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Gene noise

Shimin Zong, Xue Zeng, Tianyi Liu, Fangmin Wan, Pan Luo, Hongjun Xiao
BACKGROUND: Several case-control studies reported the relationship between single nucleotide polymorphisms (SNPs) in HSP70 genes and noise-induced hearing loss (NIHL). However, their conclusions are conflicting. This meta-analysis aims to identify the association of HSP70 variants and NIHL susceptibility. METHOD: A systematical literature search was performed in PubMed, Web of Science, EMBASE, and Wanfang Chinese database. The pooled odds radio (OR), 95% confidence interval (CI) and p value were calculated in fixed- or random-effects model according to the I2 value in the heterogeneity test...
2017: PloS One
Sibei Huo, Yachuan Zhou, Xinyu He, Mian Wan, Wei Du, Xin Xu, Ling Ye, Xuedong Zhou, Liwei Zheng
BACKGROUND: Long non-coding RNAs (LncRNAs) are non-protein coding transcripts longer than 200 nucleotides in length. Instead of being "transcriptional noise", lncRNAs are emerging as a key modulator in various biological processes and disease development. Mesenchymal stem cells can be isolated from various adult tissues, such as bone marrow and dental tissues. The differentiation processes into multiple lineages, such as osteogenic differentiation, are precisely orchestrated by molecular signals in both genetic and epigenetic ways...
November 15, 2017: Current Stem Cell Research & Therapy
Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures...
November 14, 2017: Scientific Reports
Jessica E Salvatore, Jeanne E Savage, Peter Barr, Aaron R Wolen, Fazil Aliev, Eero Vuoksimaa, Antti Latvala, Lea Pulkkinen, Richard J Rose, Jaakko Kaprio, Danielle M Dick
BACKGROUND: Characterizing aggregate genetic risk for alcohol misuse and identifying variants involved in gene-by-environment interaction (G×E) effects has so far been a major challenge. We hypothesized that functional genomic information could be used to enhance detection of polygenic signal underlying alcohol misuse, and to prioritize identification of single nucleotide polymorphisms (SNPs) most likely to exhibit G×E effects. METHODS: We examined these questions in the young adult FinnTwin12 sample (n=1170)...
November 9, 2017: Alcoholism, Clinical and Experimental Research
Sourabh Lahiri, Philippe Nghe, Sander J Tans, Martin Luc Rosinberg, David Lacoste
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback...
2017: PloS One
Qiang Yan, Stephen S Fong
Background: UP elements (upstream element) are DNA sequences upstream of a promoter that interact with the α-subunit of RNA polymerase (RNAP) and can affect transcription by altering the binding RNAP to DNA. However, details of UP element and binding affinity effects on transcriptional strength are unclear. Results: Here, we investigated the effects of UP element sequences on gene transcription, binding affinity, and gene expression noise. Addition of UP elements resulted in increased gene expression (maximum 95...
2017: Journal of Biological Engineering
Thomas E Bartlett, Sören Müller, Aaron Diaz
Single-cell transcriptomic data have rapidly become very popular in genomic science. Genomic science also has a long history of using network models to understand the way in which genes work together to carry out specific biological functions. However, working with single-cell data presents major challenges, such as zero inflation and technical noise. These challenges require methods to be specifically adapted to the context of single-cell data. Recently, much effort has been made to develop the theory behind statistical network models...
November 8, 2017: Scientific Reports
Ann-Christin Honnen, Michael T Monaghan, Igor Sharakhov
Mosquitoes (Diptera, Culicidae) occur in natural, urban, and peri-urban areas throughout the globe. Although the characteristics of urban and peri-urban habitats differ from those of natural habitats in many ways (e.g., fragmentation, pollution, noise, and light), few studies have examined the population connectivity of mosquitoes in urban areas. To obtain an overview of the species composition, we sampled mosquitoes from 23 sites in and around the city of Berlin, Germany. Of 23 species, five occurred in urban, 10 in peri-urban, and 20 in rural areas...
September 1, 2017: Journal of Insect Science
Lindsey B Turnbull, Geoffrey H Siwo, Katrina A Button-Simons, Asako Tan, Lisa A Checkley, Heather J Painter, Manuel Llinás, Michael T Ferdig
Gene expression DNA microarrays have been vital for characterizing whole-genome transcriptional profiles. Nevertheless, their effectiveness relies heavily on the accuracy of genome sequences, the annotation of gene structures, and the sequence-dependent performance of individual probes. Currently available gene expression arrays for the malaria parasite Plasmodium falciparum rely on an average of 2 probes per gene, usually positioned near the 3' end of genes; consequently, existing designs are prone to measurement bias and cannot capture complexities such as the occurrence of transcript isoforms arising from alternative splicing or alternative start/ stop sites...
2017: PloS One
Xiaomei Huang, Xi Zhou, Qing Hu, Binyu Sun, Mingming Deng, Xiaolong Qi, Muhan Lü
Esophageal cancer is a malignant digestive tract cancer with high mortality. Although studies have found that esophageal cancer is involved in a complex and important gene regulation network, the pathogenesis remains unclear. The recently described long non-coding RNAs (lncRNAs) are one effective part of the gene regulation network. However, in past decades, lncRNAs were thought to be "transcript noise" or "pseudogenes" and were thus ignored. Early studies indicated that lncRNAs play pivotal roles during evolution...
November 10, 2017: Cancer Letters
Andre J Faure, Jörn M Schmiedel, Ben Lehner
Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core promoter architecture of a gene, with CpG island promoters and a TATA box associated with low and high noise, respectively. High noise is also associated with "conflicting" chromatin states-the absence of transcription-associated histone modifications or the presence of repressive ones in active genes...
October 31, 2017: Cell Systems
Gustavo Valadares Barroso, Natasa Puzovic, Julien Y Dutheil
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generate noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, in particular owing to the advent of single cell transcriptomics...
November 2, 2017: Genetics
Elena Bidnenko, Vladimir Bidnenko
Populations of genetically identical microorganisms exhibit high degree of cell-to-cell phenotypic diversity even when grown in uniform environmental conditions. Heterogeneity is a genetically determined trait, which ensures bacterial adaptation and survival in the ever changing environmental conditions. Fluctuations in gene expression (noise) at the level of transcription initiation largely contribute to cell-to-cell variability within population. Not surprisingly, the analyses of the mechanisms driving phenotypic heterogeneity are mainly focused on the activity of promoters and transcriptional factors...
November 1, 2017: Current Genetics
Nicolas J Tourasse, Jonathan R M Millet, Denis Dupuy
Almost twenty years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms the question of how much spurious splicing is tolerated is still heavily debated. Here we gathered a compendium of 1,682 publicly available C. elegans RNA-seq datasets to increase the dynamic range of detection of RNA isoforms and obtained robust measurements of the relative abundance of each splicing event...
October 31, 2017: Genome Research
Zach Hensel
Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription...
2017: PloS One
Jianguo Xu, Tingting Zheng, Jingqing Le, Lee Jia
Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs)...
October 30, 2017: Analyst
Vasily V Ashapkin, Lyudmila I Kutueva, Boris F Vanyushin
INTRODUCTION: Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging...
October 2017: Current Genomics
V V Krasitskaya, E E Bashmakova, K G Dobretsov, N V Orlova, L A Frank
This article was designed to be the overview of the current literature publications concerning the identification of the genetic markers of susceptibility to the noise-induced loss of hearing. The analysis of these data has demonstrated that the major gene polymorphisms associated with the development of this pathological condition are localized in the genes encoding for the antioxidant systems, potassium homeostasis, and adhesion molecules as well as in the genes involved in intercellular coupling, the mechanisms underlying the cellular response to stress, activation and regulation of heat shock proteins, and signaling function of the immune system...
2017: Vestnik Otorinolaringologii
Qi-Sheng Sun, Qi-Ying Guo, Wen-Rui Jia, Zong-Yu Jin, Zhi Ji, Qiu-Lei Guo, Fang-Yuan Yang, He Zhan, He Wang, Qing-Guo Liu
OBJECTIVE: To observe the effect of twirling-reducing needling on changes of profile of differentially-expressed genes in the hypothalamus in rats with stress-induced prehypertension (SI-PHT), so as to explore its mechanism under-lying improvement of prehypertension. METHODS: Wistar male rats were randomly divided into blank control group (n=12), model group (n=12) and acupuncture group (n=10). The SI-PHT model was established by planta-electric-shock stimulation (30 V, 5 s) plus noise stimulation (80-100 db, 50 ms), twice daily, continuously for 11 days...
June 25, 2017: Zhen Ci Yan Jiu, Acupuncture Research
Xi Chen, Qiao-Ling Wang, Meng-Hui Zhang
The current study aimed to identify key genes in glaucoma based on a benchmarked dataset and gene regulatory network (GRN). Local and global noise was added to the gene expression dataset to produce a benchmarked dataset. Differentially-expressed genes (DEGs) between patients with glaucoma and normal controls were identified utilizing the Linear Models for Microarray Data (Limma) package based on benchmarked dataset. A total of 5 GRN inference methods, including Zscore, GeneNet, context likelihood of relatedness (CLR) algorithm, Partial Correlation coefficient with Information Theory (PCIT) and GEne Network Inference with Ensemble of Trees (Genie3) were evaluated using receiver operating characteristic (ROC) and precision and recall (PR) curves...
October 2017: Experimental and Therapeutic Medicine
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