Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls

Trends in Genetics : TIG
Huifen CaoPhilipp Kapranov

Abstract

The past decade has seen an explosion of interest in long noncoding RNAs (lncRNAs). However, despite the massive volume of scientific data implicating these transcripts in a plethora of molecular and cellular processes, a great deal of controversy surrounds these RNAs. One of the main reasons for this lies in the multiple unique features of lncRNAs which limit the available methods used to characterize them. Combined with their vast numbers and inadequate classification, comprehensive annotation of these transcripts becomes a daunting task. The solution to this complex challenge likely lies in deep understanding of the strengths and weaknesses of each computational and empirical approach, and integration of multiple strategies to reduce noise, authenticate the results, and classify lncRNAs. We review here both the advantages and caveats of strategies commonly used for functional characterization and annotation of lncRNAs in the context of emerging conceptual guidelines for their application.

Citations

Nov 14, 2018·Nature Structural & Molecular Biology·Minakshi GandhiSven Diederichs
Apr 24, 2019·Non-coding RNA·Marina R Hadjicharalambous, Mark A Lindsay
May 16, 2019·Journal of Zhejiang University. Science. B·Brian L GudenasLiang-Jiang Wang
Jan 25, 2020·Scientific Reports·Danilo Guillermo CeschinAndrés Venturino
Sep 19, 2020·Scientific Reports·Endika Varela-MartínezBegoña M Jugo
Feb 9, 2020·International Journal of Molecular Sciences·Marek KazimierczykJan Wrzesinski
Aug 7, 2020·Biochemical Society Transactions·Qianpeng LiLina Ma
Feb 8, 2019·Frontiers in Genetics·Ling LiXuekun Li
Nov 13, 2020·PLoS Computational Biology·Hyungtaek JungSeong-Il Eyun
Dec 18, 2020·Briefings in Bioinformatics·A T Vivek, Shailesh Kumar
Jun 26, 2020·Seminars in Cell & Developmental Biology·Tim Vierbuchen, Katherine A Fitzgerald
Nov 27, 2018·The Science of the Total Environment·Guiping HuGuang Jia
Mar 24, 2021·Nature Chemical Biology·Yue ChenPhilipp Kapranov
Mar 16, 2021·G3 : Genes - Genomes - Genetics·Mark J Bouska, Hua Bai
May 6, 2021·International Journal of Molecular Sciences·Mariana LopesRaquel Chaves
Jul 2, 2021·Frontiers in Genetics·Praveen Krishna ChitneediBeatriz Gutiérrez-Gil
Jul 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sarva KeihaniEugenio F Fornasiero
Jun 29, 2021·Frontiers in Cell and Developmental Biology·Wenlun WangLingyun Zhu
Jan 6, 2022·ELife·Maria Rodriguez-LopezJürg Bähler

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.