Abstract
The majority of the human transcriptome is defined as non-coding RNA (ncRNA), since only a small fraction of human DNA encodes for proteins, as reported by the ENCODE project. Several distinct classes of ncRNAs, such as transfer RNA, microRNA, and long non-coding RNA, have been classified, each with its own three-dimensional folding and specific function. As ncRNAs are highly abundant in living organisms and have been discovered to play important roles in many biological processes, there has been an ever increasing need to investigate the entire ncRNAome in further unbiased detail. Recently, the advent of next-generation sequencing (NGS) technologies has substantially increased the throughput of transcriptome studies, allowing an unprecedented investigation of ncRNAs, as regulatory pathways and novel functions involving ncRNAs are now also emerging. The huge amount of transcript data produced by NGS has progressively required the development and implementation of suitable bioinformatics workflows, complemented by knowledge-based approaches, to identify, classify, and evaluate the expression of hundreds of ncRNAs in normal and pathological conditions, such as cancer. In this mini-review, we present and discuss current bioinformatics advances in the development of such computational approaches to analyze and classify the ncRNA component of human transcriptome sequence data obtained from NGS technologies.
Highlights
For over five decades, the central dogma of molecular biology has represented the basis of genetics (Crick, 1970), essentially describing the genetic information flow of life in which DNA and protein, as respectively repository and functional incarnation of that information, have been viewed as the two main actors in the life of the cell, confining RNA to the role of template for protein synthesis
Output is represented by a diverse family of untranslated transcripts that play crucial roles in many biochemical cellular processes (Mattick, 2001). These non-coding RNAs are divided into two major categories most commonly according to their nucleotide sequence length: small (
Most currently available tools/pipelines for transcriptome investigation through next-generation sequencing (NGS) concentrate on detection/prediction/expression quantification of small RNAs, especially miRNAs
Summary
The central dogma of molecular biology has represented the basis of genetics (Crick, 1970), essentially describing the genetic information flow of life in which DNA and protein, as respectively repository and functional incarnation of that information, have been viewed as the two main actors in the life of the cell, confining RNA to the role of template for protein synthesis. NcRNA bioinformatics analysis through NGS output is represented by a diverse family of untranslated transcripts that play crucial roles in many biochemical cellular processes (Mattick, 2001) These non-coding RNAs (ncRNAs) are divided into two major categories most commonly according to their nucleotide sequence length: small (
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