Post-transcriptional regulation of long noncoding RNAs in cancer

Tumor Biology ◽  
2015 ◽  
Vol 36 (2) ◽  
pp. 503-513 ◽  
Author(s):  
Xuefei Shi ◽  
Ming Sun ◽  
Ying Wu ◽  
Yanwen Yao ◽  
Hongbing Liu ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Post Transcriptional Regulation

scholarly journals Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1458 ◽  
Author(s):  
Yang Zhao ◽  
Hongqi Teng ◽  
Fan Yao ◽  
Shannon Yap ◽  
Yutong Sun ◽  
...  
Keyword(s):  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Genetically Engineered ◽  
Long Noncoding Rnas ◽  
Genetically Engineered Mouse Models ◽  
Genomic Location ◽  
Bona Fide ◽  
Underlying Mechanisms ◽  
Post Transcriptional Regulation ◽  
In Cis

Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded abundant information about lncRNA functions and underlying mechanisms, albeit with many discrepancies. In this review, we elaborate on the challenges in ascribing functions to lncRNAs based on the features of lncRNAs, including the genomic location, copy number, domain structure, subcellular localization, stability, evolution, and expression pattern. We also describe a framework for the investigation of lncRNA functions and mechanisms of action. Rigorous characterization of cancer-implicated lncRNAs is critical for the identification of bona fide anticancer targets.

scholarly journals Full-length annotation with multi-strategy RNA-seq uncovers transcriptional regulation of lncRNAs in diploid cotton G. arboreum1

2020 ◽  
Author(s):  
Xiaomin Zheng ◽  
Yanjun Chen ◽  
Yifan Zhou ◽  
Danyang Li ◽  
Keke Shi ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Rna Seq ◽  
Accurate Identification ◽  
Tissue Samples ◽  
Protein Coding ◽  
Diploid Cotton ◽  
Cap Analysis

AbstractLong noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. High-throughput and accurate identification of lncRNAs is still lacking in plants. To build an accurate atlas of lncRNA in cotton, we combined Isoform-sequencing (Iso-seq), strand-specific RNA-seq (ssRNA-seq), cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA (PULL) to integrate multi-omics data. A total of 9240 lncRNAs from 21 tissue samples of the diploid cotton Gossypium arboreum were identified. We revealed that alternative usage of transcription start site (TSS) and transcription end site (TES) of lncRNAs occurs pervasively during plant growth and responses to stress. We identified the lncRNAs which co-expressed or be linked to the protein coding genes (PCGs) or GWAS studied SNPs associated with ovule and fiber development. We also mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing (ChIRP-seq) and validated the trans transcriptional regulation of lnc-Ga13g0352 via virus induced gene suppression (VIGS) assay. These findings provide valuable research resources for plant community and broaden our understandings of biogenesis and regulation function of plant lncRNAs.One sentence summaryThe full-length annotation and transcriptional regulation of long noncoding RNAs in cotton.

scholarly journals Widespread localisation of long noncoding RNAs to ribosomes: Distinguishing features and evidence for regulatory roles.

2015 ◽  
Author(s):  
Juna Carlevaro-Fita ◽  
Anisa Rahim ◽  
Roderic Guigo ◽  
Leah Vardy ◽  
Rory Johnson
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Cell Types ◽  
Long Noncoding Rnas ◽  
Open Reading Frames ◽  
Translation Machinery ◽  
Evolutionary Selection ◽  
Regulatory Interactions ◽  
Distinguishing Features ◽  
Reading Frames

The function of long noncoding RNAs (lncRNAs) depends on their location within the cell. While most studies to date have concentrated on their nuclear roles in transcriptional regulation, evidence is mounting that lncRNA also have cytoplasmic roles. Here we comprehensively map the cytoplasmic and ribosomal lncRNA population in a human cell. Three-quarters (74%) of lncRNAs are detected in the cytoplasm, the majority of which (62%) preferentially cofractionate with polyribosomes. Ribosomal lncRNA are highly expressed across tissues, under purifying evolutionary selection, and have cytoplasmic-to-nuclear ratios comparable to mRNAs and consistent across cell types. LncRNAs may be classified into three groups by their ribosomal interaction: non-ribosomal cytoplasmic lncRNAs, and those associated with either heavy or light polysomes. A number of mRNA-like features destin lncRNA for light polysomes, including capping and 5′UTR length, but not cryptic open reading frames or polyadenylation. Surprisingly, exonic retroviral sequences antagonise recruitment. In contrast, it appears that lncRNAs are recruited to heavy polysomes through basepairing to mRNAs. Finally, we show that the translation machinery actively degrades lncRNA. We propose that light polysomal lncRNAs are translationally engaged, while heavy polysomal lncRNAs are recruited indirectly. These findings point to extensive and reciprocal regulatory interactions between lncRNA and the translation machinery.

scholarly journals When Long Noncoding RNAs Meet Genome Editing in Pluripotent Stem Cells

2017 ◽  
Vol 2017 ◽  
pp. 1-13
Author(s):  
Fuquan Chen ◽  
Jiaojiao Ji ◽  
Jian Shen ◽  
Xinyi Lu
Keyword(s):  
Stem Cells ◽  
Transcriptional Regulation ◽  
Genome Editing ◽  
Pluripotent Stem Cells ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Biological Processes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Past

Most of the human genome can be transcribed into RNAs, but only a minority of these regions produce protein-coding mRNAs whereas the remaining regions are transcribed into noncoding RNAs. Long noncoding RNAs (lncRNAs) were known for their influential regulatory roles in multiple biological processes such as imprinting, dosage compensation, transcriptional regulation, and splicing. The physiological functions of protein-coding genes have been extensively characterized through genome editing in pluripotent stem cells (PSCs) in the past 30 years; however, the study of lncRNAs with genome editing technologies only came into attentions in recent years. Here, we summarize recent advancements in dissecting the roles of lncRNAs with genome editing technologies in PSCs and highlight potential genome editing tools useful for examining the functions of lncRNAs in PSCs.

scholarly journals Emerging Roles of Long Noncoding RNAs in Immuno-Oncology

2021 ◽  
Vol 9 ◽  
Author(s):  
Xin Wang ◽  
Xu Wang ◽  
Midie Xu ◽  
Weiqi Sheng
Keyword(s):  
Tumor Microenvironment ◽  
Chromatin Remodeling ◽  
Immune Cells ◽  
Tumor Development ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Cancer Development ◽  
Immune Recognition ◽  
Tumor Surveillance ◽  
Post Transcriptional Regulation

Long noncoding RNAs (lncRNAs), defined as ncRNAs no longer than 200 nucleotides, play an important role in cancer development. Accumulating research on lncRNAs offers a compelling new aspect of genome modulation, in which they are involved in chromatin remodeling, transcriptional and post-transcriptional regulation, and cross-talk with other nucleic acids. Increasing evidence suggests that lncRNAs reshape the tumor microenvironment (TME), which accounts for tumor development and progression. At the same time, the insightful findings on lncRNAs in immune recognition and evasion in tumor-infiltrating immune cells raise concerns with regard to immuno-oncology. In this review, we describe the essential characteristics of lncRNAs, elucidate functions of immune components engaged in tumor surveillance, and present some instructive examples in this new area.

Sign in / Sign up

Export Citation Format

Share Document