Non‐coding RNAs: biological functions and applications

Santosh, Baby; Varshney, Akhil; Yadava, Pramod Kumar

doi:10.1002/cbf.3079

Cited by 149 publications

(100 citation statements)

References 87 publications

(164 reference statements)

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“…These include long RNAs (lncRNAs), and many small noncoding RNAs such as miRNAs (microRNAs), siRNAs (small interfering RNAs), and piRNAs (Piwi-interacting RNAs). These mRNA-like molecules do not code for proteins but rather play key regulatory roles in a variety of cellular processes by modulating the levels and translation of other RNAs, including those coding for proteins [77]. Thus, it becomes important to briefly describe the biochemical constitution and function of these molecules.…”

Section: Epigenetic Regulation By Non-coding Rnasmentioning

confidence: 99%

The Triple-Code Model for Pancreatic Cancer

Lomberk¹,

Urrutia²

2015

Surgical Clinics of North America

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Pancreatic adenocarcinoma (PDAC) is a lethal and painful disease, which has become one of the most frequent causes of death by malignant diseases around the world. Unfortunately, for the most part, this disease remains incurable. Significant advances in the field of genetics, particularly during the last two decades, has led to the proposal of a progression model, by which this cancer evolves by the accumulation of mutations and deletions in key oncogenes and tumor suppressor genes. This model has been remarkably useful for the development of tumor markers as well as elegant animal models. In spite of these strengths, this model does not take into consideration concepts and methodologies that have been derived from the field of epigenetics nor studies in the field of nuclear structure and function. Since our laboratory has been long been an advocate of these changes as critical for the pathobiology of pancreatic cancer, in this article, we describe an updated, more comprehensive model, which includes these concepts. With the widespread utilization of next generation sequencing for identifying both genetic and epigenetic changes genome-wide, we believe that the framework of this model will help to further identify and validate not only more but better markers for pancreatic cancer. In addition, as opposed to genetic changes, epigenetic alterations are amenable to pharmacological manipulations, consequently the familiarization with this model will help to better understand the potential beneficial effects of this type of therapy for this disease. Thus, we are optimistic that this new integrated paradigm will contribute to advance this field of research not only from a mechanistic point of view, but also from a translational one.

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Section: Epigenetic Regulation By Non-coding Rnasmentioning

confidence: 99%

The Triple-Code Model for Pancreatic Cancer

Lomberk¹,

Urrutia²

2015

Surgical Clinics of North America

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“…Alternative splicing (AS) is a ubiquitous phenomenon occurring across all eukaryotic organisms as many biological processes are regulated through this type of post-transcriptional process, leading to the production of more than one coding or noncoding transcript from a single locus [1–3]. Several types of AS events occur during precursor mRNA (pre-mRNA) splicing, including exon skipping, intron retention, and/or the use of alternative acceptor and donor splice sites, producing transcripts with premature stop codons and altered coding potential [4].…”

Section: Introductionmentioning

confidence: 99%

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Aghamirzaie

Collakova

et al. 2016

BMC Genomics

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BackgroundAlternative splicing has been proposed to increase transcript diversity and protein plasticity in eukaryotic organisms, but the extent to which this is the case is currently unclear, especially with regard to the diversification of molecular function. Eukaryotic splicing involves complex interactions of splicing factors and their targets. Inference of co-splicing networks capturing these types of interactions is important for understanding this crucial, highly regulated post-transcriptional process at the systems level.ResultsFirst, several transcript and protein attributes, including coding potential of transcripts and differences in functional domains of proteins, were compared between splice variants and protein isoforms to assess transcript and protein diversity in a biological system. Alternative splicing was shown to increase transcript and function-related protein diversity in developing Arabidopsis embryos. Second, CoSpliceNet, which integrates co-expression and motif discovery at splicing regulatory regions to infer co-splicing networks, was developed. CoSpliceNet was applied to temporal RNA sequencing data to identify candidate regulators of splicing events and predict RNA-binding motifs, some of which are supported by prior experimental evidence. Analysis of inferred splicing factor targets revealed an unexpected role for the unfolded protein response in embryo development.ConclusionsThe methods presented here can be used in any biological system to assess transcript diversity and protein plasticity and to predict candidate regulators, their targets, and RNA-binding motifs for splicing factors. CoSpliceNet is freely available at http://delasa.github.io/co-spliceNet/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3172-6) contains supplementary material, which is available to authorized users.

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“…lncRNA). According to function, ncRNAs are classified as (1) housekeeping or translation-related ncRNAs: they are constitutively expressed and crucial for normal cellular function and viability and include tRNA, rRNA and snoRNA and (2) regulatory ncRNAs and include miRNA, lncRNA, siRNA and piRNA [22,23]. The biogenesis of these various types of ncRNAs has been discussed extensively [23][24][25][26].…”

Section: Non-coding Rnas: Biosynthesis and Classificationmentioning

confidence: 99%

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

Ngoc¹,

Ibeagha‐Awemu²

2017

Current Topics in Lactation

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The ruminant mammary gland (MG) is an important organ charged with the production of milk for young and human nourishment. ) are a class of untranslated RNA molecules that function to regulate gene expression, associated biochemical pathways and cellular functions and are involved in many biological processes. This chapter presents a review of the current state of knowledge on the role of ncRNAs (particularly miRNAs and lncRNAs) in the MG and lactation processes, lactation signalling pathways, lipid metabolism, MG health of ruminants as well as miRNA roles in milk recipients. Finally, the potential application of new genome editing technology for ncRNA studies in MG development, the lactation process and milk components is presented.

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Non‐coding RNAs: biological functions and applications

Cited by 149 publications

References 87 publications

The Triple-Code Model for Pancreatic Cancer

The Triple-Code Model for Pancreatic Cancer

CoSpliceNet: a framework for co-splicing network inference from transcriptomics data

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

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