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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/29908293/reversible-rna-modification-n-1-methyladenosine-m-1-a-in-mrna-and-trna
#1
REVIEW
Chi Zhang, Guifang Jia
More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6 -methyladenosine (m6 A), N1 -methyladenosine (m1 A) has been found as a reversible modification in tRNA and mRNA. m1 A occurs at positions 9, 14, and 58 of tRNA, with m1 A58 being critical for tRNA stability. Other than the hundreds of m1 A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1 A also identifies >20 m1 A sites in mitochondrial genes...
June 14, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29908294/tet2-regulates-osteoclast-differentiation-by-interacting-with-runx1-and-maintaining-genomic-5-hydroxymethylcytosine-5hmc
#2
Yajing Chu, Zhigang Zhao, David Wayne Sant, Ganqian Zhu, Sarah M Greenblatt, Lin Liu, Jinhuan Wang, Zeng Cao, Jeanette Cheng Tho, Shi Chen, Xiaochen Liu, Peng Zhang, Jaroslaw P Maciejewski, Stephen Nimer, Gaofeng Wang, Weiping Yuan, Feng-Chun Yang, Mingjiang Xu
As a dioxygenase, Ten-Eleven Translocation 2 (TET2) catalyzes subsequent steps of 5-methylcytosine (5mC) oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hematopoietic stem cells, but its impact on mature hematopoietic cells is not well-characterized. Here we show that Tet2 plays an essential role in osteoclastogenesis. Deletion of Tet2 impairs the differentiation of osteoclast precursor cells (macrophages) and their maturation into bone-resorbing osteoclasts in vitro...
June 13, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30037509/corrigendum-to-goldclip-gel-omitted-ligation-dependent-clip-genomics-proteomics-bioinformatics-16-2-2018-136-143
#3
Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J Hannon, Yang Yu
No abstract text is available yet for this article.
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30010036/5-hydroxymethylome-in-circulating-cell-free-dna-as-a-potential-biomarker-for-non-small-cell-lung-cancer
#4
Ji Zhang, Xiao Han, Chunchun Gao, Yurong Xing, Zheng Qi, Ruijuan Liu, Yueqin Wang, Xiaojian Zhang, Yun-Gui Yang, Xiangnan Li, Baofa Sun, Xin Tian
Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30010035/a-systems-biology-approach-for-studying-heterotopic-ossification-proteomic-analysis-of-clinical-serum-and-tissue-samples
#5
LETTER
Erin L Crowgey, Jennifer T Wyffels, Patrick M Osborn, Thomas T Wood, Laura E Edsberg
Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO+ ) and without (HO- ) heterotopic ossification...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30005964/identification-and-analysis-of-human-sex-biased-micrornas
#6
Chunmei Cui, Weili Yang, Jiangcheng Shi, Yong Zhou, Jichun Yang, Qinghua Cui, Yuan Zhou
Sex differences are widely observed under various circumstances ranging from physiological processes to therapeutic responses, and a myriad of sex-biased genes have been identified. In recent years, transcriptomic datasets of microRNAs (miRNAs), an important class of non-coding RNAs, become increasingly accessible. However, comprehensive analysis of sex difference in miRNA expression has not been performed. Here, we identified the differentially-expressed miRNAs between males and females by examining the transcriptomic datasets available in public databases and conducted a systemic analysis of their biological characteristics...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29981854/genome-wide-microrna-expression-profiles-in-copd-early-predictors-for-cancer-development
#7
Andreas Keller, Tobias Fehlmann, Nicole Ludwig, Mustafa Kahraman, Thomas Laufer, Christina Backes, Claus Vogelmeier, Caroline Diener, Frank Biertz, Christian Herr, Rudolf A Jörres, Hans-Peter Lenhof, Eckart Meese, Robert Bals
Chronic obstructive pulmonary disease (COPD) significantly increases the risk of developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development independent of the tumor type...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29753129/applications-of-rna-indexes-for-precision-oncology-in-breast-cancer
#8
REVIEW
Liming Ma, Zirui Liang, Hui Zhou, Lianghu Qu
Precision oncology aims to offer the most appropriate treatments to cancer patients mainly based on their individual genetic information. Genomics has provided numerous valuable data on driver mutations and risk loci; however, it remains a formidable challenge to transform these data into therapeutic agents. Transcriptomics describes the multifarious expression patterns of both mRNAs and non-coding RNAs (ncRNAs), which facilitates the deciphering of genomic codes. In this review, we take breast cancer as an example to demonstrate the applications of these rich RNA resources in precision medicine exploration...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29730207/sports1-0-a-tool-for-annotating-and-profiling-non-coding-rnas-optimized-for-rrna-and-trna-derived-small-rnas
#9
Junchao Shi, Eun-A Ko, Kenton M Sanders, Qi Chen, Tong Zhou
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipelineoptimized for rRNA- and tRNA-derived sRNAs (SPORTS1...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29730206/comparative-analysis-of-human-genes-frequently-and-occasionally-regulated-by-m-6-a-modification
#10
Yuan Zhou, Qinghua Cui
The m6 A modification has been implicated as an important epitranscriptomic marker, which plays extensive roles in the regulation of transcript stability, splicing, translation, and localization. Nevertheless, only some genes are repeatedly modified across various conditions and the principle of m6 A regulation remains elusive. In this study, we performed a systems-level analysis of human genes frequently regulated by m6 A modification (m6 Afreq genes) and those occasionally regulated by m6 A modification (m6 Aocca genes)...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29723684/the-role-of-exportin-5-in-microrna-biogenesis-and-cancer
#11
REVIEW
Ke Wu, Juan He, Wenchen Pu, Yong Peng
MicroRNAs (miRNAs) are conserved small non-coding RNAs that play an important role in the regulation of gene expression and participate in a variety of biological processes. The biogenesis of miRNAs is tightly controlled at multiple steps, such as transcription of miRNA genes, processing by Drosha and Dicer, and transportation of precursor miRNAs (pre-miRNAs) from the nucleus to the cytoplasm by exportin-5 (XPO5). Given the critical role of nuclear export of pre-miRNAs in miRNA biogenesis, any alterations of XPO5, resulting from either genetic mutation, epigenetic change, abnormal expression level or posttranslational modification, could affect miRNA expression and thus have profound effects on tumorigenesis...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29715522/yth-domain-a-family-of-n-6-methyladenosine-m-6-a-readers
#12
REVIEW
Shanhui Liao, Hongbin Sun, Chao Xu
Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N6 -methyladenosine (m6 A) is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs (lncRNAs). In mammalian cells, m6 A can be incorporated by a methyltransferase complex and removed by demethylases, which ensures that the m6 A modification is reversible and dynamic...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29709557/structural-insights-into-n-6-methyladenosine-m-6-a-modification-in-the-transcriptome
#13
REVIEW
Jinbo Huang, Ping Yin
More than 100 types of chemical modifications in RNA have been well documented. Recently, several modifications, such as N6 -methyladenosine (m6 A), have been detected in mRNA, opening the window into the realm of epitranscriptomics. The m6 A modification is the most abundant modification in mRNA and non-coding RNA (ncRNA). At the molecular level, m6 A affects almost all aspects of mRNA metabolism, including splicing, translation, and stability, as well as microRNA (miRNA) maturation, playing essential roles in a range of cellular processes...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29709556/goldclip-gel-omitted-ligation-dependent-clip
#14
Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J Hannon, Yang Yu
Protein-RNA interaction networks are essential to understand gene regulation control. Identifying binding sites of RNA-binding proteins (RBPs) by the UV-crosslinking and immunoprecipitation (CLIP) represents one of the most powerful methods to map protein-RNA interactions in vivo. However, the traditional CLIP protocol is technically challenging, which requires radioactive labeling and suffers from material loss during PAGE-membrane transfer procedures. Here we introduce a super-efficient CLIP method (GoldCLIP) that omits all gel purification steps...
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29691129/corrigendum-to-pharmacogenomics-of-drug-metabolizing-enzymes-and-transporters-relevance-to-precision-medicine-genomics-proteomics-bioinformatics-14-5-2016-298-313
#15
Shabbir Ahmed, Zhan Zhou, Jie Zhou, Shu-Qing Chen
No abstract text is available yet for this article.
April 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29522900/deep-learning-and-its-applications-in-biomedicine
#16
REVIEW
Chensi Cao, Feng Liu, Hai Tan, Deshou Song, Wenjie Shu, Weizhong Li, Yiming Zhou, Xiaochen Bo, Zhi Xie
Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein sequences. Learning from these data facilitates the understanding of human health and disease. Developed from artificial neural networks, deep learning-based algorithms show great promise in extracting features and learning patterns from complex data. The aim of this paper is to provide an overview of deep learning techniques and some of the state-of-the-art applications in the biomedical field...
February 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29505855/the-immunome-of-colon-cancer-functional-in-silico-analysis-of-antigenic-proteins-deduced-from-igg-microarray-profiling
#17
Johana A Luna Coronell, Khulan Sergelen, Philipp Hofer, István Gyurján, Stefanie Brezina, Peter Hettegger, Gernot Leeb, Karl Mach, Andrea Gsur, Andreas Weinhäusel
Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens (DIRAGs) could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer (CRC) patients and 32 controls using proteins isolated from 15,417 human cDNA expression clones on microarrays. 671 unique DIRAGs were identified and 632 were more highly reactive in CRC samples...
February 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29496591/lessons-learned-as-president-of-the-institute-for-systems-biology-2000-2018
#18
EDITORIAL
Leroy E Hood
No abstract text is available yet for this article.
February 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29474889/human-gut-microbiota-and-gastrointestinal-cancer
#19
REVIEW
Changting Meng, Chunmei Bai, Thomas D Brown, Leroy E Hood, Qiang Tian
Human gut microbiota play an essential role in both healthy and diseased states of humans. In the past decade, the interactions between microorganisms and tumors have attracted much attention in the efforts to understand various features of the complex microbial communities, as well as the possible mechanisms through which the microbiota are involved in cancer prevention, carcinogenesis, and anti-cancer therapy. A large number of studies have indicated that microbial dysbiosis contributes to cancer susceptibility via multiple pathways...
February 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29474888/preprocessing-of-2-dimensional-gel-electrophoresis-images-applied-to-proteomic-analysis-a-review
#20
REVIEW
Manuel Mauricio Goez, Maria Constanza Torres-Madroñero, Sarah Röthlisberger, Edilson Delgado-Trejos
Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction...
February 2018: Genomics, Proteomics & Bioinformatics
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