SyntDB: defining orthologues of human long noncoding RNAs across primates

Bryzghalov, Oleksii; Szcześniak, Michał Wojciech; Makałowska, Izabela

doi:10.1093/nar/gkz941

Cited by 22 publications

(33 citation statements)

References 41 publications

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“…Recent studies have shown that several lncRNAs have conserved syntenic location (Herrera-úbeda et al 2019; Bryzghalov et al 2020; Amaral et al 2018). Hezroni et al were also able to detect several syntenically conserved lncRNAs even when the sequence was not conserved (Hezroni et al 2015).…”

Section: Resultsmentioning

confidence: 99%

“…Unlike protein coding (PC) genes, lncRNAs do not have conserved sequence similarity and rapid evolutionary turnover renders the identification of orthologs challenging. The few studies that investigated the conservation of lncRNAs found little evidence of sequence conservation (Necsulea et al 2014), while other studies attempted to identify lncRNA homologs based on syntenic organization (Hezroni et al 2015; Chen et al 2016; Bryzghalov et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology

Gandhi¹,

Witten²,

deMajo

et al. 2021

Preprint

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Cardiovascular disease (CVD) remains the leading cause of death worldwide. A deeper characterization of the regional transcription patterns within different heart chambers may aid to improve our understanding of the molecular mechanisms involved in the function of the heart as well as our ability to develop novel therapeutic strategies. Here, we determined differentially expressed protein coding, long non-coding (lncRNA) and circular RNA (CircRNA) genes within various heart chambers across seven vertebrate species. We identified chamber specific genes, lncRNAs and pathways that are evolutionarily conserved in vertebrates. Further, we identified lncRNA homologs based on sequence, secondary structure, synteny and expressional conservation. Interestingly, most lncRNAs were found to be syntenically conserved. Various factors affect the co-expression patterns of transcripts including (i) genomic overlap, (ii) strandedness and (iii) transcript biotype. We also provide a catalogue of CircRNAs which are abundantly expressed across vertebrate hearts. Finally, we established a repository called EvoACTG (http://evoactg.uni-muenster.de/), which provides information about the conserved expression patterns for both PC genes and non-coding RNAs (ncRNAs) in the various heart chambers, and may serve as a community resource for investigators interested in the (patho)-physiology of CVD. We believe that this study will inform researchers working in the field of cardiovascular biology to explore the conserved yet intertwined nature of both coding and non-coding cardiac transcriptome across various popular model organisms in CVD research.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology

Gandhi¹,

Witten²,

deMajo

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…As a result, one obtains a set of lncRNAs in the GTF and FASTA formats as well as a tab-separated text file with the detailed annotation data. The overall lncRNA search procedure represents a modification of previously published protocols and was previously applied by us in large-scale studies [ 4 , 24 ].…”

Section: Methodsmentioning

confidence: 99%

“…It should be noted, however, that there are diverse patterns of lncRNA conservation, which are believed to reflect their mode of action [ 3 ]. Most often, lncRNAs show only positional conservation, with the sequence itself showing little or no similarity to the assumed homologue (referred to as a syntenic homologue or syntolog) [ 4 ]. They are expected to exert their functions, such as cotranscriptional recruitment of the complex epigenetic machinery that mediates histone modifications, in a sequence-independent manner, leading to transcriptional regulation of genes in cis [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

lncEvo: automated identification and conservation study of long noncoding RNAs

2021

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Background Long noncoding RNAs represent a large class of transcripts with two common features: they exceed an arbitrary length threshold of 200 nt and are assumed to not encode proteins. Although a growing body of evidence indicates that the vast majority of lncRNAs are potentially nonfunctional, hundreds of them have already been revealed to perform essential gene regulatory functions or to be linked to a number of cellular processes, including those associated with the etiology of human diseases. To better understand the biology of lncRNAs, it is essential to perform a more in-depth study of their evolution. In contrast to protein-encoding transcripts, however, they do not show the strong sequence conservation that usually results from purifying selection; therefore, software that is typically used to resolve the evolutionary relationships of protein-encoding genes and transcripts is not applicable to the study of lncRNAs. Results To tackle this issue, we developed lncEvo, a computational pipeline that consists of three modules: (1) transcriptome assembly from RNA-Seq data, (2) prediction of lncRNAs, and (3) conservation study—a genome-wide comparison of lncRNA transcriptomes between two species of interest, including search for orthologs. Importantly, one can choose to apply lncEvo solely for transcriptome assembly or lncRNA prediction, without calling the conservation-related part. Conclusions lncEvo is an all-in-one tool built with the Nextflow framework, utilizing state-of-the-art software and algorithms with customizable trade-offs between speed and sensitivity, ease of use and built-in reporting functionalities. The source code of the pipeline is freely available for academic and nonacademic use under the MIT license at https://gitlab.com/spirit678/lncrna_conservation_nf.

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“…lncRNAs are defined as transcripts of more than 200 nucleotides in length that are not translated into proteins. An increased number of studies highlight their important biological roles in processes such as post-transcriptional regulation, cell cycle regulation and cell apoptosis, and protein localization ( Bryzghalov et al, 2020 ). circRNAs are a recently identified genetic element that are covalently closed and evolutionarily conserved.…”

Section: Introductionmentioning

confidence: 99%

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

et al. 2020

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RNA in milk exosomes can be absorbed in the mammalian intestinal tract and function in gene expression regulations. Our previous work demonstrated that porcine milk exosomes (PME) contain large amounts of miRNAs and mRNAs. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are of particular interest, given their key role in diverse biological processes of animals. However, the expression profiles and the potential functions of lncRNAs and circRNAs in PME are still unknown. In the present study, we isolated PME by ultracentrifugation and performed a comprehensive analysis of lncRNA and circRNA in PME by using RNA sequencing. As a result, 2,466 novel lncRNAs, 809 annotated lncRNAs, and 61 circRNAs were identified in PME. The lncRNAs shared similar characteristics with other mammals in terms of length, exon number, and open reading frames. However, lncRNAs showed a higher level compared with mRNAs. Eight lncRNAs and five circRNAs in PME were selected for PCR identification. A functional enrichment analysis on the target genes of lncRNAs indicated that these genes were involved in cellular macromolecule metabolic, RNA metabolic, and immune processes. The circRNAs host genes were enriched in nucleic acid binding and adherence junction. We also evaluated the potential interaction targets between miRNAs and PME lncRNAs or circRNAs, and the results showed that the PME lncRNAs and the circRNAs have a high density of miRNA target sites. The top 20 highly expressed lncRNAs were found to interact with the proliferation-related miRNAs, and the circRNAs potentially targeted many miRNAs that are associated with the intestinal barrier. This study is the first to provide a resource for lncRNA and circRNA research of porcine milk. Moreover, the potential interaction between lncRNA/circRNA and miRNA is revealed. The present study expands our knowledge of non-coding RNAs in milk, and additional research is necessary to confirm their exactly physiological functions.

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SyntDB: defining orthologues of human long noncoding RNAs across primates

Cited by 22 publications

References 41 publications

Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology

Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology

lncEvo: automated identification and conservation study of long noncoding RNAs

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

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