Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Schor, Ignacio E.; Bussotti, Giovanni; Maleš, Matilda; Forneris, Mattia; Viales, Rebecca R.; Enright, Anton J.; Furlong, Eileen E. M.

doi:10.1016/j.cub.2018.09.026

Cited by 46 publications

(40 citation statements)

References 82 publications

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“…Furthermore, we also found GO terms related to stress tolerance, including response to stimulus (nine genes), signaling (three genes), and transporter activity (six genes), suggesting that some lncRNAs might contribute to drought stress tolerance via control of target gene expression. with bidirectional promoters, RNA-mediated enhancement, and genomic imprinting [45][46][47][48]. To identify potential mRNA targets of drought-responsive tomato lncRNA, we initially predicted potential mRNA targets by searching 100 kb upstream and downstream of each lncRNA.…”

Section: Functional Characterization Of Drought-responsive Tomato Lonmentioning

confidence: 99%

Identification and Functional Prediction of Drought-Responsive Long Non-Coding RNA in Tomato

Eom

Lee²,

Lee³

et al. 2019

Agronomy

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In higher plants, several lines of evidence suggest that long non-coding RNAs (lncRNAs) may play important roles in the regulation of various biological processes by regulating gene expression. In this study, we identified a total of 521 lncRNAs, classified as intergenic, intronic, sense, and natural antisense lncRNAs, from RNA-seq data of drought-exposed tomato leaves. A further 244 drought-responsive tomato lncRNAs were predicted to be putative targets of 92 tomato miRNAs. Expression pattern and preliminary functional analysis of potential mRNA targets suggested that drought-responsive tomato lncRNAs play important roles in a variety of biological processes via lncRNA–mRNA co-expression. Taken together, these data present a comprehensive view of drought-responsive tomato lncRNAs that serve as a starting point for understanding the role of long intergenic non-coding RNAs in the regulatory mechanisms underlying drought responses in crops.

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Section: Functional Characterization Of Drought-responsive Tomato Lonmentioning

confidence: 99%

Identification and Functional Prediction of Drought-Responsive Long Non-Coding RNA in Tomato

Eom

Lee²,

Lee³

et al. 2019

Agronomy

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“…Recent advances based on RNA sequencing efforts documented several classes of long and short noncoding RNAs transcribed in the promoter regions proximal the transcription start sites (TSS) of most annotated genes, bona fide involved in the regulation of transcription initiation [1]. Among them, the promoter-associated noncoding RNAs (named interchangeably pancRNAs or pncRNAs) have now been described in all eukaryotic species, from yeast to human [1][2][3][4][5][6][7][8][9]. PancRNAs are defined as transcripts transcribed within a few hundred bases from the TSSs of protein-coding or non-coding genes.…”

Section: Introductionmentioning

confidence: 99%

Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer

Chellini

Frezza

Paronetto

2020

J Exp Clin Cancer Res

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In-depth analysis of global RNA sequencing has enabled a comprehensive overview of cellular transcriptomes and revealed the pervasive transcription of divergent RNAs from promoter regions across eukaryotic genomes. These studies disclosed that genomes encode a vast repertoire of RNAs beyond the well-known protein-coding messenger RNAs. Furthermore, they have provided novel insights into the regulation of eukaryotic epigenomes, and transcriptomes, including the identification of novel classes of noncoding transcripts, such as the promoterassociated noncoding RNAs (pancRNAs). PancRNAs are defined as transcripts transcribed within few hundred bases from the transcription start sites (TSSs) of protein-coding or non-coding genes. Unlike the long transacting ncRNAs that regulate expression of target genes located in different chromosomal domains and displaying their function both in the nucleus and in the cytoplasm, the pancRNAs operate as cis-acting elements in the transcriptional regulation of neighboring genes. PancRNAs are very recently emerging as key players in the epigenetic regulation of gene expression programs in development and diseases. Herein, we review the complex epigenetic network driven by pancRNAs in eukaryotic cells, their impact on physiological and pathological states, which render them promising targets for novel therapeutic strategies.

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“…Many studies have described the developmental and tissue-specific expression of these transcripts in different organisms (eg. human, mouse, or fruit fly) [147][148][149]. However, it was only recently that it became possible to study lncRNAs at the single-cell level with a genome-wide approach by using scRNA-seq.…”

Section: Single-cell Analysis Of Lncrnasmentioning

confidence: 99%

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

Alessio

Bonadio

Buson

et al. 2020

IJMS

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In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.Int. J. Mol. Sci. 2020, 21, 302 2 of 32 not achieved by transcription factors (TFs) alone because of their low number (approximately 1500 in mammals [4]) compared to genes to regulate (90% of the genome is transcribed in human [5]). A single TF is estimated to regulate only ten thousand genes according to Chromatin immunoprecipitation and DNA sequencing experiments (ChIp-seq) [6]. Moreover, the involvement of non-coding RNAs in gene expression regulation was evident [7,8]. The evidence that the non-protein coding component of the human genome is actively transcribed and carries out crucial functions limits the importance of coding genes in genome regulation. Non-coding transcripts become one of the stars of modern biology, especially because of their involvement in a wide range of regulatory processes and changed the association of non-coding regions to junk DNA [3].The genome of multicellular eukaryotes is mostly comprised of non-coding DNA (less than 2% of the human genome codes for proteins [9] while 90% of the human genome is transcribed). Non-coding DNA is transcribed into different classes of non-coding RNAs (ncRNAs) that include structural RNAs (rRNAs and tRNAs) and regulatory RNAs [10]. rRNAs and tRNAs are involved in mRNA translation and can be long or short in size. Regulatory RNAs are further divided into three classes: Small, medium, and long non-coding RNAs. Small non-coding RNAs are between 20 and 50 nucleotides long and include microRNAs (miRNAs) that participate in post-transcriptional regulation [11], small interfering RNAs (siRNAs) that are double-stranded RNAs involved in gene silencing through RNA interfering pathway [12], piwi interacting R...

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Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Cited by 46 publications

References 82 publications

Identification and Functional Prediction of Drought-Responsive Long Non-Coding RNA in Tomato

Identification and Functional Prediction of Drought-Responsive Long Non-Coding RNA in Tomato

Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

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