The origins and evolutionary history of human non-coding RNA regulatory networks

Sherafatian, Masih; Mowla, Seyed Javad

doi:10.1142/s0219720017500056

Cited by 8 publications

(7 citation statements)

References 27 publications

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“…The understanding of when, where and to what extent a gene is expressed, can elucidate the regulatory mechanisms and biological pathways that lead to, maintain or reverse multiple drug-resistance in cancer treatment. Almost twenty years ago, the non-coding RNAs (ncRNAs) were discovered [ 2 , 3 ] and provided a breakthrough in our understanding of the functionality of the human genome. To take advantage of the large and rapidly increasing body of genome-scale sequence information, new technologies are required to exploit this information by characterizing biological processes and by studying the synchronous expression of a high number of genes.…”

Section: Introductionmentioning

confidence: 99%

The Non-Coding RNA GAS5 and Its Role in Tumor Therapy-Induced Resistance

Lambrou

Hatziagapiou

Zaravinos

2020

IJMS

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The growth arrest-specific transcript 5 (GAS5) is a >200-nt lncRNA molecule that regulates several cellular functions, including proliferation, apoptosis, invasion and metastasis, across different types of human cancers. Here, we reviewed the current literature on the expression of GAS5 in leukemia, cervical, breast, ovarian, prostate, urinary bladder, lung, gastric, colorectal, liver, osteosarcoma and brain cancers, as well as its interaction with various miRNAs and its effect on therapy-related resistance in these malignancies. The general consensus is that GAS5 acts as a tumor suppressor across different tumor types and that its up-regulation results in tumor sensitization to chemotherapy or radiotherapy. GAS5 seems to play a previously unappreciated, but significant role in tumor therapy-induced resistance.

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Section: Introductionmentioning

confidence: 99%

The Non-Coding RNA GAS5 and Its Role in Tumor Therapy-Induced Resistance

Lambrou

Hatziagapiou

Zaravinos

2020

IJMS

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“…Twenty-nine of these downregulated lncRNAs targeted genes encoded ribosomal proteins, indicating the important role of TOR in regulating the cotton ribosome biogenesis. Transposons associate with the origins and transcribed regions of lncRNAs and eventually drive lncRNA expression (Ponting et al, 2009; Kapusta et al, 2013; Xu et al, 2015; Wang et al, 2016a,b; Sherafatian and Mowla, 2017). We analyzed the potential transposons that targeted these ribosome-related lncRNAs (Supplementary Table 4B).…”

Section: Resultsmentioning

confidence: 99%

“…Taken together with the expression patterns of GhTOR genes under different stresses (Figure 5 and Supplementary Figure 1), our results indicated that TOR may directly regulate these potential stress-related lncRNAs and play a vital role in plant stress response. In addition, it is well-known that transposons associate with lncRNA origins and lncRNAs' transcribed regions, eventually driving expression of lncRNAs, and microRNA can also target lncRNAs (Ponting et al, 2009; Kapusta et al, 2013; Xu et al, 2015; Wang et al, 2016a,b; Sherafatian and Mowla, 2017). To confirm the lncRNAs' functions selected in the present study, transposons and miRNAs related with these selected lncRNAs were analyzed (Supplementary Tables 4–6).…”

Section: Discussionmentioning

confidence: 99%

Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton

Song

Yang

et al. 2019

Front. Genet.

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TOR (Target of Rapamycin) kinase is an evolutionarily conserved protein kinase, which integrates stress-related cues with growth and metabolic outputs. Long non-coding RNAs (lncRNAs) play a vital role in the regulation of eukaryotic genes. However, little is known about TOR's function in regulating the expression of lncRNAs in plants. In this study, four putative homologous genes encoding the TOR protein were identified by utilizing the recently completed cotton genome. Pharmacological experiments with TOR inhibitor AZD8055 and on silencing GhTOR genes resulted in obvious cotton growth retardation, indicating the conserved role of TOR in plant growth. The expression pattern analyses in different tissues reveal that TOR may play a role in root development, and the transcript levels of TOR genes were changed under different stress conditions. Importantly, we found TOR may be a key player in regulating the expression of long non-coding RNAs (lncRNAs). A total of 10,315 lncRNAs were discovered in cotton seedlings, 90.7% of which were long intergenic ncRNAs. Moreover, we identified the differentially expressed lncRNAs, of which 296 were significantly upregulated and 105 were downregulated in TOR inactivated plants. GO and KEGG analyses of differentially expressed lncRNA neighboring genes reveal that these differentially expressed lncRNA-targeted genes are involved in many life processes, including stress response, glutathione, and ribosomes in cotton. A series of differentially expressed lncRNAs potentially involved in plant stress response was identified under TOR inhibition. Collectively, these results suggest that cotton TOR proteins may directly modulate the expression of putative stress-related lncRNAs and eventually play a potential role in the cotton stress response.

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“…The non-coding RNA networks [26,27] are currently under intense investigation, both for evolutionary studies as well as for the elucidation of their multiple roles in the development of disease.…”

Section: Fig 4 (Color Online)mentioning

confidence: 99%

“…Genome studies have revealed an extensive map of genetic variation within the human genome, with changes of all possible kinds, predominantly single nucleotide variants (polymorphisms) (SNP). Additionally, a plethora of non-coding RNA is being reported [27] that form the machinery for the fine tuning of gene expression and affect disease outcome. This wealth of data has been exploited by the use of computer software used to assemble the enormous sequence data in regions of high variability and to produce databases of human mapped variation (e.g.…”

Section: Genome-wide Association Studiesmentioning

confidence: 99%

Genetic Complexity of the Human Genome in Health and Disease: Basic Concepts

Athanassiadou

2020

Nonlinear Phenomena in Complex Systems

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Determination of the DNA sequence of the human genome, revealing extensive genetic variation, and the mapping of the genes and the various regulatory elements of genome function within the genomic DNA, has revolutionized the way we view the states of health and disease in our time. Genetic complexity of the genome is manifested on different levels. The first level refers to the expression of protein coding genes, as regulated by their individual promoter in linear proximity. The next level of genetic complexity involves long distance action by far away enhancers, interacting with promoters through DNA looping. This 3- dimensional (3D) regulation is further developing by chromosome folding into the so called transcription factories, for fully physiological expression. Chromosome folding, mediated by specific genetic elements - insulators - is adding to the genetic complexity by facilitating movements of chromatin of specific genomic regions - the so-called topologically associated domains (TAD) in support of transcription and other cellular functions. Further genetic complexity has emerged with the finding that over 75% of the genome is transcribed and except of the coding genes, a plethora of RNA transcripts are produced - the non-coding RNA - that has important regulatory roles in the gene expression context. The great variation of genome sequence and regulatory elements of the genome architecture are exploited in studies of genome-wide association with disease, in the framework of Precision Medicine and in general of Genomic Medicine.

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The origins and evolutionary history of human non-coding RNA regulatory networks

Cited by 8 publications

References 27 publications

The Non-Coding RNA GAS5 and Its Role in Tumor Therapy-Induced Resistance

The Non-Coding RNA GAS5 and Its Role in Tumor Therapy-Induced Resistance

Target of Rapamycin (TOR) Regulates the Expression of lncRNAs in Response to Abiotic Stresses in Cotton

Genetic Complexity of the Human Genome in Health and Disease: Basic Concepts

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