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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/29037489/latent-hiv-1-tar-regulates-7sk-responsive-p-tefb-target-genes-and-targets-cellular-immune-responses-in-the-absence-of-tat
#1
Sebastian Eilebrecht, Bernd-Joachim Benecke, Arndt G Benecke
The transactivating response element (TAR) structure of the nascent HIV-1 transcript is critically involved in the recruitment of inactive positive transcription elongation factor b (P-TEFb) to the promoter proximal paused RNA polymerase II. The viral transactivator Tat is responsible for subsequent P-TEFb activation in order to start efficient viral transcription elongation. In the absence of the viral transactivator of transcription (Tat), e.g., during latency or in early stages of HIV transcription, TAR mediates an interaction of P-TEFb with its inhibitor hexamethylene bis-acetamide-inducible proteins 1 (HEXIM1), keeping P-TEFb in its inactive form...
October 13, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29031844/alternative-polyadenylation-methods-findings-and-impacts
#2
REVIEW
Wei Chen, Qi Jia, Yifan Song, Haihui Fu, Gang Wei, Ting Ni
Alternative polyadenylation (APA), a phenomenon that RNA molecules with different 3' ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells...
October 11, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29031843/rna-regulations-and-functions-decoded-by-transcriptome-wide-rna-structure-probing
#3
REVIEW
Meiling Piao, Lei Sun, Qiangfeng Cliff Zhang
RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes...
October 11, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29031842/ribosome-profiling-reveals-genome-wide-cellular-translational-regulation-upon-heat-stress-in-escherichia-coli
#4
Yanqing Zhang, Zhengtao Xiao, Qin Zou, Jianhuo Fang, Qifan Wang, Xuerui Yang, Ning Gao
Heat shock response is a classical stress-induced regulatory system in bacteria, characterized by extensive transcriptional reprogramming. To compare the impact of heat stress on the transcriptome and translatome in Escherichia coli, we conducted ribosome profiling in parallel with RNA-Seq to investigate the alterations in transcription and translation efficiency when E. coli cells were exposed to a mild heat stress (from 30°C to 45°C). While general changes in ribosome footprints correlate with the changes of mRNA transcripts upon heat stress, a number of genes show differential changes at the transcription and translation levels...
October 11, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017968/author-s-reply-comments-on-vitamin-pharmacogenomics-new-insight-into-individual-differences-in-diseases-and-drug-responses
#5
LETTER
Wei Zhang
No abstract text is available yet for this article.
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017967/non-coding-rnas-and-their-roles-in-stress-response-in-plants
#6
REVIEW
Jingjing Wang, Xianwen Meng, Oxana B Dobrovolskaya, Yuriy L Orlov, Ming Chen
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance...
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017966/comments-on-vitamin-pharmacogenomics-new-insight-into-individual-differences-in-diseases-and-drug-responses
#7
LETTER
Tom Greenfield
No abstract text is available yet for this article.
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28942262/engineering-novel-molecular-beacon-constructs-to-study-intracellular-rna-dynamics-and-localization
#8
REVIEW
Zhao Ma, Xiaotian Wu, Christopher J Krueger, Antony K Chen
With numerous advancements in novel biochemical techniques, our knowledge of the role of RNAs in the regulation of cellular physiology and pathology has grown significantly over the past several decades. Nevertheless, detailed information regarding RNA processing, trafficking, and localization in living cells has been lacking due to technical limitations in imaging single RNA transcripts in living cells with high spatial and temporal resolution. In this review, we discuss techniques that have shown great promise for single RNA imaging, followed by highlights in our recent work in the development of molecular beacons (MBs), a class of nanoscale oligonucleotide-probes, for detecting individual RNA transcripts in living cells...
September 20, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28882787/steering-against-wind-a-new-network-of-namirnas-and-enhancers
#9
Ying Liang, Qingping Zou, Wenqiang Yu
MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs with regulatory functions. Traditionally, miRNAs are thought to play a negative regulatory role in the cytoplasm by binding to the 3'UTR of target genes to degrade mRNA or inhibit translation. However, it remains a challenge to interpret the potential function of many miRNAs located in the nucleus. Recently, we reported a new type of miRNAs present in the nucleus, which can activate gene expression by binding to the enhancer, and named them Nuclear Activating miRNAs (NamiRNAs)...
September 4, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28813639/exploitation-of-gene-expression-and-cancer-biomarkers-in-paving-the-path-to-era-of-personalized-medicine
#10
REVIEW
Hala Fawzy Mohamed Kamel, Hiba Saeed A Bagader Al-Amodi
Cancer therapy agents have been used extensively as cytotoxic drugs against tissue or organ of a specific type of cancer. With the better understanding of molecular mechanisms underlying carcinogenesis and cellular events during cancer progression and metastasis, it is now possible to use targeted therapy for these molecular events. Targeted therapy is able to identify cancer patients with dissimilar genetic defects at cellular level for the same cancer type and consequently requires individualized approach for treatment...
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28811232/cyp2a6-polymorphisms-associate-with-outcomes-of-s-1-plus-oxaliplatin-chemotherapy-in-chinese-gastric-cancer-patients
#11
LETTER
Lin Yang, Shanshan Zou, Chang Shu, Yan Song, Yong-Kun Sun, Wen Zhang, Aiping Zhou, Xinghua Yuan, Yi Yang, Songnian Hu
Gastric carcinoma is a heterogeneous malignant disease involving genetic factors. To identify predictive markers for gastric cancer treatment in Chinese patients, we evaluated the association between polymorphisms of the gene encoding cytochrome P450 2A6 (CYP2A6) and outcomes of S-1 plus oxaliplatin (SOX) chemotherapy treatment. Clinical data on 60 consecutive gastric cancer patients receiving SOX regimen were collected prospectively. We sequenced all exons of CYP2A6 and a total of 22 different polymorphisms were detected in the present study...
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28811231/a-step-forward-in-precision-medicine-on-one-belt-one-road
#12
EDITORIAL
Jun Yu
No abstract text is available yet for this article.
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28797870/future-strategies-on-glioma-research-from-big-data-to-the-clinic
#13
Hang Cao, Feiyifan Wang, Xue-Jun Li
No abstract text is available yet for this article.
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28642113/paralog-divergent-features-may-help-reduce-off-target-effects-of-drugs-hints-from-glucagon-subfamily-analysis
#14
Zhining Sa, Jingqi Zhou, Yangyun Zou, Zhixi Su, Xun Gu
Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II) of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs) at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes...
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28549934/in-vitro-metabolomic-approaches-to-investigating-the-potential-biological-effects-of-phenolic-compounds-an-update
#15
REVIEW
Úrsula Catalán, Laura Barrubés, Rosa Maria Valls, Rosa Solà, Laura Rubió
Dietary phenolic compounds (PCs) have been receiving interest for their presumed roles in disease prevention. However, there is a lack of studies on the underlying molecular mechanisms. In this regard, in vitrometabolomic approaches are suitable for the investigation of the molecular changes in response to PC exposure. Up to date, the biological effects of PCs have only been examined for PCs from rosemary (Rosmarinus officinalis), olive oil, and resveratrol using cell-based metabolomic approach, although transcriptomic and/or proteomic studies have also been conducted in the same in vitro cell experiment in some cases...
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602845/silencing-of-transposable-elements-by-pirnas-in-drosophila-an-evolutionary-perspective
#16
REVIEW
Shiqi Luo, Jian Lu
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602844/primate-specific-long-non-coding-rnas-and-micrornas
#17
REVIEW
Hassaan Mehboob Awan, Abdullah Shah, Farooq Rashid, Ge Shan
Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602785/downregulation-of-mir-503-promotes-escc-cell-proliferation-migration-and-invasion-by-targeting-cyclin-d1
#18
Lanfang Jiang, Zitong Zhao, Leilei Zheng, Liyan Xue, Qimin Zhan, Yongmei Song
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers in China, but the underlying molecular mechanism of ESCC is still unclear. Involvement of microRNAs has been demonstrated in cancer initiation and progression. Despite the reported function of miR-503 in several human cancers, its detailed anti-oncogenic role and clinical significance in ESCC remain undefined. In this study, we examined miR-503 expression by qPCR and found the downregulation of miR-503 expression in ESCC tissue relative to adjacent normal tissues...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28599852/non-coding-transcripts-from-enhancers-new-insights-into-enhancer-activity-and-gene-expression-regulation
#19
REVIEW
Hongjun Chen, Guangshi Du, Xu Song, Ling Li
Long non-coding RNAs (lncRNAs) have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological processes. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs (eRNAs). The eRNAs are not merely the by-product of the enhancer transcription...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28533025/enhancer-derived-rna-a-primer
#20
REVIEW
Feng Liu
Enhancer-derived RNAs (eRNAs) are a group of RNAs transcribed by RNA polymerase II from the domain of transcription enhancers, a major type of cis-regulatory elements in the genome. The correlation between eRNA production and enhancer activity has stimulated studies on the potential role of eRNAs in transcriptional regulation. Additionally, eRNA has also served as a marker for global identification of enhancers. Here I review the brief history and fascinating properties of eRNAs.
June 2017: Genomics, Proteomics & Bioinformatics
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