Articles

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

Brucella melitensis bacteria cause persistent, intracellular infections in small ruminants as well as in humans, leading to significant morbidity and economic loss worldwide. The majority of experiments on the tr...

Authors: Paola M. Boggiatto, Daniel Fitzsimmons, Darrell O. Bayles, David Alt, Catherine E. Vrentas and Steven C. Olsen

Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression

Core canonical histones are required in the S phase of the cell cycle to pack newly synthetized DNA, therefore the expression of their genes is highly activated during DNA replication. In mammalian cells, this...

Authors: Aleksandra Brzek, Marlena Cichocka, Jakub Dolata, Wojciech Juzwa, Daniel Schümperli and Katarzyna Dorota Raczynska

Evaluation of suitable reference genes for qRT-PCR normalization in strawberry (Fragaria × ananassa) under different experimental conditions

Strawberry has received much attention due to its nutritional value, unique flavor, and attractive appearance. The availability of the whole genome sequence and multiple transcriptome databases allows the grea...

Authors: Yunting Zhang, Xiaorui Peng, Yi Liu, Yali Li, Ya Luo, Xiaorong Wang and Haoru Tang

Laser capture microdissection for transcriptomic profiles in human skin biopsies

The acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-...

Authors: Silvia Santoro, Ignazio Diego Lopez, Raffaella Lombardi, Andrea Zauli, Ana Maria Osiceanu, Melissa Sorosina, Ferdinando Clarelli, Silvia Peroni, Daniele Cazzato, Margherita Marchi, Angelo Quattrini, Giancarlo Comi, Raffaele Adolfo Calogero, Giuseppe Lauria and Filippo Martinelli Boneschi

Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides

Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recently, it has been demonstrated that gastric cancer cells display a specific miRNA expression profile, with increasing eviden...

Authors: Joana Filipa Lima, Joana Carvalho, Inês Pinto-Ribeiro, Carina Almeida, Jesper Wengel, Laura Cerqueira, Céu Figueiredo, Carla Oliveira and Nuno Filipe Azevedo

Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the heter...

Authors: Yiming K. Chang, Zheng Zuo and Gary D. Stormo

pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor

Bicarbonate-based peritoneal dialysis (PD) fluids enhance the migratory capacity and damage-repair ability of human peritoneal mesothelial cells by upregulating AQP1. However, little is known about the underly...

Authors: Yihui Zhai, Hong Xu, Qian Shen, Franz Schaefer, Claus P. Schmitt, Jing Chen, Haimei Liu, Jialu Liu and Jiaojiao Liu

A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone

Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employ...

Authors: Neftali Vazquez, Lilia Sanchez, Rebecca Marks, Eduardo Martinez, Victor Fanniel, Alma Lopez, Andrea Salinas, Itzel Flores, Jesse Hirschmann, Robert Gilkerson, Erin Schuenzel, Robert Dearth, Reginald Halaby, Wendy Innis-Whitehouse and Megan Keniry

Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples

Glomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve r...

Authors: Clemens L. Bockmeyer, Juliane Wittig, Karen Säuberlich, Philipp Selhausen, Marc Eßer, Philip Zeuschner, Friedrich Modde, Kerstin Amann and Christoph Daniel

Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5′-phosphate-dependent exonuclease in Candida albicans and other yeasts

Messenger RNA (mRNA) represents a small percentage of RNAs in a cell, with ribosomal RNA (rRNA) making up the bulk of it. To isolate mRNA from eukaryotes, typically poly-A selection is carried out. Recently, a...

Authors: Jacob Fleischmann and Miguel A. Rocha

An optimized rapid bisulfite conversion method with high recovery of cell-free DNA

Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DN...

Authors: Shaohua Yi, Fei Long, Juanbo Cheng and Daixin Huang

Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939

Cholangiocarcinoma is one of the deadly disease with poor 5-year survival and poor response to conventional therapies. Previously, we found that p27kip1 nuclear-cytoplasmic translocation confers proliferation ...

Authors: Jun Yang, Yan Liu, Bing Wang, Hongzhen Lan, Ying Liu, Fei Chen, Ju Zhang and Jian Luo

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA–pr...

Authors: Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon and Enni Markkanen

Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries

We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage...

Authors: Gorantla Venkata Raghuram, Deepika Gupta, Siddharth Subramaniam, Ashwini Gaikwad, Naveen Kumar Khare, Malcolm Nobre, Naveen Kumar Nair and Indraneel Mittra

Interaction between NFATc2 and the transcription factor Sp1 in pancreatic carcinoma cells PaTu 8988t

Nuclear factors of activated T-cells (NFATs) have been mainly characterized in the context of immune response regulation because, as transcription factors, they have the ability to induce gene transcription. N...

Authors: Manuela Malsy, Bernhard Graf and Katrin Almstedt

Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA

RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. ...

Authors: Leslie C. Sutherland, Philippe Thibault, Mathieu Durand, Elvy Lapointe, Jose M. Knee, Ariane Beauvais, Irina Kalatskaya, Sarah C. Hunt, Julie J. Loiselle, Justin G. Roy, Sarah J. Tessier, Gustavo Ybazeta, Lincoln Stein, Rashmi Kothary, Roscoe Klinck and Benoit Chabot

Growth arrest specific gene 2 in tilapia (Oreochromis niloticus): molecular characterization and functional analysis under low-temperature stress

Growth arrest specific 2 (gas2) gene is a component of the microfilament system that plays a major role in the cell cycle, regulation of microfilaments, and cell morphology during apoptotic processes. However, li...

Authors: ChangGeng Yang, Fan Wu, Xing Lu, Ming Jiang, Wei Liu, Lijuan Yu, Juan Tian and Hua Wen

Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands

G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands D...

Authors: Daniyah H. Bay, Annika Busch, Fred Lisdat, Keisuke Iida, Kazunori Ikebukuro, Kazuo Nagasawa, Isao Karube and Wataru Yoshida

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interes...

Authors: Gaurav G. Shimpi, Sergio Vargas, Angelo Poliseno and Gert Wörheide

Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis

The denervated hippocampus provides a proper microenvironment for the survival and neuronal differentiation of neural progenitors. While thousands of lncRNAs were identified, only a few lncRNAs that regulate n...

Authors: Bingying Deng, Xiang Cheng, Haoming Li, Jianbing Qin, Meiling Tian and Guohua Jin

Early growth response protein 1 regulates promoter activity of α-plasma membrane calcium ATPase 2, a major calcium pump in the brain and auditory system

Along with sodium/calcium (Ca²⁺) exchangers, plasma membrane Ca²⁺ ATPases (ATP2Bs) are main regulators of intracellular Ca²⁺ levels. There are four ATP2B paralogs encoded by four different genes. Atp2b2 encodes t...

Authors: Rebecca R. Minich, Jin Li and Bruce L. Tempel

hSSB1 associates with and promotes stability of the BLM helicase

Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functi...

Authors: Laura V. Croft, Nicholas W. Ashton, Nicolas Paquet, Emma Bolderson, Kenneth J. O’Byrne and Derek J. Richard

Selective measurement of α smooth muscle actin: why β-actin can not be used as a housekeeping gene when tissue fibrosis occurs

Prevalence of fibroproliferative diseases, including chronic kidney disease is rapidly increasing and has become a major public health problem worldwide. Fibroproliferative diseases are characterized by increa...

Authors: Apor Veres-Székely, Domonkos Pap, Erna Sziksz, Eszter Jávorszky, Réka Rokonay, Rita Lippai, Kálmán Tory, Andrea Fekete, Tivadar Tulassay, Attila J. Szabó and Ádám Vannay

Erratum to: RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions

Authors: Shubham Goyal, Takahiro Suzuki, Jing‑Ru Li, Shiori Maeda, Mami Kishima, Hajime Nishimura, Yuri Shimizu and Harukazu Suzuki

Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells

Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has ...

Authors: Tianyi Li, Hongying Diao, Lei Zhao, Yue Xing, Jichang Zhang, Ning Liu, Youyou Yan, Xin Tian, Wei Sun and Bin Liu

RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions

SPI1 is an essential transcription factor (TF) for the hematopoietic lineage, in which its expression is tightly controlled through a −17-kb upstream regulatory region and a promoter region. Both regulatory re...

Authors: Shubham Goyal, Takahiro Suzuki, Jing-Ru Li, Shiori Maeda, Mami Kishima, Hajime Nishimura, Yuri Shimizu and Harukazu Suzuki

Immunoglobulin T from sea bass (Dicentrarchus labrax L.): molecular characterization, tissue localization and expression after nodavirus infection

Immunoglobulins (Igs) are fundamental components of the adaptive immune system of vertebrates, with the IgT/IgZ isotype specific of Teleosts. In this paper we describe the identification of an IgT heavy chain ...

Authors: Francesco Buonocore, Valentina Stocchi, Noelia Nunez-Ortiz, Elisa Randelli, Marco Gerdol, Alberto Pallavicini, Angelo Facchiano, Chiara Bernini, Laura Guerra, Giuseppe Scapigliati and Simona Picchietti

Properties of STAT1 and IRF1 enhancers and the influence of SNPs

STAT1 and IRF1 collaborate to induce interferon-γ (IFNγ) stimulated genes (ISGs), but the extent to which they act alone or together is unclear. The effect of single nucleotide polymorphisms (SNPs) on in vivo ...

Authors: Mohamed Abou El Hassan, Katherine Huang, Manoja B. K. Eswara, Zhaodong Xu, Tao Yu, Arthur Aubry, Zuyao Ni, Izzy Livne-bar, Monika Sangwan, Mohamad Ahmad and Rod Bremner

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective ...

Authors: Toshiki Aiba, Toshiyuki Saito, Akiko Hayashi, Shinji Sato, Harunobu Yunokawa, Toru Maruyama, Wataru Fujibuchi, Hisaka Kurita, Chiharu Tohyama and Seiichiroh Ohsako

Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae)

MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have be...

Authors: Kang-Sheng Ma, Fen Li, Ying Liu, Ping-Zhuo Liang, Xue-Wei Chen and Xi-Wu Gao

Binding affinity of five PBPs to Ostrinia sex pheromones

Pheromone binding proteins (PBPs) of male Lepidoptera function in chemical communication, mate attraction and recognition. Directional selection was previously predicted between PBP3 orthologs of Ostrinia furnaca...

Authors: Tiantao Zhang, Yaqi Sun, Kevin W. Wanner, Brad S. Coates, Kanglai He and Zhenying Wang

Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants

Farnesyl pyrophosphate synthase (FPS) belongs to the short-chain prenyltransferase family, and it performs a conserved and essential role in the terpenoid biosynthesis pathway. However, its classification, evo...

Authors: Jieying Qian, Yong Liu, Naixia Chao, Chengtong Ma, Qicong Chen, Jian Sun and Yaosheng Wu

Transcriptional regulation of human sperm-associated antigen 16 gene by S-SOX5

The mammalian sperm-associated antigen 16 gene (Spag16) uses alternative promoters to produce two major transcript isoforms (Spag16L and Spag16S) and encode proteins that are involved in the cilia/flagella format...

Authors: Ling Zhang, Yunhao Liu, Wei Li, Qiaoling Zhang, Yanwei Li, Junpin Liu, Jie Min, Chaofan Shuang, Shizheng Song and Zhibing Zhang

Heterogeneous pattern of DNA methylation in developmentally important genes correlates with its chromatin conformation

DNA methylation is a major epigenetic modification, playing a crucial role in the development and differentiation of higher organisms. DNA methylation is also known to regulate transcription by gene repression...

Authors: Puja Sinha, Kiran Singh and Manisha Sachan

Novel insight into the composition of human single-stranded DNA-binding protein 1 (hSSB1)-containing protein complexes

Single-stranded DNA-binding proteins are essential cellular components required for the protection, metabolism and processing of single-stranded DNA. Human single-stranded DNA-binding protein 1 (hSSB1) is one ...

Authors: Nicholas W. Ashton, Dorothy Loo, Nicolas Paquet, Kenneth J. O’Byrne and Derek J. Richard

3C-digital PCR for quantification of chromatin interactions

Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin inte...

Authors: Meijun Du and Liang Wang

Ataxia telangiectasia mutated (ATM) interacts with p400 ATPase for an efficient DNA damage response

Ataxia telangiectasia mutated (ATM) and TRRAP proteins belong to the phosphatidylinositol 3-kinase-related kinase family and are involved in DNA damage repair and chromatin remodeling. ATM is a checkpoint kina...

Authors: Rebecca J. Smith, Matthew S. Savoian, Lauren E. Weber and Jeong Hyeon Park

RNA polymerase II depletion promotes transcription of alternative mRNA species

Cells respond to numerous internal and external stresses, such as heat, cold, oxidative stress, DNA damage, and osmotic pressure changes. In most cases, the primary response to stress is transcriptional induct...

Authors: Lijian Yu, Mayuri Rege, Craig L. Peterson and Michael R. Volkert

Distinct recruitment of human eIF4E isoforms to processing bodies and stress granules

Eukaryotic translation initiation factor 4E (eIF4E) plays a pivotal role in the control of cap-dependent translation initiation, modulates the fate of specific mRNAs, occurs in processing bodies (PBs) and is r...

Authors: Klara Frydryskova, Tomas Masek, Katerina Borcin, Silvia Mrvova, Veronica Venturi and Martin Pospisek

Nucleophosmin: from structure and function to disease development

Nucleophosmin (NPM1) is a critical cellular protein that has been implicated in a number of pathways including mRNA transport, chromatin remodeling, apoptosis and genome stability. NPM1 function is a critical ...

Authors: Joseph K. Box, Nicolas Paquet, Mark N. Adams, Didier Boucher, Emma Bolderson, Kenneth J. O’Byrne and Derek J. Richard

Myelodysplasia-associated mutations in serine/arginine-rich splicing factor SRSF2 lead to alternative splicing of CDC25C

Serine–arginine rich splicing factor 2 (SRSF2) is a protein known for its role in RNA splicing and genome stability. It has been recently discovered that SRSF2, along with other splicing regulators, is frequen...

Authors: Lindsey Skrdlant, Jeremy M. Stark and Ren-Jang Lin

MicroRNA 433 regulates nonsense-mediated mRNA decay by targeting SMG5 mRNA

Nonsense-mediated mRNA decay (NMD) is a RNA quality surveillance system for eukaryotes. It prevents cells from generating deleterious truncated proteins by degrading abnormal mRNAs that harbor premature termin...

Authors: Yi Jin, Fang Zhang, Zhenfa Ma and Zhuqing Ren

Stearoyl-CoA desaturase 1 expression is downregulated in liver and udder during E. coli mastitis through enhanced expression of repressive C/EBP factors and reduced expression of the inducer SREBP1A

Stearoyl-CoA desaturase 1 (SCD1) desaturates long chain fatty acids and is therefore a key enzyme in fat catabolism. Its synthesis is downregulated in liver during illnesses caused by high levels of circulatin...

Authors: Tianle Xu, Xiangzhen Shen and Hans-Martin Seyfert

Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein

In contrast to rat and mouse databases, the NCBI gene database lists the human dual-endothelin1/VEGFsp receptor (DEspR, formerly Dear) as a unitary transcribed pseudogene due to a stop [TGA]-codon at codon#14 in ...

Authors: Victoria L. M. Herrera, Martin Steffen, Ann Marie Moran, Glaiza A. Tan, Khristine A. Pasion, Keith Rivera, Darryl J. Pappin and Nelson Ruiz-Opazo

Strong preference of BRCA1 protein to topologically constrained non-B DNA structures

The breast and ovarian cancer susceptibility gene BRCA1 encodes a multifunctional tumor suppressor protein BRCA1, which is involved in regulating cellular processes such as cell cycle, transcription, DNA repair, ...

Authors: Václav Brázda, Lucia Hároníková, Jack C. C. Liao, Helena Fridrichová and Eva B. Jagelská

Erratum to: Gene expression profiling of the venom gland from the Venezuelan mapanare (Bothrops colombiensis) using expressed sequence tags (ESTs)

Authors: Montamas Suntravat, Néstor L. Uzcategui, Chairat Atphaisit, Thomas J. Helmke, Sara E. Lucena, Elda E. Sánchez and Alexis Rodríguez-Acosta

A potential role for protein palmitoylation and zDHHC16 in DNA damage response

Cells respond to DNA damage by activating the phosphatidylinositol-3 kinase-related kinases, p53 and other pathways to promote cell cycle arrest, apoptosis, and/or DNA repair. Here we report that protein palmi...

Authors: Na Cao, Jia-Kai Li, Yu-Qing Rao, Huijuan Liu, Ji Wu, Baojie Li, Peiquan Zhao, Li Zeng and Jing Li

Mice lacking microRNAs in Pax8-expressing cells develop hypothyroidism and end-stage renal failure

Non-coding RNAs have gained increasing attention during the last decade. The first large group of non-coding RNAs to be characterized systematically starting at the beginning of the 21st century were small oli...

Authors: Malte P. Bartram, Elena Amendola, Thomas Benzing, Bernhard Schermer, Gabriella de Vita and Roman-Ulrich Müller

Signal transducer and activator of transcription STAT5 is recruited to c-Myc super-enhancer

c-Myc has been proposed as a putative target gene of signal transducer and activator of transcription 5 (STAT5). No functional STAT5 binding site has been identified so far within the

Authors: Sophia Pinz, Samy Unser and Anne Rascle

Immunoblot screening of CRISPR/Cas9-mediated gene knockouts without selection

Targeted genomic editing using the CRISPR/Cas9 methodology has opened exciting new avenues in probing gene function in virtually any model system, including cultured mammalian cells. Depending on the desired m...

Authors: Jason A. Estep, Erin L. Sternburg, Gissell A. Sanchez and Fedor V. Karginov