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

Abstract

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...

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

“…The transcriptional regulation of lncRNAs could be predicted as cis and trans , and could have a positive or negative effect on gene expression [ 7 ]. It is noteworthy that lncRNA regulates the expression of a target gene by cis -regulation, which is restricted to the chromosome from which it is transcribed, while a lncRNA role in trans -regulation is predicted when it affects genes on other chromosomes at the expression level [ 6 , 7 ]. We hypothesized that the DElncRNA target genes could act through cis - or trans -regulating mechanisms, thereby affecting sperm freezability.…”

“…Spermatozoa comprise a wide repertoire of RNAs that are implicated in several biological processes associated with spermatogenesis, fertilization and embryo development [ 1 , 2 , 3 , 4 , 5 ]. In eukaryotes, the vast majority of gene transcripts are non-coding RNAs (ncRNAs) [ 6 ]. While once thought to be “junk” in the sequences of genomes, accumulating evidence has shown that ncRNAs are implicated in numerous important biological processes, such as transcription, splicing, translation, epigenetic modifications, cell development and differentiation [ 3 , 5 , 6 , 7 , 8 ].…”

“…While once thought to be “junk” in the sequences of genomes, accumulating evidence has shown that ncRNAs are implicated in numerous important biological processes, such as transcription, splicing, translation, epigenetic modifications, cell development and differentiation [ 3 , 5 , 6 , 7 , 8 ]. Recently, several reports have focused on the biological functions of long non-coding RNAs (lncRNAs) [ 4 , 6 , 8 ]. Evidence has shown that the lncRNAs represent the largest part of the transcriptome in mammals, but only a small proportion has been functionally characterized [ 7 ].…”

Roles for the long non-coding RNAPax6os1/PAX6-AS1in pancreatic beta cell identity and function

“…LncRNAs may regulate gene expression through a number of different mechanisms. These include chromatin remodelling, activation/repression of transcription factors in the nucleus as well as modulation of mRNA/protein stability in the cytoplasm 26,27 . Therefore, the subcellular localization of a lncRNA may provide a reliable indicator of its mechanism(s) of action.…”

Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship

“…Well-known and characterized ncRNA classes include ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), playing pivotal roles in translation. Research focused on other ncRNA classes, such as long intergenic non-coding RNAs (lincRNAs) and microRNAs (miRNAs), have identified that transcripts from these classes serve important regulatory roles in coding transcription [ 11 , 12 ]. Less well characterized ncRNA classes emerge from functional genomic elements, such as enhancer RNAs (eRNAs), promoter proximal transcripts (PROMPTs), or telomeric repeat containing RNAs (TERRAs).…”