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https://www.readbyqxmd.com/read/29329249/scaffolding-for-repair-understanding-molecular-functions-of-the-smc5-6-complex
#1
REVIEW
Mariana Diaz, Ales Pecinka
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex...
January 12, 2018: Genes
https://www.readbyqxmd.com/read/29329216/an-introduction-to-integrative-genomics-and-systems-medicine-in-cancer
#2
EDITORIAL
Xiaolong Cheng, Victor X Jin
In this Special Issue (SI), with a theme of "Integrative Genomics and Systems Medicine in Cancer", we have collected a total of 12 research and review articles from researchers in the field of genomics and systems medicine[...].
January 12, 2018: Genes
https://www.readbyqxmd.com/read/29324704/dissection-of-myogenic-differentiation-signatures-in-chickens-by-rna-seq-analysis
#3
Tingting Li, Genxi Zhang, Pengfei Wu, Lian Duan, Guohui Li, Qiuhong Liu, Jinyu Wang
A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29324691/physiological-and-comparative-genomic-analysis-of-arthrobacter-sp-srs-w-1-2016-provides-insights-on-niche-adaptation-for-survival-in-uraniferous-soils
#4
Ashvini Chauhan, Ashish Pathak, Rajneesh Jaswal, Bobby Edwards Iii, Demario Chappell, Christopher Ball, Reyna Garcia-Sillas, Paul Stothard, John Seaman
Arthrobacter sp. strain SRS-W-1-2016 was isolated on high concentrations of uranium (U) from the Savannah River Site (SRS) that remains co-contaminated by radionuclides, heavy metals, and organics. SRS is located on the northeast bank of the Savannah River (South Carolina, USA), which is a U.S. Department of Energy (DOE) managed ecosystem left historically contaminated from decades of nuclear weapons production activities. Predominant contaminants within the impacted SRS environment include U and Nickel (Ni), both of which can be transformed microbially into less toxic forms via metal complexation mechanisms...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29324689/characterization-of-translationally-controlled-tumour-protein-from-the-sea-anemone-anemonia-viridis-and-transcriptome-wide-identification-of-cnidarian-homologues
#5
Aldo Nicosia, Carmelo Bennici, Girolama Biondo, Salvatore Costa, Marilena Di Natale, Tiziana Masullo, Calogera Monastero, Maria Antonietta Ragusa, Marcello Tagliavia, Angela Cuttitta
Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29324665/genome-wide-methylation-patterns-in-androgen-independent-prostate-cancer-cells-a-comprehensive-analysis-combining-medip-bisulfite-rna-and-microrna-sequencing-data
#6
Yumin Wang, Tingting Qin, Wangqiang Hu, Binghua Chen, Meijie Dai, Gang Xu
This study aimed to investigate the mechanisms underlying the development of the androgen-independent phenotype in prostate cancer. Methylation patterns were detected in androgen-independent and androgen-dependent lymph node carcinoma of the prostate (LNCaP) prostate carcinoma cells based on methylated DNA immunoprecipitation-bisulfite sequencing data and differentially methylated regions (DMRs) were identified. Differentially expressed genes (DEGs) and micro RNAs (miRNAs) with DMRs (named MDEGs and MDEmiRNAs) were identified by combining transcriptome and methylation data, and transcription factor (TF)-DEGs with DMRs in promoter (PMDEGs) and MDEmiRNA-MDEGs networks were constructed...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29320459/the-landscape-of-small-non-coding-rnas-in-triple-negative-breast-cancer
#7
Yan Guo, Hui Yu, Jing Wang, Quanhu Sheng, Shilin Zhao, Ying-Yong Zhao, Brian D Lehmann
Triple-negative breast cancer (TNBC) is an operational term for breast cancers lacking targetable estrogen receptor expression and HER2 amplifications. TNBC is, therefore, inherently heterogeneous, and is associated with worse prognosis, greater rates of metastasis, and earlier onset. TNBC displays mutational and transcriptional diversity, and distinct mRNA transcriptional subtypes exhibiting unique biology. High-throughput sequencing has extended cancer research far beyond protein coding regions that include non-coding small RNAs, such as miRNA, isomiR, tRNA, snoRNAs, snRNA, yRNA, 7SL, and 7SK...
January 10, 2018: Genes
https://www.readbyqxmd.com/read/29320452/structural-and-evolutionary-relationships-in-the-giant-sex-chromosomes-of-three-microtus-species
#8
Luz Lamelas, María Arroyo, Francisco Javier Fernández, Juan Alberto Marchal, Antonio Sánchez
The genus Microtus has high karyotypic diversity. The existence of notable differences in the length of its sex chromosomes contributes to this variation. Variations in size are attributed to the enlargement of their heterochromatin content, which is of such magnitude in some species that they are referred to as "giant sex chromosomes". Here, we perform an intra- and interspecific analysis of the molecular composition of the heterochromatic blocks in three species with giant sex chromosomes (Microtus chrotorrhinus, M...
January 10, 2018: Genes
https://www.readbyqxmd.com/read/29320387/identification-of-inherited-retinal-disease-associated-genetic-variants-in-11-candidate-genes
#9
Galuh D N Astuti, L Ingeborgh van den Born, M Imran Khan, Christian P Hamel, Béatrice Bocquet, Gaël Manes, Mathieu Quinodoz, Manir Ali, Carmel Toomes, Martin McKibbin, Mohammed E El-Asrag, Lonneke Haer-Wigman, Chris F Inglehearn, Graeme C M Black, Carel B Hoyng, Frans P M Cremers, Susanne Roosing
Inherited retinal diseases (IRDs) display an enormous genetic heterogeneity. Whole exome sequencing (WES) recently identified genes that were mutated in a small proportion of IRD cases. Consequently, finding a second case or family carrying pathogenic variants in the same candidate gene often is challenging. In this study, we searched for novel candidate IRD gene-associated variants in isolated IRD families, assessed their causality, and searched for novel genotype-phenotype correlations. Whole exome sequencing was performed in 11 probands affected with IRDs...
January 10, 2018: Genes
https://www.readbyqxmd.com/read/29315268/mirna-influences-in-neuroblast-modulation-an-introspective-analysis
#10
REVIEW
Vanessa Zammit, Byron Baron, Duncan Ayers
Neuroblastoma (NB) is the most common occurring solid paediatric cancer in children under the age of five years. Whether of familial or sporadic origin, chromosome abnormalities contribute to the development of NB and cause dysregulation of microRNAs (miRNAs). MiRNAs are small non-coding, single stranded RNAs that target messenger RNAs at the post-transcriptional levels by repressing translation within all facets of human physiology. Such gene 'silencing' activities by miRNAs allows the development of regulatory feedback loops affecting multiple functions within the cell, including the possible differentiation of neural stem cell (NSC) lineage selection...
January 9, 2018: Genes
https://www.readbyqxmd.com/read/29315258/methods-for-using-small-non-coding-rnas-to-improve-recombinant-protein-expression-in-mammalian-cells
#11
REVIEW
Sarah Inwood, Michael J Betenbaugh, Joseph Shiloach
The ability to produce recombinant proteins by utilizing different "cell factories" revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic...
January 9, 2018: Genes
https://www.readbyqxmd.com/read/29315242/nf-kappab-two-sides-of-the-same-coin
#12
REVIEW
Bruno R B Pires, Rafael C M C Silva, Gerson M Ferreira, Eliana Abdelhay
Nuclear Factor-kappa B (NF-κB) is a transcription factor family that regulates a large number of genes that are involved in important physiological processes, including survival, inflammation, and immune responses. More recently, constitutive expression of NF-κB has been associated with several types of cancer. In addition, microorganisms, such as viruses and bacteria, cooperate in the activation of NF-κB in tumors, confirming the multifactorial role of this transcription factor as a cancer driver. Recent reports have shown that the NF-κB signaling pathway should receive attention for the development of therapies...
January 9, 2018: Genes
https://www.readbyqxmd.com/read/29315229/the-aging-mitochondria
#13
REVIEW
Pierre Theurey, Paola Pizzo
Mitochondrial dysfunction is a central event in many pathologies and contributes as well to age-related processes. However, distinguishing between primary mitochondrial dysfunction driving aging and a secondary mitochondrial impairment resulting from other cell alterations remains challenging. Indeed, even though mitochondria undeniably play a crucial role in aging pathways at the cellular and organismal level, the original hypothesis in which mitochondrial dysfunction and production of free radicals represent the main driving force of cell degeneration has been strongly challenged...
January 9, 2018: Genes
https://www.readbyqxmd.com/read/29315213/identification-of-transposable-elements-contributing-to-tissue-specific-expression-of-long-non-coding-rnas
#14
Takafumi Chishima, Junichi Iwakiri, Michiaki Hamada
It has been recently suggested that transposable elements (TEs) are re-used as functional elements of long non-coding RNAs (lncRNAs). This is supported by some examples such as the human endogenous retrovirus subfamily H (HERVH) elements contained within lncRNAs and expressed specifically in human embryonic stem cells (hESCs), as required to maintain hESC identity. There are at least two unanswered questions about all lncRNAs. How many TEs are re-used within lncRNAs? Are there any other TEs that affect tissue specificity of lncRNA expression? To answer these questions, we comprehensively identify TEs that are significantly related to tissue-specific expression levels of lncRNAs...
January 9, 2018: Genes
https://www.readbyqxmd.com/read/29316729/wnt-rspo-and-hippo-signalling-in-the-intestine-and-intestinal-stem-cells
#15
REVIEW
Vitezslav Kriz, Vladimir Korinek
In this review, we address aspects of Wnt, R-Spondin (RSPO) and Hippo signalling, in both healthy and transformed intestinal epithelium. In intestinal stem cells (ISCs), the Wnt pathway is essential for intestinal crypt formation and renewal, whereas RSPO-mediated signalling mainly affects ISC numbers. In human colorectal cancer (CRC), aberrant Wnt signalling is the driving mechanism initiating this type of neoplasia. The signalling role of the RSPO-binding transmembrane proteins, the leucine-rich-repeat-containing G-protein-coupled receptors (LGRs), is possibly more pleiotropic and not only limited to the enhancement of Wnt signalling...
January 8, 2018: Genes
https://www.readbyqxmd.com/read/29304028/high-density-single-nucleotide-polymorphism-snp-mapping-and-quantitative-trait-loci-qtl-analysis-in-a-biparental-spring-triticale-population-localized-major-and-minor-effect-fusarium-head-blight-resistance-and-associated-traits-qtl
#16
Raman Dhariwal, George Fedak, Yves Dion, Curtis Pozniak, André Laroche, François Eudes, Harpinder Singh Randhawa
Triticale (xTriticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits (ergot, grain protein content, test weight, yield, plant height and lodging) followed by single nucleotide polymorphism (SNP) genotyping...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29304022/muscle-specific-mis-splicing-and-heart-disease-exemplified-by-rbm20
#17
REVIEW
Maimaiti Rexiati, Mingming Sun, Wei Guo
Alternative splicing is an essential post-transcriptional process to generate multiple functional RNAs or proteins from a single transcript. Progress in RNA biology has led to a better understanding of muscle-specific RNA splicing in heart disease. The recent discovery of the muscle-specific splicing factor RNA-binding motif 20 (RBM20) not only provided great insights into the general alternative splicing mechanism but also demonstrated molecular mechanism of how this splicing factor is associated with dilated cardiomyopathy...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29303998/linking-dna-damage-and-age-related-promoter-dna-hyper-methylation-in-the-intestine
#18
Torsten Thalheim, Maria Herberg, Joerg Galle
Aberrant DNA methylation in stem cells is a hallmark of aging and tumor development. Here, we explore whether and how DNA damage repair might impact on these time-dependent changes, in particular in proliferative intestinal stem cells. We introduce a 3D multiscale computer model of intestinal crypts enabling simulation of aberrant DNA and histone methylation of gene promoters during aging. We assume histone state-dependent activity of de novo DNA methyltransferases (DNMTs) and methylation-dependent binding of maintenance DNMTs to CpGs...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29303984/transcription-factor-and-lncrna-regulatory-networks-identify-key-elements-in-lung-adenocarcinoma
#19
Dan Li, William Yang, Jialing Zhang, Jack Y Yang, Renchu Guan, Mary Qu Yang
Lung cancer is the second most commonly diagnosed carcinoma and is the leading cause of cancer death. Although significant progress has been made towards its understanding and treatment, unraveling the complexities of lung cancer is still hampered by a lack of comprehensive knowledge on the mechanisms underlying the disease. High-throughput and multidimensional genomic data have shed new light on cancer biology. In this study, we developed a network-based approach integrating somatic mutations, the transcriptome, DNA methylation, and protein-DNA interactions to reveal the key regulators in lung adenocarcinoma (LUAD)...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29300342/snca-is-a-functionally-low-expressed-gene-in-lung-adenocarcinoma
#20
Yuanliang Yan, Zhijie Xu, Xiaofang Hu, Long Qian, Zhi Li, Yangying Zhou, Shuang Dai, Shuangshuang Zeng, Zhicheng Gong
There is increasing evidence for the contribution of synuclein alpha (SNCA) to the etiology of neurological disorders, such as Parkinson's disease (PD). However, little is known about the detailed role of SNCA in human cancers, especially lung cancers. Here, we evaluated the effects of SNCA on the occurrence and prognosis of lung adenocarcinoma (ADC). Comprehensive bioinformatics analyses of data obtained from the Oncomine platform, the human protein atlas (HPA) project and the cancer cell line encyclopedia (CCLE) demonstrated that SNCA expression was significantly reduced in both ADC tissues and cancer cells...
January 4, 2018: Genes
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