Articles

MicroRNA-19a regulates lipopolysaccharide-induced endothelial cell apoptosis through modulation of apoptosis signal-regulating kinase 1 expression

MicroRNAs, small non-encoding RNAs that post-transcriptionally modulate expression of their target genes, have been implicated as critical regulatory molecules in endothelial cells.

Authors: Wei-Long Jiang, Yu-Feng Zhang, Qing-Qing Xia, Jian Zhu, Xin Yu, Tao Fan and Feng Wang

Annual acknowledgement of reviewers

The editors of BMC Molecular Biology would like to thank all our reviewers who have contributed to the journal in Volume 15 (2014).

Authors: Tim Sands

Lowering the quantification limit of the Qubit^TM RNA HS Assay using RNA spike-in

RNA quantification is often a prerequisite for most RNA analyses such as RNA sequencing. However, the relatively low sensitivity and large sample consumption of traditional RNA quantification methods such as U...

Authors: Xin Li, Iddo Z Ben-Dov, Maurizio Mauro and Zev Williams

An Rb1-dependent amplification loop between Ets1 and Zeb1 is evident in thymocyte differentiation and invasive lung adenocarcinoma

Ras pathway mutation leads to induction and Erk phosphorylation and activation of the Ets1 transcription factor. Ets1 in turn induces cyclin E and cyclin dependent kinase (cdk) 2 to drive cell cycle progressio...

Authors: Kevin C Dean, Li Huang, Yao Chen, Xiaoqin Lu and Yongqing Liu

Nop17 is a key R2TP factor for the assembly and maturation of box C/D snoRNP complex

Box C/D snoRNPs are responsible for rRNA methylation and processing, and are formed by snoRNAs and four conserved proteins, Nop1, Nop56, Nop58 and Snu13. The snoRNP assembly is a stepwise process, involving ot...

Authors: Marcela B Prieto, Raphaela C Georg, Fernando A Gonzales-Zubiate, Juliana S Luz and Carla C Oliveira

Mechanical stimulation of human tendon stem/progenitor cells results in upregulation of matrix proteins, integrins and MMPs, and activation of p38 and ERK1/2 kinases

Tendons are dense connective tissues subjected periodically to mechanical stress upon which complex responsive mechanisms are activated. These mechanisms affect not only the development of these tissues but al...

Authors: Cvetan Popov, Martina Burggraf, Ludwika Kreja, Anita Ignatius, Matthias Schieker and Denitsa Docheva

Pre-amplification in the context of high-throughput qPCR gene expression experiment

With the introduction of the first high-throughput qPCR instrument on the market it became possible to perform thousands of reactions in a single run compared to the previous hundreds. In the high-throughput r...

Authors: Vlasta Korenková, Justin Scott, Vendula Novosadová, Marie Jindřichová, Lucie Langerová, David Švec, Monika Šídová and Robert Sjöback

Wnt antagonist, secreted frizzled-related protein 1, is involved in prenatal skeletal muscle development and is a target of miRNA-1/206 in pigs

The Wnt signaling pathway is involved in the control of cell proliferation and differentiation during skeletal muscle development. Secreted frizzled-related proteins (SFRPs), such as SFRP1, function as inhibitors...

Authors: Yalan Yang, Wei Sun, Ruiqi Wang, Chuzhao Lei, Rong Zhou, Zhonglin Tang and Kui Li

Fluorescence-based monitoring of ribosome assembly landscapes

Ribosomes and functional complexes of them have been analyzed at the atomic level. Far less is known about the dynamic assembly and degradation events that define the half-life of ribosomes and guarantee their...

Authors: Rainer Nikolay, Renate Schloemer, Silke Mueller and Elke Deuerling

Efficient 5′-3′ DNA end resection by HerA and NurA is essential for cell viability in the crenarchaeon Sulfolobus islandicus

ATPase/Helicases and nucleases play important roles in homologous recombination repair (HRR). Many of the mechanistic details relating to these enzymes and their function in this fundamental and complicated DN...

Authors: Qihong Huang, Linlin Liu, Junfeng Liu, Jinfeng Ni, Qunxin She and Yulong Shen

MKL1 inhibits cell cycle progression through p21 in podocytes

The glomerular podocyte is a highly specialized cell type with the ability to ultrafilter blood and support glomerular capillary pressure. However, little is known about the genetic programs leading to this fu...

Authors: Shuang Yang, Lingjia Liu, Pengjuan Xu and Zhuo Yang

Molecular characterization of the piggyBac-like element, a candidate marker for phylogenetic research of Chilo suppressalis (Walker) in China

Transposable elements (TEs, transposons) are mobile genetic DNA sequences. TEs can insert copies of themselves into new genomic locations and they have the capacity to multiply. Therefore, TEs have been crucia...

Authors: Guang-Hua Luo, Xiao-Huan Li, Zhao-Jun Han, Hui-Fang Guo, Qiong Yang, Min Wu, Zhi-Chun Zhang, Bao-Sheng Liu, Lu Qian and Ji-Chao Fang

Néstor-Guillermo Progeria Syndrome: a biochemical insight into Barrier-to-Autointegration Factor 1, alanine 12 threonine mutation

Premature aging syndromes recapitulate many aspects of natural aging and provide an insight into this phenomenon at a molecular and cellular level. The progeria syndromes appear to cause rapid aging through di...

Authors: Nicolas Paquet, Joseph K Box, Nicholas W Ashton, Amila Suraweera, Laura V Croft, Aaron J Urquhart, Emma Bolderson, Shu-Dong Zhang, Kenneth J O’Byrne and Derek J Richard

Efficient isolation of specific genomic regions retaining molecular interactions by the iChIP system using recombinant exogenous DNA-binding proteins

Comprehensive understanding of mechanisms of genome functions requires identification of molecules interacting with genomic regions of interest in vivo. We previously developed the insertional chromatin immunopre...

Authors: Toshitsugu Fujita and Hodaka Fujii

Downregulation of microRNA-100 protects apoptosis and promotes neuronal growth in retinal ganglion cells

Retinal ganglion cells (RGCs) are preferentially lost in glaucoma or optic neuritis. In the present study, we investigated the protective effect of mircoRNA 100 (miR-100) against oxidative stress induced apopt...

Authors: Ning Kong, Xiaohe Lu and Bin Li

Establishment of a quantitative PCR system for discriminating chitinase-like proteins: catalytically inactive breast regression protein-39 and Ym1 are constitutive genes in mouse lung

Mice and humans produce chitinase-like proteins (CLPs), which are highly homologous to chitinases but lack chitinolytic activity. Mice express primarily three CLPs, including breast regression protein-39 (BRP-...

Authors: Misa Ohno, Yuta Kida, Masayoshi Sakaguchi, Yasusato Sugahara and Fumitaka Oyama

Expression of GBGT1 is epigenetically regulated by DNA methylation in ovarian cancer cells

The GBGT1 gene encodes the globoside alpha-1,3-N-acetylgalactosaminyltransferase 1. This enzyme catalyzes the last step in the multi-step biosynthesis of the Forssman (Fs) antigen, a pentaglycosyl ceramide of the...

Authors: Francis Jacob, Megan P Hitchins, André Fedier, Kevin Brennan, Sheri Nixdorf, Neville F Hacker, Robyn Ward and Viola A Heinzelmann-Schwarz

Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms

Previous studies suggested that nucleosomes are enriched with single nucleotide polymorphisms (SNPs) in humans and that the occurrence of mutations is closely associated with CpG dinucleotides. We aimed to det...

Authors: Hongde Liu, Jinchen Zhai, Kun Luo and Lingjie Liu

Pax8 modulates the expression of Wnt4 that is necessary for the maintenance of the epithelial phenotype of thyroid cells

The transcription factor Pax8 is expressed during thyroid development and is involved in the morphogenesis of the thyroid gland and maintenance of the differentiated phenotype. In particular, Pax8 has been shown ...

Authors: Maria Grazia Filippone, Tina Di Palma, Valeria Lucci and Mariastella Zannini

Wingless gene cloning and its role in manipulating the wing dimorphism in the white-backed planthopper, Sogatella furcifera

Wingless gene (Wg) plays a fundamental role in regulating the segment polarity and wing imaginal discs of insects. The rice planthoppers have an obvious wing dimorphism, and the long- and short-winged forms exist...

Authors: Ju-Long Yu, Zhi-Fang An and Xiang-Dong Liu

Requirements for resuming translation in chimeric transfer-messenger RNAs of Escherichia coli and Mycobacterium tuberculosis

Trans-translation is catalyzed by ribonucleprotein complexes composed of SmpB protein and transfer-messenger RNA. They release stalled ribosomes from truncated mRNAs and tag defective proteins for proteolytic deg...

Authors: Iwona K Wower, Christian Zwieb and Jacek Wower

Insight into the cellular involvement of the two reverse gyrases from the hyperthermophilic archaeon Sulfolobus solfataricus

Reverse gyrases are DNA topoisomerases characterized by their unique DNA positive-supercoiling activity. Sulfolobus solfataricus, like most Crenarchaeota, contains two genes each encoding a reverse gyrase. We sho...

Authors: Mohea Couturier, Anna H Bizard, Florence Garnier and Marc Nadal

Visualization of the physical and functional interaction between hMYH and hRad9 by Dronpa bimolecular fluorescence complementation

Human MutY glycosylase homolog (hMYH), a component of the base excision repair pathway, is responsible for the generation of apurinic/apyrimidinic sites. Rad9-Rad1-Hus1 (9-1-1) is a heterotrimeric protein comp...

Authors: Lia Agustina, Soo-Hyun Hahm, Se Hee Han, An Hue Vy Tran, Ji Hyung Chung, Jong-Hwa Park, Jin Woo Park and Ye Sun Han

Erratum to: Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermussp. enzyme family

Authors: Agnieszka Zylicz-Stachula, Janusz M Bujnicki and Piotr M Skowron

Genetic transformation of Fusarium avenaceum by Agrobacterium tumefaciens mediated transformation and the development of a USER-Brick vector construction system

The plant pathogenic and saprophytic fungus Fusarium avenaceum causes considerable in-field and post-field losses worldwide due to its infections of a wide range of different crops. Despite its significant impact...

Authors: Lisette Quaade Sørensen, Erik Lysøe, Jesper Erup Larsen, Paiman Khorsand-Jamal, Kristian Fog Nielsen and Rasmus John Normand Frandsen

Egr-1 regulates the transcription of NGX6 gene through a Sp1/Egr-1 overlapping site in the promoter

As a novel candidate metastasis suppressor gene, Nasopharyngeal carcinoma-associated gene 6 (NGX6) is involved in cellular growth, cell cycle progression and tumor angiogenesis. Previous studies have shown tha...

Authors: Minji Liu, Xiaoyan Wang, Ya Peng, Shourong Shen and Guiyuan Li

Exploring the transcription activator-like effectors scaffold versatility to expand the toolbox of designer nucleases

The past decade has seen the emergence of several molecular tools that render possible modification of cellular functions through accurate and easy addition, removal, or exchange of genomic DNA sequences. Amon...

Authors: Alexandre Juillerat, Marine Beurdeley, Julien Valton, Séverine Thomas, Gwendoline Dubois, Mikhail Zaslavskiy, Jérome Mikolajczak, Fabian Bietz, George H Silva, Aymeric Duclert, Fayza Daboussi and Philippe Duchateau

Ribonomic analysis of human DZIP1 reveals its involvement in ribonucleoprotein complexes and stress granules

DZIP1 (DAZ-interacting protein 1) has been described as a component of the Hh signaling pathway with a putative regulatory role in ciliogenesis. DZIP1 interacts with DAZ RNA binding proteins in embryonic stem ...

Authors: Patrícia ShigunovShigunov, Jose Sotelo-Silveira, Marco Augusto Stimamiglio, Crisciele Kuligovski, Florencia Irigoín, Jose L Badano, David Munroe, Alejandro Correa and Bruno Dallagiovanna

Identification of a common reference gene pair for qPCR in human mesenchymal stromal cells from different tissue sources treated with VEGF

Human mesenchymal stromal cells from the bone marrow (BMSCs) are widely used as experimental regenerative treatment of ischemic heart disease, and the first clinical trials using adipose-derived stromal cells ...

Authors: Josefine Tratwal, Bjarke Follin, Annette Ekblond, Jens Kastrup and Mandana Haack-Sørensen

Single and combinatorial chromatin coupling events underlies the function of transcript factor krüppel-like factor 11 in the regulation of gene networks

Krüppel-like factors (KLFs) are a group of master regulators of gene expression conserved from flies to human. However, scant information is available on either the mechanisms or functional impact of the coupl...

Authors: Ezequiel Calvo, Adrienne Grzenda, Gwen Lomberk, Angela Mathison, Juan Iovanna and Raul Urrutia

Validation of housekeeping gene and impact on normalized gene expression in clear cell Renal Cell Carcinoma: critical reassessment of YBX3/ZONAB/CSDA expression

YBX3/ZONAB/CSDA is an epithelial-specific transcription factor acting in the density-based switch between proliferation and differentiation. Our laboratory reported overexpression of YBX3 in clear cell renal c...

Authors: Sébastien Dupasquier, Anne-Sophie Delmarcelle, Etienne Marbaix, Jean-Pierre Cosyns, Pierre J Courtoy and Christophe E Pierreux

Differential regulation of the α-globin locus by Krüppel-like factor 3 in erythroid and non-erythroid cells

Krüppel-like Factor 3 (KLF3) is a broadly expressed zinc-finger transcriptional repressor with diverse biological roles. During erythropoiesis, KLF3 acts as a feedback repressor of a set of genes that are acti...

Authors: Alister PW Funnell, Douglas Vernimmen, Wooi F Lim, Ka Sin Mak, Beeke Wienert, Gabriella E Martyn, Crisbel M Artuz, Jon Burdach, Kate GR Quinlan, Douglas R Higgs, Emma Whitelaw, Richard CM Pearson and Merlin Crossley

A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity

Many studies of the eukaryotic transcription mechanism and its regulation rely on in vitro assays. Conventional RNA polymerase II transcription assays are based on radioactive labelling of the newly synthesized R...

Authors: Cristina Voss, Brita Schmitt, Susanne Werner-Simon, Christian Lutz, Werner Simon and Jan Anderl

Fidelity of end joining in mammalian episomes and the impact of Metnase on joint processing

Double Stranded Breaks (DSBs) are the most serious form of DNA damage and are repaired via homologous recombination repair (HRR) or non-homologous end joining (NHEJ). NHEJ predominates in mammalian cells at mo...

Authors: Abhijit Rath, Robert Hromas and Arrigo De Benedetti

Inverted terminal repeats of adeno-associated virus decrease random integration of a gene targeting fragment in Saccharomyces cerevisiae

Homologous recombination mediated gene targeting is still too inefficient to be applied extensively in genomics and gene therapy. Although sequence-specific nucleases could greatly stimulate gene targeting eff...

Authors: Alvaro Galli and Tiziana Cervelli

Cooperative activation of Xenopus rhodopsin transcription by paired-like transcription factors

In vertebrates, rod photoreceptor-specific gene expression is regulated by the large Maf and Pax-like transcription factors, Nrl/LNrl and Crx/Otx5. The ubiquitous occurrence of their target DNA binding sites t...

Authors: Sarah E Reks, Vera McIlvain, Xinming Zhuo and Barry E Knox

Spdef deletion rescues the crypt cell proliferation defect in conditional Gata6 null mouse small intestine

GATA transcription factors are essential for self-renewal of the small intestinal epithelium. Gata4 is expressed in the proximal 85% of small intestine while Gata6 is expressed throughout the length of small inte...

Authors: Boaz E Aronson, Kelly A Stapleton, Laurens ATM Vissers, Eva Stokhuijzen, Hanneke Bruijnzeel and Stephen D Krasinski

Annual acknowledgement of reviewers

The editors of BMC Molecular Biology would like to thank all our reviewers who have contributed to the journal in Volume 14 (2013).

Authors: Tim Sands

MicroRNA miR-378 promotes BMP2-induced osteogenic differentiation of mesenchymal progenitor cells

MicroRNAs (miRNAs) are a family of small, non-coding single-stranded RNA molecules involved in post-transcriptional regulation of gene expression. As such, they are believed to play a role in regulating the st...

Authors: Marlinda Hupkes, Ana M Sotoca, José M Hendriks, Everardus J van Zoelen and Koen J Dechering

Dissecting domains necessary for activation and repression of splicing by muscleblind-like protein 1

Alternative splicing contributes to the diversity of the proteome, and provides the cell with an important additional layer of regulation of gene expression. Among the many RNA binding proteins that regulate a...

Authors: Christopher Edge, Clare Gooding and Christopher WJ Smith

Differential regulation of the rainbow trout (Oncorhynchus mykiss) MT-A gene by nuclear factor interleukin-6 and activator protein-1

Previously we have identified a distal region of the rainbow trout (Oncorhynchus mykiss) metallothionein-A (rtMT-A) enhancer region, being essential for free radical activation of the rtMT-A gene. The distal prom...

Authors: Peter Kling, Carina Modig, Huthayfa Mujahed, Hazem Khalaf, Jonas von Hofsten and Per-Erik Olsson

An aryl hydrocarbon receptor induces VEGF expression through ATF4 under glucose deprivation in HepG2

Aryl hydrocarbon receptor (AhR) not only regulates drug-metabolizing enzyme expression but also regulates cancer malignancy. The steps to the development of malignancy include angiogenesis that is induced by t...

Authors: Jun Terashima, Chie Tachikawa, Kenzo Kudo, Wataru Habano and Shogo Ozawa

MAR-mediated integration of plasmid vectors for in vivo gene transfer and regulation

The in vivo transfer of naked plasmid DNA into organs such as muscles is commonly used to assess the expression of prophylactic or therapeutic genes in animal disease models.

Authors: Stefania Puttini, Ruthger W van Zwieten, Damien Saugy, Małgorzata Lekka, Florence Hogger, Deborah Ley, Andrzej J Kulik and Nicolas Mermod

Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries

Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated ...

Authors: Katie Rose Boissonneault, Brooks M Henningsen, Stephen S Bates, Deborah L Robertson, Sean Milton, Jerry Pelletier, Deborah A Hogan and David E Housman

Identification of an NF-κB p50/p65-responsive site in the human MIR155HG promoter

MicroRNA-155 (miR-155) is the diced product of the MIR155HG gene. miR-155 regulates the expression of many immune-specific transcripts, is overexpressed in many human lymphomas, and has oncogenic activity in mous...

Authors: Ryan C Thompson, Iosif Vardinogiannis and Thomas D Gilmore

3′ terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing

Post-transcriptional 3′ end processing is a key component of RNA regulation. The abundant and essential RNA subunit of RNase MRP has been proposed to function in three distinct cellular compartments and theref...

Authors: Katherine C Goldfarb and Thomas R Cech

VprBP (DCAF1): a promiscuous substrate recognition subunit that incorporates into both RING-family CRL4 and HECT-family EDD/UBR5 E3 ubiquitin ligases

The terminal step in the ubiquitin modification system relies on an E3 ubiquitin ligase to facilitate transfer of ubiquitin to a protein substrate. The substrate recognition and ubiquitin transfer activities o...

Authors: Tadashi Nakagawa, Koushik Mondal and Patrick C Swanson

Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells

Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In ...

Authors: Liesbeth Vossaert, Thomas O’Leary, Christophe Van Neste, Björn Heindryckx, Jo Vandesompele, Petra De Sutter and Dieter Deforce

Pseudo attP sites in favor of transgene integration and expression in cultured porcine cells identified by streptomyces phage phiC31 integrase

Phage PhiC31 integrase integrates attB-containing plasmid into pseudo attP site in eukaryotic genomes in a unidirectional site-specific manner and maintains robust transgene expression. Few studies, however, e...

Authors: Yanzhen Bi, Ximei Liu, Long Zhang, Changwei Shao, Zhuo Ma, Zaidong Hua, Liping Zhang, Li Li, Wenjun Hua, Hongwei Xiao, Qingxin Wei and Xinmin Zheng

Molecular cloning and RNA interference-mediated functional characterization of a Halloween gene spook in the white-backed planthopper Sogatella furcifera

Ecdysteroid hormones ecdysone and 20-hydroxyecdysone play fundamental roles in insect postembryonic development and reproduction. Five cytochrome P450 monooxygenases (CYPs), encoded by Halloween genes, have be...

Authors: Shuang Jia, Pin-Jun Wan, Li-Tao Zhou, Li-Li Mu and Guo-Qing Li