LncRNAs in vertebrates: Advances and challenges

Abstract

Beyond the handful of classic and well-characterized long noncoding RNAs (lncRNAs), more recently, hundreds of thousands of lncRNAs have been identified in multiple species including bacteria, plants and vertebrates, and the number of newly annotated lncRNAs continues to increase as more transcriptomes are analyzed. In vertebrates, the expression of many lncRNAs is highly regulated, displaying discrete temporal and spatial expression patterns, suggesting roles in a wide range of developmental processes and setting them apart from classic housekeeping ncRNAs. In addition, the deregulation of a subset of these lncRNAs has been linked to the development of several diseases, including cancers, as well as developmental anomalies. However, the majority of vertebrate lncRNA functions remain enigmatic. As such, a major task at hand is to decipher the biological roles of lncRNAs and uncover the regulatory networks upon which they impinge. This review focuses on our emerging understanding of lncRNAs in vertebrate animals, highlighting some recent advances in their functional analyses across several species and emphasizing the current challenges researchers face to characterize lncRNAs and identify their in vivo functions.

Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer

“…LncRNAs are defined as RNAs longer than 200 nucleotides that do not encode proteins [1]. Like mRNAs, lncRNAs can be regulated by transcription factors, undergo post-transcriptional processing, form complex secondary and tertiary structures and exhibit tissue- and development-specific expression [2, 3]. LncRNAs differ from mRNAs in that their primary structures are generally poorly conserved between species and they are expressed at very low to moderate levels, relative to mRNAs [2, 3].…”

“…Like mRNAs, lncRNAs can be regulated by transcription factors, undergo post-transcriptional processing, form complex secondary and tertiary structures and exhibit tissue- and development-specific expression [2, 3]. LncRNAs differ from mRNAs in that their primary structures are generally poorly conserved between species and they are expressed at very low to moderate levels, relative to mRNAs [2, 3]. While the molecular functions of most lncRNAs remain largely unknown, there is growing evidence that lncRNAs have functional roles in cell biology and development [4, 5].…”

“…Mechanistically, lncRNAs have been shown to modulate gene expression at the level of transcription by associating with DNA and chromatin modifying complexes, thereby mediating alteration of the local epigenetic landscape [1, 6]. LncRNAs have also been shown to act as decoys for transcription factors [7], regulate protein activity [2, 8], and function as structural components in subcellular structures like nuclear paraspeckles [3, 9]. A growing list of lncRNAs are being identified as dysregulated in cancer cells, and several studies have shown that lncRNAs can contribute to the etiology of diseases like prostate cancer [10–12].…”

The Long Non‐Coding RNA Transcriptome Landscape in CHO Cells Under Batch and Fed‐Batch Conditions

“…Our approach allowed the identification of previously undescribed lncRNAs in CHO along with mRNAs to identify the connections between them and compared these with existent literature. This network of reciprocal interactions is beginning to be unveiled in other organisms and our work will help pave the way for the definition of new layers of regulation involving single transcripts or even entire pathways in CHO.…”

State of the art technologies to explore long non‐coding RNAs in cancer

“…Among transcripts encoded by these regions are long non-coding RNAs [5]. Most lncRNAs are transcribed by RNA polymerase II [1], and similar to protein-coding RNAs, can be subjected to post-transcriptional modifications, including 5 0 -end capping, 3 0 -end polyadenylation, splicing [6][7][8][9][10][11] N 6 adenosine methylation (m 6 A) [12] and A-to-I editing [13]. Due to not having a comprehensive knowledge of their function, LncRNAs are categorized based on their location relative to the protein-coding genes as: sense (which are transcribed from sense strand of protein-coding genes and overlap one or more exons and introns), antisense (which are transcribed from the antisense strand of protein-coding genes), bidirectional (which are located 1 kb away from promoters of protein-coding genes in the opposite direction), intronic (which are located between exons of protein-coding genes) and intergenic (which are located between two protein-coding genes) [5,7,14,15].…”