Protein-coding genes and long noncoding RNAs are differentially expressed in dasatinib-treated chronic myeloid leukemia patients with resistance to imatinib

Hematology ◽  
2013 ◽  
Vol 19 (1) ◽  
pp. 31-41 ◽  
Author(s):  
Rosana A. Silveira ◽  
Angela A. Fachel ◽  
Yuri B. Moreira ◽  
Carmino A. De Souza ◽  
Fernando F. Costa ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Tianqi Xia ◽  
Bikash Ranjan Giri ◽  
Jingyi Liu ◽  
Pengfei Du ◽  
Xue Li ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Schistosoma Japonicum ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Protein Coding ◽  
Altered Expression ◽  
Protein Coding Genes

Abstract Background Schistosomiasis is a chronic, debilitating infectious disease caused by members of the genus Schistosoma. Previous findings have suggested a relationship between infection with Schistosoma spp. and alterations in the liver and spleen of infected animals. Recent reports have shown the regulatory role of noncoding RNAs, such as long noncoding RNAs (lncRNAs), in different biological processes. However, little is known about the role of lncRNAs in the mouse liver and spleen during Schistosoma japonicum infection. Methods In this study, we identified and investigated lncRNAs using standard RNA sequencing (RNA-Seq). The biological functions of the altered expression of lncRNAs and their target genes were predicted using bioinformatics. Ten dysregulated lncRNAs were selected randomly and validated in reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) experiments. Results Our study identified 29,845 and 33,788 lncRNAs from the liver and spleen, respectively, of which 212 were novel lncRNAs. We observed that 759 and 789 of the lncRNAs were differentially expressed in the respective organs. The RT-qPCR results correlated well with the sequencing data. In the liver, 657 differentially expressed lncRNAs were predicted to target 2548 protein-coding genes, whereas in the spleen 660 differentially expressed lncRNAs were predicted to target 2673 protein-coding genes. Moreover, functional annotation showed that the target genes of the differentially expressed lncRNAs were associated with cellular processes, metabolic processes, and binding, and were significantly enriched in metabolic pathways, the cell cycle, ubiquitin-mediated proteolysis, and pathways in cancer. Conclusions Our study showed that numerous lncRNAs were differentially expressed in S. japonicum-infected liver and spleen compared to control liver and spleen; this suggested that lncRNAs may be involved in pathogenesis in the liver and spleen during S. japonicum infection.

Identify the critical protein‐coding genes and long noncoding RNAs in cardiac myxoma

2019 ◽  
Vol 120 (8) ◽  
pp. 13441-13452 ◽  
Author(s):  
Nan Cheng ◽  
Yuanbin Wu ◽  
Huajun Zhang ◽  
Yi Guo ◽  
Huimin Cui ◽  
...  
Keyword(s):  
Cardiac Myxoma ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection

2020 ◽  
Vol 15 (9) ◽  
pp. 577-593
Author(s):  
Rafeed Rahman Turjya ◽  
Md. Abdullah-Al-Kamran Khan ◽  
Abul Bashar Mir Md. Khademul Islam
Keyword(s):  
Viral Infections ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Suppressive Effect ◽  
Long Noncoding Rnas ◽  
Lung Epithelial Cells ◽  
Differentially Expressed ◽  
Protein Coding ◽  
Cellular Survival ◽  
Viral Proliferation

Background: Regulatory roles of long noncoding RNAs (lncRNAs) during viral infection has become more evident in last decade, but are yet to be explored for SARS-CoV-2. Materials & methods: We analyzed RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells to identify differentially expressed genes. Results: Our analyses uncover 21 differentially expressed lncRNAs broadly involved in cell survival and regulation of gene expression. These lncRNAs can directly interact with six differentially expressed protein-coding genes, and ten host genes that interact with SARS-CoV-2 proteins. Also, they can block the suppressive effect of nine microRNAs induced in viral infections. Conclusion: Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome.

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 Long Noncoding RNAs in Acute Myeloid Leukemia: Functional Characterization and Clinical Relevance

Cancers ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1638 ◽  
Author(s):  
Morgane Gourvest ◽  
Pierre Brousset ◽  
Marina Bousquet
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Noncoding Rnas ◽  
Genetic Alterations ◽  
Long Noncoding Rnas ◽  
Leukemic Cells ◽  
Protein Coding ◽  
Acute Myeloid

Acute Myeloid Leukemia (AML) is the most common form of leukemia in adults with an incidence of 4.3 per 100,000 cases per year. Historically, the identification of genetic alterations in AML focused on protein-coding genes to provide biomarkers and to understand the molecular complexity of AML. Despite these findings and because of the heterogeneity of this disease, questions as to the molecular mechanisms underlying AML development and progression remained unsolved. Recently, transcriptome-wide profiling approaches have uncovered a large family of long noncoding RNAs (lncRNAs). Larger than 200 nucleotides and with no apparent protein coding potential, lncRNAs could unveil a new set of players in AML development. Originally considered as dark matter, lncRNAs have critical roles to play in the different steps of gene expression and thus affect cellular homeostasis including proliferation, survival, differentiation, migration or genomic stability. Consequently, lncRNAs are found to be differentially expressed in tumors, notably in AML, and linked to the transformation of healthy cells into leukemic cells. In this review, we aim to summarize the knowledge concerning lncRNAs functions and implications in AML, with a particular emphasis on their prognostic and therapeutic potential.

scholarly journals GIC: A computational method for predicting the essentiality of long noncoding lncRNAs

2017 ◽  
Author(s):  
Pan Zeng ◽  
Ji Chen ◽  
Yuan Zhou ◽  
Jichun Yang ◽  
Qinghua Cui
Keyword(s):  
Computational Methods ◽  
High Performance ◽  
Noncoding Rnas ◽  
Web Server ◽  
Long Noncoding Rnas ◽  
Computational Method ◽  
Biological Molecules ◽  
Sequence Information ◽  
Protein Coding ◽  
Protein Coding Genes

ABSTRACTMeasuring the essentiality of genes is critically important in biology and medicine. Some bioinformatic methods have been developed for this issue but none of them can be applied to long noncoding RNAs (lncRNAs), one big class of biological molecules. Here we developed a computational method, GIC (Gene Importance Calculator), which can predict the essentiality of both protein-coding genes and lncRNAs based on RNA sequence information. For identifying the essentiality of protein-coding genes, GIC is competitive with well-established computational scores. More important, GIC showed a high performance for predicting the essentiality of lncRNAs. In an independent mouse lncRNA dataset, GIC achieved an exciting performance (AUC=0.918). In contrast, the traditional computational methods are not applicable to lncRNAs. As a public web server, GIC is freely available at http://www.cuilab.cn/gic/.

scholarly journals Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs

2018 ◽  
Vol 9 ◽  
Author(s):  
Pan Zeng ◽  
Ji Chen ◽  
Yuhong Meng ◽  
Yuan Zhou ◽  
Jichun Yang ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Comparative genomics in the search for conserved long noncoding RNAs

2021 ◽  
Author(s):  
Michał Wojciech Szcześniak ◽  
Magdalena Regina Kubiak ◽  
Elżbieta Wanowska ◽  
Izabela Makałowska
Keyword(s):  
Comparative Genomics ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Model Organisms ◽  
Biological Functions ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Homologous Genes ◽  
Four Levels ◽  
Review Current

Abstract Long noncoding RNAs (lncRNAs) have emerged as prominent regulators of gene expression in eukaryotes. The identification of lncRNA orthologs is essential in efforts to decipher their roles across model organisms, as homologous genes tend to have similar molecular and biological functions. The relatively high sequence plasticity of lncRNA genes compared with protein-coding genes, makes the identification of their orthologs a challenging task. This is why comparative genomics of lncRNAs requires the development of specific and, sometimes, complex approaches. Here, we briefly review current advancements and challenges associated with four levels of lncRNA conservation: genomic sequences, splicing signals, secondary structures and syntenic transcription.

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