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ChIP-seq OR RNA-seq

Zuhong He, Qiaojun Fang, He Li, Buwei Shao, Yuan Zhang, Yuhua Zhang, Xiao Han, Rongrong Guo, Cheng Cheng, Lingna Guo, Lusen Shi, Ao Li, Chenjie Yu, Weijia Kong, Chunjie Zhao, Xia Gao, Renjie Chai
The development of therapeutic interventions for hearing loss requires a detailed understanding of the genes and proteins involved in hearing. The FOXG1 protein plays an important role in early neural development and in a variety of neurodevelopmental disorders. Previous studies have shown that there are severe deformities in the inner ear in Foxg1 knockout mice, but due to the postnatal lethality of Foxg1 knockout mice, the role of FOXG1 in hair cell (HC) development and survival during the postnatal period has not been investigated...
October 15, 2018: Neuropharmacology
Peter W Inglis, Marilia de Castro R Pappas, Lucileide V Resende, Dario Grattapaglia
Modern genotyping techniques, such as SNP analysis and genotyping by sequencing (GBS), are hampered by poor DNA quality and purity, particularly in challenging plant species, rich in secondary metabolites. We therefore investigated the utility of a pre-wash step using a buffered sorbitol solution, prior to DNA extraction using a high salt CTAB extraction protocol, in a high throughput or miniprep setting. This pre-wash appears to remove interfering metabolites, such as polyphenols and polysaccharides, from tissue macerates...
2018: PloS One
Xiang Hu, Wen Chen, Jing Li, Shulan Huang, Xuling Xu, Xuan Zhang, Shuanglin Xiang, Changning Liu
There is emerging evidence showing that lncRNAs can be involved in various critical biological processes. Zebrafish is a fully developed model system being used in a variety of basic research and biomedical studies. Hence, it is an ideal model organism to study the functions and mechanisms of lncRNAs. Here, we constructed ZFLNC-a comprehensive database of zebrafish lncRNA that is dedicated to providing a zebrafish-based platform for deep exploration of zebrafish lncRNAs and their mammalian counterparts to the relevant academic communities...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Patricia Sieber, Kerstin Voigt, Philipp Kämmer, Sascha Brunke, Stefan Schuster, Jörg Linde
Alternative splicing (AS) is an important regulatory mechanism in eukaryotes but only little is known about its impact in fungi. Human fungal pathogens are of high clinical interest causing recurrent or life-threatening infections. AS can be well-investigated genome-wide and quantitatively with the powerful technology of RNA-Seq. Here, we systematically studied AS in human fungal pathogens based on RNA-Seq data. To do so, we investigated its effect in seven fungi during conditions simulating ex vivo infection processes and during in vitro stress...
2018: Frontiers in Microbiology
Erin L Sternburg, Jason A Estep, Daniel K Nguyen, Yahui Li, Fedor V Karginov
Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3' untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. To assess the extent of such co-regulatory control, we took a global experimental approach followed by targeted validation to examine interactions between two well-characterized and highly conserved RBPs, Argonaute2 (AGO2) and Pumilio (PUM1 and PUM2)...
October 17, 2018: Scientific Reports
Chaoyang Ye, Daniel J Ho, Marilisa Neri, Chian Yang, Tripti Kulkarni, Ranjit Randhawa, Martin Henault, Nadezda Mostacci, Pierre Farmer, Steffen Renner, Robert Ihry, Leandra Mansur, Caroline Gubser Keller, Gregory McAllister, Marc Hild, Jeremy Jenkins, Ajamete Kaykas
Here we report Digital RNA with pertUrbation of Genes (DRUG-seq), a high-throughput platform for drug discovery. Pharmaceutical discovery relies on high-throughput screening, yet current platforms have limited readouts. RNA-seq is a powerful tool to investigate drug effects using transcriptome changes as a proxy, yet standard library construction is costly. DRUG-seq captures transcriptional changes detected in standard RNA-seq at 1/100th the cost. In proof-of-concept experiments profiling 433 compounds across 8 doses, transcription profiles generated from DRUG-seq successfully grouped compounds into functional clusters by mechanism of actions (MoAs) based on their intended targets...
October 17, 2018: Nature Communications
Katherine L James, Thushan de Silva, Katherine Brown, Hilton Whittle, Stephen Taylor, Gilean McVean, Joakim Esbjörnsson, Sarah L Rowland-Jones
Accurate determination of the genetic diversity present in the HIV quasi-species is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in co-infected subjects. The majority of traditional and next generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population...
October 17, 2018: Journal of Virology
Lucas Busta, Won Yim, Evan William LaBrant, Peng Wang, Lindsey Grimes, Kiah Malyszka, John C Cushman, Patricia Santos, Dylan K Kosma, Edgar B Cahoon
Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is unknown. To begin filling this gap, and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp...
October 17, 2018: Plant Physiology
Zhengyun Xiao, Guo Cheng, Yang Jiao, Chen Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng, Junling Jia
Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative accuracy and uniform coverage with a complete strand of origin information as bulk RNA-seq. Most importantly, Holo-Seq can simultaneously observe small RNAs and mRNAs in a single cell...
October 17, 2018: Genome Biology
Takae Kiyama, Ching-Kang Chen, Steven W Wang, Ping Pan, Zhenlin Ju, Jing Wang, Shinako Takada, William H Klein, Chai-An Mao
BACKGROUND: Mitochondrial dysfunction has been implicated in the pathologies of a number of retinal degenerative diseases in both the outer and inner retina. In the outer retina, photoreceptors are particularly vulnerable to mutations affecting mitochondrial function due to their high energy demand and sensitivity to oxidative stress. However, it is unclear how defective mitochondrial biogenesis affects neural development and contributes to neural degeneration. In this report, we investigated the in vivo function of nuclear respiratory factor 1 (Nrf1), a major transcriptional regulator of mitochondrial biogenesis in both proliferating retinal progenitor cells (RPCs) and postmitotic rod photoreceptor cells (PRs)...
October 17, 2018: Molecular Neurodegeneration
Nicholas Petronella, Jennifer Ronholm, Menka Suresh, Jennifer Harlow, Oksana Mykytczuk, Nathalie Corneau, Sabah Bidawid, Neda Nasheri
BACKGROUND: Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome. METHOD: A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples...
October 17, 2018: BMC Infectious Diseases
María Verónica Prego-Faraldo, Luisa Martínez, Josefina Méndez
The harmful effects of diarrhetic shellfish poisoning (DSP) toxins on mammalian cell lines have been widely assessed. Studies in bivalves suggest that mussels display a resistance to the cytogenotoxic effects of DSP toxins. Further, it seems that the bigger the exposure, the more resistant mussels become. To elucidate the early genetic response of mussels against these toxins, the digestive gland and the gill transcriptomes of Mytilus galloprovincialis after Prorocentrum lima exposure (100,000 cells/L, 48 h) were de novo assembled based on the sequencing of 8 cDNA libraries obtained using an Illumina HiSeq 2000 platform...
October 16, 2018: Toxins
Arpita Chowdhury, Abhishek Aich, Gaurav Jain, Katharina Wozny, Christian Lüchtenborg, Magnus Hartmann, Olaf Bernhard, Martina Balleiniger, Ezzaldin Ahmed Alfar, Anke Zieseniss, Karl Toischer, Kaomei Guan, Silvio O Rizzoli, Britta Brügger, Andrè Fischer, Dörthe M Katschinski, Peter Rehling, Jan Dudek
Mitochondria fulfill vital metabolic functions and act as crucial cellular signaling hubs, integrating their metabolic status into the cellular context. Here, we show that defective cardiolipin remodeling, upon loss of the cardiolipin acyl transferase tafazzin, decreases HIF-1α signaling in hypoxia. Tafazzin deficiency does not affect posttranslational HIF-1α regulation but rather HIF-1α gene expression, a dysfunction recapitulated in iPSC-derived cardiomyocytes from Barth syndrome patients with tafazzin deficiency...
October 16, 2018: Cell Reports
T L Masters, C A Hilker, P R Jeraldo, A V Bhagwate, K E Greenwood-Quaintance, B W Eckloff, N Chia, A D Hanssen, M P Abdel, J Z Yao, J Jen, R Patel
With the emergence of RNA sequencing technologies, metatranscriptomic studies are rapidly gaining attention as they simultaneously provide insight into gene expression profiles and therefore disease association pathways of microbial pathogens and their hosts. This approach, therefore, holds promise for applicability in infectious disease diagnostics. A challenge of this approach in the clinical setting is the low amount and quality of RNA, especially microbial RNA in most clinically-infected specimens. Here, we compared two commercially available stranded cDNA library preparation kits, the NuGEN Ovation SoLo RNA-Seq System and the Illumina TruSeq Stranded Total RNA, using RNA extracted from synovial and sonicate fluids from a subject with periprosthetic joint infection...
October 14, 2018: Journal of Microbiological Methods
Jianlu Kong, Wenjie Sun, Wenyuan Zhu, Chuanxia Liu, Honghe Zhang, Huiming Wang
BACKGROUND AND OBJECTIVES: Long noncoding RNAs (lncRNAs) play key roles in carcinoma metastasis. We aimed to investigate lncRNA LINC01133 in oral squamous cell carcinoma (OSCC) metastasis. METHODS: The RNA levels of LINC01133 and growth and differentiation factor 15 (GDF15) in tissue samples from OSCC patients, and OSCC cell lines were tested by real-time quantitative polymerase chain reaction (RT-qPCR). SPSS20.0 was used to perform statistical analysis of LINC01133 expression in clinical samples and correlate expression of LINC01133 and GDF15...
October 17, 2018: Journal of Surgical Oncology
David Pincus, Jayamani Anandhakumar, Prathapan Thiru, Michael J Guertin, Alexander M Erkine, David S Gross
Heat Shock Factor 1 is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting Heat Shock Element (HSE) across the eukaryotic lineage. In budding yeast, Hsf1 drives the transcription of ∼20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here, we combine Hsf1 ChIP-seq, nascent RNA-seq and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome...
October 17, 2018: Molecular Biology of the Cell
Naresh V R Mutha, Waleed K Mohammed, Natalio Krasnogor, Geok Y A Tan, Siew Woh Choo, Nicholas S Jakubovics
Cell-cell interactions between genetically distinct bacteria, known as coaggregation, are important for the formation of mixed-species biofilms such as dental plaque. Interactions lead to gene regulation in the partner organisms that may be critical for adaptation and survival in mixed-species biofilms. Here, gene regulation responses to coaggregation between Streptococcus gordonii and Fusobacterium nucleatum were studied using dual RNA-Seq. Initially, S. gordonii DL1 was shown to coaggregate strongly with F...
October 17, 2018: Molecular Oral Microbiology
Simone Altmann, Jose M Muino, Vivien Lortzing, Ronny Brandt, Axel Himmelbach, Lothar Altschmied, Monika Hilker
Plant responses to insect egg depositions are known to shape subsequent defensive responses to larvae hatching from the eggs. Elm (Ulmus minor) leaves, on which elm leaf beetles laid their eggs, mount a more efficient defense against larvae hatching from the eggs. However, the molecular mechanisms of this egg-mediated, improved defense are insufficiently understood and have so far only been studied in annual plants. We analyzed the dynamics of transcriptomic changes in larval feeding-damaged elm leaves with and without prior egg deposition using de novo assembled RNA-seq data...
October 17, 2018: Molecular Ecology
Sihyung Park, Seung Hyun Ahn, Eun Sol Cho, You Kyung Cho, Eun-Sook Jang, Sung Wook Chi
High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP, also called CLIP-Seq) has been used to map global RNA-protein interactions. However, a critical caveat of HITS-CLIP results is that they contain non-linear background noise-different extent of non-specific interactions caused by individual transcript abundance-that has been inconsiderately normalized, resulting in sacrifice of sensitivity. To properly deconvolute RNA-protein interactions, we have implemented CLIPick, a flexible peak calling pipeline for analyzing HITS-CLIP data, which statistically determines the signal-to-noise ratio for each transcript based on the expression-dependent background simulation...
October 17, 2018: Nucleic Acids Research
Shayoni Ray, Samrawit Gebre, Homer Fogle, Daniel C Berrios, Peter B Tran, Jonathan M Galazka, Sylvain V Costes
Motivation: - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. Results: - The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated "omics" (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms...
October 17, 2018: Bioinformatics
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