu Pan ◽

Wen-chang Lin

Keyword(s):

Human Genome ◽

Expression Profiles ◽

Tissue Expression ◽

Human Protein ◽

Clear Understanding ◽

Overlapping Genes ◽

Genome Sequences ◽

Protein Coding ◽

Protein Coding Genes ◽

Overlapping Gene

Abstract The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5ʹ-tandem overlapping and 3ʹ-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

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LncTarD: a manually-curated database of experimentally-supported functional lncRNA–target regulations in human diseases

Nucleic Acids Research ◽

10.1093/nar/gkz985 ◽

2019 ◽

Cited By ~ 4

Author(s):

Hongying Zhao ◽

Jian Shi ◽

Yunpeng Zhang ◽

Aimin Xie ◽

Lei Yu ◽

...

Keyword(s):

Molecular Mechanisms ◽

Sequence Data ◽

Human Diseases ◽

Regulatory Mechanisms ◽

Biological Functions ◽

Functional Dynamics ◽

Disease Associations ◽

Non Coding Rnas ◽

User Friendly ◽

Pan Cancer

Abstract Long non-coding RNAs (lncRNAs) are associated with human diseases. Although lncRNA–disease associations have received significant attention, no online repository is available to collect lncRNA-mediated regulatory mechanisms, key downstream targets, and important biological functions driven by disease-related lncRNAs in human diseases. We thus developed LncTarD (http://biocc.hrbmu.edu.cn/LncTarD/ or http://bio-bigdata.hrbmu.edu.cn/LncTarD), a manually-curated database that provides a comprehensive resource of key lncRNA–target regulations, lncRNA-influenced functions, and lncRNA-mediated regulatory mechanisms in human diseases. LncTarD offers (i) 2822 key lncRNA–target regulations involving 475 lncRNAs and 1039 targets associated with 177 human diseases; (ii) 1613 experimentally-supported functional regulations and 1209 expression associations in human diseases; (iii) important biological functions driven by disease-related lncRNAs in human diseases; (iv) lncRNA–target regulations responsible for drug resistance or sensitivity in human diseases and (v) lncRNA microarray, lncRNA sequence data and transcriptome data of an 11 373 pan-cancer patient cohort from TCGA to help characterize the functional dynamics of these lncRNA–target regulations. LncTarD also provides a user-friendly interface to conveniently browse, search, and download data. LncTarD will be a useful resource platform for the further understanding of functions and molecular mechanisms of lncRNA deregulation in human disease, which will help to identify novel and sensitive biomarkers and therapeutic targets.

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