Articles

A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector

Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloni...

Authors: Raquel Buj, Noa Iglesias, Anna M Planas and Tomàs Santalucía

Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus

In continuing our research into the new family of bifunctional restriction endonucleases (REases), we describe the cloning of the tsoIRM gene. Currently, the family includes six thermostable enzymes: TaqII, Tth11...

Authors: Piotr M Skowron, Jolanta Vitkute, Danute Ramanauskaite, Goda Mitkaite, Joanna Jezewska-Frackowiak, Joanna Zebrowska, Agnieszka Zylicz-Stachula and Arvydas Lubys

APOBEC3 inhibits DEAD-END function to regulate microRNA activity

The RNA binding protein DEAD-END (DND1) is one of the few proteins known to regulate microRNA (miRNA) activity at the level of miRNA-mRNA interaction. DND1 blocks miRNA interaction with the 3′-untranslated reg...

Authors: Sara Ali, Namrata Karki, Chitralekha Bhattacharya, Rui Zhu, Donna A MacDuff, Mark D Stenglein, April J Schumacher, Zachary L Demorest, Reuben S Harris, Angabin Matin and Sita Aggarwal

Loss of CARM1 is linked to reduced HuR function in replicative senescence

The co-activator-associated arginine methyltransferase 1 (CARM1) catalyzes the methylation of HuR. However, the functional impact of this modification is not fully understood. Here, we investigated the influen...

Authors: Lijun Pang, Haiyan Tian, Na Chang, Jie Yi, Lixiang Xue, Bin Jiang, Myriam Gorospe, Xiaowei Zhang and Wengong Wang

Tip110 interacts with YB-1 and regulates each other’s function

Tip110 plays important roles in tumor immunobiology, pre-mRNA splicing, expression regulation of viral and host genes, and possibly protein turnover. It is clear that our understanding of Tip110 biological fun...

Authors: Khalid Amine Timani, Ying Liu and Johnny J He

How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population

Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied int...

Authors: Ellen De Keyser, Laurence Desmet, Erik Van Bockstaele and Jan De Riek

Identification of nucleotides and amino acids that mediate the interaction between ribosomal protein L30 and the SECIS element

Ribosomal protein L30 belongs to the L7Ae family of RNA-binding proteins, which recognize diverse targets. L30 binds to kink-turn motifs in the 28S ribosomal RNA, L30 pre-mRNA, and mature L30 mRNA. L30 has a n...

Authors: Abby L Bifano, Tarik Atassi, Tracey Ferrara and Donna M Driscoll

Characterization of Stra8 in Southern catfish (Silurus meridionalis): evidence for its role in meiotic initiation

RA (retinoic acid) signal pathway has been proved to be required for germ cell meiotic initiation in mammals, aves and amphibians. Stra8 (Stimulated by retinoic acid gene 8) is an important factor in RA signal...

Authors: Ranran Dong, Shijie Yang, Jing Jiao, Tingru Wang, Hongjuan Shi, Linyan Zhou, Yaoguang Zhang and Deshou Wang

Screening and analysis of PoAkirin1 and two related genes in response to immunological stimulants in the Japanese flounder (Paralichthys olivaceus)

A member of the NF-κB signaling pathway, PoAkirin1, was cloned from a full-length cDNA library of Japanese flounder (Paralichthys olivaceus). The full-length cDNA comprises a 5′UTR of 202 bp, an open reading fram...

Authors: Chang-Geng Yang, Xian-Li Wang, Bo Zhang, Bing Sun, Shan-Shan Liu and Song-Lin Chen

Human single-stranded DNA binding proteins are essential for maintaining genomic stability

The double-stranded conformation of cellular DNA is a central aspect of DNA stabilisation and protection. The helix preserves the genetic code against chemical and enzymatic degradation, metabolic activation, ...

Authors: Nicholas W Ashton, Emma Bolderson, Liza Cubeddu, Kenneth J O’Byrne and Derek J Richard

Annual acknowledgement of manuscript reviewers

The editors of BMC Molecular Biology would like to thank all of our reviewers who have contributed to the journal in Volume 13 (2012).

Authors: Christopher Morrey

Identification of differences in microRNA transcriptomes between porcine oxidative and glycolytic skeletal muscles

MicroRNAs (miRNAs) are a type of non-coding small RNA ~22 nucleotides in length that regulate the expression of protein coding genes at the post-transcriptional level. Glycolytic and oxidative myofibers, the t...

Authors: Yingkai Liu, Mingzhou Li, Jideng Ma, Jie Zhang, Chaowei Zhou, Tao Wang, Xiaolian Gao and Xuewei Li

Single cell transcriptomic analysis of prostate cancer cells

The ability to interrogate circulating tumor cells (CTC) and disseminated tumor cells (DTC) is restricted by the small number detected and isolated (typically <10). To determine if a commercially available tec...

Authors: Christopher J Welty, Ilsa Coleman, Roger Coleman, Bryce Lakely, Jing Xia, Shu Chen, Roman Gulati, Sandy R Larson, Paul H Lange, Bruce Montgomery, Peter S Nelson, Robert L Vessella and Colm Morrissey

Multiple tandem splicing silencer elements suppress aberrant splicing within the long exon 26 of the human Apolipoprotein B gene

Apolipoprotein B (APOB) is an integral component of the chylomicron and the atherogenic lipoproteins LDL and Lp(a). Exon 26 of the APOB pre-mRNA is unusually long at 7,572 nt and is constitutively spliced. It is ...

Authors: Umasuthan Srirangalingam, Scott A Akker, Dennis Norman, Naveenan Navaratnam, Shern L Chew and Bernard Khoo

Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling

T-cell intracellular antigen (TIA) proteins function as regulators of cell homeostasis. These proteins control gene expression globally at multiple levels in response to dynamic regulatory changes and environm...

Authors: Carmen Sánchez-Jiménez, Isabel Carrascoso, Juan Barrero and José M Izquierdo

UtroUp is a novel six zinc finger artificial transcription factor that recognises 18 base pairs of the utrophin promoter and efficiently drives utrophin upregulation

Duchenne muscular dystrophy (DMD) is the most common X-linked muscle degenerative disease and it is due to the absence of the cytoskeletal protein dystrophin. Currently there is no effective treatment for DMD....

Authors: Annalisa Onori, Cinzia Pisani, Georgios Strimpakos, Lucia Monaco, Elisabetta Mattei, Claudio Passananti and Nicoletta Corbi

The ICP22 protein selectively modifies the transcription of different kinetic classes of pseudorabies virus genes

Pseudorabies virus (PRV), an alpha-herpesvirus of swine, is a widely used model organism in investigations of the molecular pathomechanisms of the herpesviruses. This work is the continuation of our earlier st...

Authors: Irma F Takács, Dóra Tombácz, Beáta Berta, István Prazsák, Nándor Póka and Zsolt Boldogkői

Drosophila MOF controls Checkpoint protein2 and regulates genomic stability during early embryogenesis

In Drosophila embryos, checkpoints maintain genome stability by delaying cell cycle progression that allows time for damage repair or to complete DNA synthesis. Drosophila MOF, a member of MYST histone acetyl tra...

Authors: Sreerangam NCVL Pushpavalli, Arpita Sarkar, M Janaki Ramaiah, Debabani Roy Chowdhury, Utpal Bhadra and Manika Pal-Bhadra

Alternative splicing of the neurofibromatosis type 1 pre-mRNA is regulated by the muscleblind-like proteins and the CUG-BP and ELAV-like factors

Alternative splicing is often subjected to complex regulatory control that involves many protein factors and cis-acting RNA sequence elements. One major challenge is to identify all of the protein players and def...

Authors: Victoria A Fleming, Cuiyu Geng, Andrea N Ladd and Hua Lou

Directional telomeric silencing and lack of canonical B1 elements in two silencer Autonomously Replicating Sequences in S. cerevisiae

Autonomously Replicating Sequences (ARS) in S. cerevisiae serve as origins of DNA replication or as components of cis-acting silencers, which impose positional repression at the mating type loci and at the telome...

Authors: Patricia Chisamore-Robert, Samantha Peeters, Kristina Shostak and Krassimir Yankulov

Escherichia coli RecG functionally suppresses human Bloom syndrome phenotypes

Defects in the human BLM gene cause Bloom syndrome, notable for early development of tumors in a broad variety of tissues. On the basis of sequence similarity, BLM has been identified as one of the five human hom...

Authors: Michael W Killen, Dawn M Stults, William A Wilson and Andrew J Pierce

Cloning, ligand-binding, and temporal expression of ecdysteroid receptors in the diamondback moth, Plutella xylostella

The diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), is a devastating pest of cruciferous crops worldwide, and has developed resistance to a wide range of insecticides, including diacylhydra...

Authors: Baozhen Tang, Wei Dong, Pei Liang, Xuguo Zhou and Xiwu Gao

Adenylate kinase 2 (AK2) promotes cell proliferation in insect development

Adenylate kinase 2 (AK2) is a phosphotransferase that catalyzes the reversible reaction 2ADP(GDP) ↔ ATP(GTP) + AMP and influences cellular energy homeostasis. However, the role of AK2 in regulating cell prolif...

Authors: Ru-Ping Chen, Chun-Yan Liu, Hong-Lian Shao, Wei-Wei Zheng, Jin-Xing Wang and Xiao-Fan Zhao

A MultiSite Gateway^TM vector set for the functional analysis of genes in the model Saccharomyces cerevisiae

Recombinatorial cloning using the Gateway^TM technology has been the method of choice for high-throughput omics projects, resulting in the availability of entire ORFeomes in Gateway^TM compatible vectors. The Multi...

Authors: Astrid Nagels Durand, Tessa Moses, Rebecca De Clercq, Alain Goossens and Laurens Pauwels

A novel 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) splice variant with an alternative exon 1 potentially encoding an extended N-terminus

The major rate-limiting enzyme for de novo cholesterol synthesis is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR). HMGCR is sterically inhibited by statins, the most commonly prescribed drugs for the...

Authors: Camilla Stormo, Marianne K Kringen, Runa M Grimholt, Jens P Berg and Armin P Piehler

Regulation of GAD65 expression by SMAR1 and p53 upon Streptozotocin treatment

GAD65 (Glutamic acid decarboxylase 65 KDa isoform) is one of the most important auto-antigens involved in Type 1 diabetes induction. Although it serves as one of the first injury markers of β-islets, the mecha...

Authors: Sandeep Singh, Varsheish Raina, Pavithra Lakshminarsimhan Chavali, Taronish Dubash, Sreenath Kadreppa, Pradeep Parab and Samit Chattopadhyay

Clock-controlled mir-142-3p can target its activator, Bmal1

microRNAs (miRNAs) are shown to be involved in the regulation of circadian clock. However, it remains largely unknown whether miRNAs can regulate the core clock genes (Clock and Bmal1).

Authors: Xiaochao Tan, Peng Zhang, Lan Zhou, Bin Yin, Hui Pan and Xiaozhong Peng

Structural/functional analysis of the human OXR1 protein: identification of exon 8 as the anti-oxidant encoding function

The human OXR1 gene belongs to a class of genes with conserved functions that protect cells from reactive oxygen species (ROS). The gene was found using a screen of a human cDNA library by its ability to suppr...

Authors: Kenan C Murphy and Michael R Volkert

Dual regulation of P-glycoprotein expression by Trichostatin A in cancer cell lines

It has been reported that the histone deacetylase inhibitor (iHDAc) trichostatin A (TSA) induces an increase in MDR1 gene transcription (ABCB1). This result would compromise the use of iHDACs in combination wi...

Authors: Trinidad Mata Balaguer, Angeles Gómez-Martínez, Pilar García-Morales, Javier Lacueva, Rafael Calpena, Lourdes Rocamora Reverte, Natividad Lopez Riquelme, Isabel Martinez-Lacaci, José A Ferragut and Miguel Saceda

Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase – engineering a thermostable ATP independent enzyme

RNA ligases are essential reagents for many methods in molecular biology including NextGen RNA sequencing. To prevent ligation of RNA to itself, ATP independent mutant ligases, defective in self-adenylation, a...

Authors: Alexander M Zhelkovsky and Larry A McReynolds

G-quadruplex recognition activities of E. Coli MutS

Guanine quadruplex (G4 DNA) is a four-stranded structure that contributes to genome instability and site-specific recombination. G4 DNA folds from sequences containing tandemly repetitive guanines, sequence mo...

Authors: Edward A Ehrat, Bradley R Johnson, Jonathan D Williams, Glen M Borchert and Erik D Larson

Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment

The selection of stable and suitable reference genes for real-time quantitative PCR (RT-qPCR) is a crucial prerequisite for reliable gene expression analysis under different experimental conditions. The presen...

Authors: Qingdi Quentin Li, Jeff Skinner and John E Bennett

Interaction of C/EBP-beta and NF-Y factors constrains activity levels of the nutritionally controlled promoter IA expressing the acetyl-CoA carboxylase-alpha gene in cattle

The enzyme acetyl-CoA carboxylase-alpha (ACC-α) is rate limiting for de novo fatty acid synthesis. Among the four promoters expressing the bovine gene, promoter IA (PIA) is dominantly active in lipogenic tissu...

Authors: Xuanming Shi, Cornelia C Metges and Hans-Martin Seyfert

SPRR2A enhances p53 deacetylation through HDAC1 and down regulates p21 promoter activity

Small proline rich protein (SPRR) 2A is one of 14 SPRR genes that encodes for a skin cross-linking protein, which confers structural integrity to the cornified keratinocyte cell envelope. New evidence, however...

Authors: Yoshiaki Mizuguchi, Susan Specht, John G Lunz III, Kumiko Isse, Natasha Corbitt, Toshihiro Takizawa and Anthony J Demetris

The Saccharomyces cerevisiae Hot1p regulated gene YHR087W (HGI1) has a role in translation upon high glucose concentration stress

While growing in natural environments yeasts can be affected by osmotic stress provoked by high glucose concentrations. The response to this adverse condition requires the HOG pathway and involves transcriptio...

Authors: M Gomar-Alba, E Jiménez-Martí and M del Olmo

PIM-1 kinase interacts with the DNA binding domain of the vitamin D receptor: a further kinase implicated in 1,25-(OH)₂D₃ signaling

The vitamin D3 receptor (VDR) is responsible for mediating the pleiotropic and, in part, cell-type-specific effects of 1,25-dihydroxyvitamin D3 (calcitriol) on the cardiovascular and the muscle system, on the ...

Authors: Christina J Maier, Richard H Maier, Raphaela Rid, Andrea Trost, Harald Hundsberger, Andreas Eger, Helmut Hintner, Johann W Bauer and Kamil Onder

Complementation between inactive fragments of SssI DNA methyltransferase

Silencing mammalian genes by targeted DNA (cytosine-5) methylation of selected CG sites in the genome would be a powerful technique to analyze epigenomic information and to study the roles of DNA methylation i...

Authors: Krystyna Ślaska-Kiss, Edit Tímár and Antal Kiss

Plasticity of DNA methylation in mouse T cell activation and differentiation

Circulating CD4⁺ T helper cells are activated through interactions with antigen presenting cells and undergo differentiation into specific T helper cell subsets depending on the type of antigen encountered. In ad...

Authors: Yan Li, Guobing Chen, Lina Ma, Stephen J Ohms, Chao Sun, M Frances Shannon and Jun Y Fan

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

The organization of eukaryotic DNA into chromatin has a strong influence on the accessibility and regulation of genetic information. The locations and occupancies of a principle component of chromatin, nucleos...

Authors: Jason M Rizzo, Jonathan E Bard and Michael J Buck

Erratum to: LIM kinase 1 - dependent cofilin 1 pathway and actin dynamics mediate nuclear retinoid receptor function in T lymphocytes

Authors: Mohammad Ishaq, Bor-Ruei Lin, Marjorie Bosche, Xin Zheng, Jun Yang, Dawei Huang, Richard A Lempicki, Angelica Aguilera-Gutierrez and Ven Natarajan

Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities

We previously defined a family of restriction endonucleases (REases) from Thermus sp., which share common biochemical and biophysical features, such as the fusion of both the nuclease and methyltransferase (MTase...

Authors: Agnieszka Zylicz-Stachula, Olga Zolnierkiewicz, Arvydas Lubys, Danute Ramanauskaite, Goda Mitkaite, Janusz M Bujnicki and Piotr M Skowron

High recovery of cell-free methylated DNA based on a rapid bisulfite-treatment protocol

Detection of cell-free methylated DNA in plasma is a promising tool for tumour diagnosis and monitoring. Due to the very low amounts of cell-free DNA in plasma, analytical sensitivity is of utmost importance. ...

Authors: Inge Søkilde Pedersen, Henrik Bygum Krarup, Ole Thorlacius-Ussing and Poul Henning Madsen

The leukemia associated nuclear corepressor ETO homologue genes MTG16 and MTGR1 are regulated differently in hematopoietic cells

MTG16, MTGR1 and ETO are nuclear transcriptional corepressors of the human ETO protein family. MTG16 is implicated in hematopoietic development and in controlling erythropoiesis/megakaryopoiesis. Furthermore, ...

Authors: Ram Ajore, Parveen Kumar, Rakesh Singh Dhanda, Urban Gullberg and Inge Olsson

Control of progesterone receptor transcriptional synergy by SUMOylation and deSUMOylation

Covalent modification of nuclear receptors by the Small Ubiquitin-like Modifier (SUMO) is dynamically regulated by competing conjugation/deconjugation steps that modulate their overall transcriptional activity...

Authors: Hany A Abdel-Hafiz and Kathryn B Horwitz

Novel polysome messages and changes in translational activity appear after induction of adipogenesis in 3T3-L1 cells

Control of translation allows for rapid adaptation of the cell to stimuli, rather than the slower transcriptional control. We presume that translational control is an essential process in the control of adipog...

Authors: Carolin Fromm-Dornieden, Silvia von der Heyde, Oleksandr Lytovchenko, Gabriela Salinas-Riester, Bertram Brenig, Tim Beissbarth and Bernhard G Baumgartner

EGF activates TTP expression by activation of ELK-1 and EGR-1 transcription factors

Tristetraprolin (TTP) is a key mediator of processes such as inflammation resolution, the inhibition of autoimmunity and in cancer. It carries out this role by the binding and degradation of mRNA transcripts, ...

Authors: Magdalena Florkowska, Piotr Tymoszuk, Aleksandra Balwierz, Anna Skucha, Jakub Kochan, Mateusz Wawro, Krystyna Stalinska and Aneta Kasza

Protein kinase CK2 localizes to sites of DNA double-strand break regulating the cellular response to DNA damage

The DNA-dependent protein kinase (DNA-PK) is a nuclear complex composed of a large catalytic subunit (DNA-PKcs) and a heterodimeric DNA-targeting subunit Ku. DNA-PK is a major component of the non-homologous e...

Authors: Birgitte B Olsen, Shih-Ya Wang, Tina H Svenstrup, Benjamin PC Chen and Barbara Guerra

An evaluation of oligonucleotide-based therapeutic strategies for polyQ diseases

RNA interference (RNAi) and antisense strategies provide experimental therapeutic agents for numerous diseases, including polyglutamine (polyQ) disorders caused by CAG repeat expansion. We compared the potenti...

Authors: Agnieszka Fiszer, Marta Olejniczak, Pawel M Switonski, Joanna P Wroblewska, Joanna Wisniewska-Kruk, Agnieszka Mykowska and Wlodzimierz J Krzyzosiak

A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter

The human papillomavirus (HPV) E2 protein is a multifunctional DNA-binding protein. The transcriptional activity of HPV E2 is mediated by binding to its specific binding sites in the upstream regulatory region...

Authors: Chen Gao, Ming-Ming Pan, Yan-Jun Lei, Li-Qing Tian, Hui-Ying Jiang, Xiao-Li Li, Qi Shi, Chan Tian, Yu-Kang Yuan, Gui-Xiang Fan and Xiao-Ping Dong

Transcriptional activation of microRNA-34a by NF-kappa B in human esophageal cancer cells

miR-34a functions as an important tumor suppressor during the process of carcinogenesis. However, the mechanism of miR-34a dysregulation in human malignancies has not been well elucidated. Our study aimed to f...

Authors: Juan Li, Kai Wang, Xuedan Chen, Hui Meng, Min Song, Yan Wang, Xueqing Xu and Yun Bai