Computational Approaches to Predict Protein Interaction

Chang, Tien-Hao

doi:10.5772/38340

Cited by 1 publication

(1 citation statement)

References 45 publications

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“…These algorithms have been applied to create computational tools and web servers to predict RNA/protein interaction partners. A detailed description of these tools is beyond the scope of this review but those readers who seek more insights will find it useful to read the manuscript from the Dobbs' lab (Muppirala et al, 2013 ) and book chapters (Chang, 2012 ; Meller and Porollo, 2012 ). More recently, an innovative large-scale pipeline has been developed by Ribeiro and colleagues to identify candidate lncRNAs acting as scaffolding molecules for protein complexes (Ribeiro et al, 2017 ).…”

Section: New Technologies For the Study Of Lncrnas/protein Interactiomentioning

confidence: 99%

The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

Cipriano

Ballarino

2018

Front. Mol. Biosci.

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The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.

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