Articles

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

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

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

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

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

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

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

A reliable method for quantification of splice variants using RT-qPCR

The majority of protein isoforms arise from alternative splicing of the encoding primary RNA transcripts. To understand the significance of single splicing events, reliable techniques are needed to determine t...

Authors: Julia Camacho Londoño and Stephan E. Philipp

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

Bothrops colombiensis is a highly dangerous pit viper and responsible for over 70 % of snakebites in Venezuela. Although the composition in B. colombiensis venom has been identified us...

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

Knockdown of SALL4 inhibits the proliferation and reverses the resistance of MCF-7/ADR cells to doxorubicin hydrochloride

Breast cancer is the most frequent malignancy in women and drug resistance is the major obstacle for its successful chemotherapy. In the present study, we analyzed the involvement of an oncofetal gene, sal-lik...

Authors: Yuan-Yuan Chen, Zhi-Zhen Li, Yuan-Yuan Ye, Feng Xu, Rui-Jie Niu, Hong-Chen Zhang, Yi-Jian Zhang, Ying-Bin Liu and Bao-San Han

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 16 (2015).

Authors: Timothy R. Sands

What is normal? Next generation sequencing-driven analysis of the human circulating miRNAOme

MicroRNAs (miRNAs) are short non-protein-coding RNA species that have a regulatory function in modulating protein translation and degradation of specific mRNAs. MicroRNAs are estimated to target approximately...

Authors: D. P. Tonge and T. W. Gant

TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint

The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activi...

Authors: Sanket Awate and Arrigo De Benedetti

Erratum to: Temperature-induced variation in gene expression burst size in metazoan cells

Authors: Ophélie Arnaud, Sam Meyer, Elodie Vallin, Guillaume Beslon and Olivier Gandrillon

Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays

The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no informat...

Authors: Quirino Alves de Lima Neto, Francisco Ferreira Duarte Junior, Paulo Sérgio Alves Bueno, Flavio Augusto Vicente Seixas, Madzia Pauline Kowalski, Eyemen Kheir, Torsten Krude and Maria Aparecida Fernandez

microRNA-150 promotes cervical cancer cell growth and survival by targeting FOXO4

Dysregulation of microRNA-150 (miR-150) is commonly observed in solid tumor and has been reported to be involved in multiple important biological processes, such as cell proliferation, apoptosis, and metastasi...

Authors: Jun Li, Lina Hu, Chao Tian, Feng Lu, Jia Wu and Li Liu

Transfection of Sertoli cells with androgen receptor alters gene expression without androgen stimulation

Androgens play an important role for the development of male fertility and gained interest as growth and survival factors for certain types of cancer. Androgens act via the androgen receptor (AR/Ar), which is inv...

Authors: D. Fietz, M. Markmann, D. Lang, L. Konrad, J. Geyer, S. Kliesch, T. Chakraborty, H. Hossain and M. Bergmann

Conserved and highly expressed tRNA derived fragments in zebrafish

Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identifi...

Authors: Ana Raquel Soares, Noémia Fernandes, Marisa Reverendo, Hugo Rafael Araújo, José Luís Oliveira, Gabriela M. R. Moura and Manuel A. S. Santos

Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

Orphan nuclear receptor estrogen related receptor β (Esrrb or ERRβ) is well known in stem cells and early embryonic development. However, little is known about its function in cancer.

Authors: Yuan Lu, Jilong Li, Jianlin Cheng and Dennis B. Lubahn

Temperature-induced variation in gene expression burst size in metazoan cells

Gene expression is an inherently stochastic process, owing to its dynamic molecular nature. Protein amount distributions, which can be acquired by cytometry using a reporter gene, can inform about the mechanis...

Authors: Ophélie Arnaud, Sam Meyer, Elodie Vallin, Guillaume Beslon and Olivier Gandrillon

Genes targeted by the Hedgehog-signaling pathway can be regulated by Estrogen related receptor β

Nuclear receptor family member, Estrogen related receptor β, and the Hedgehog signal transduction pathway are both reported to relate to tumorigenesis and induced pluripotent stem cell reprogramming. We hypoth...

Authors: Yuan Lu, Jilong Li, Jianlin Cheng and Dennis B. Lubahn

DNA double-strand break repair is impaired in presenescent Syrian hamster fibroblasts

Studies of DNA damage response are critical for the comprehensive understanding of age-related changes in cells, tissues and organisms. Syrian hamster cells halt proliferation and become presenescent after sev...

Authors: Ljudmila Solovjeva, Denis Firsanov, Anastasia Vasilishina, Vadim Chagin, Nadezhda Pleskach, Andrey Kropotov and Maria Svetlova

The elongation factor eEF3 (Yef3) interacts with mRNA in a translation independent manner

mRNA binding proteins (RBPs) constitute 10–15 % of the eukaryotic proteome and play important part in post-transcriptional regulation of gene expression. Due to the instability of RNA and the transient nature ...

Authors: Nitzan Samra, Avigail Atir-Lande, Lilach Pnueli and Yoav Arava

Deciphering targeting rules of splicing modulator compounds: case of TG003

Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the d...

Authors: Maki Sakuma, Kei Iida and Masatoshi Hagiwara

RE1 silencing transcription factor (REST) negatively regulates ALL1-fused from chromosome 1q (AF1q) gene transcription

ALL1-fused from chromosome 1q (AF1q), originally considered as an oncogenic factor, has been implicated in neuronal development; however, its upstream regulatory mechanisms in neural system remained elusive.

Authors: Yuanyuan Hu, Qianwen Sun, Chen Zhang, Qingquan Sha and Xiulian Sun

TRIM28 as a novel transcriptional elongation factor

TRIM28 is a multidomain protein with versatile functions in transcription and DNA repair. Recently it was shown that this factor plays unanticipated roles in transcriptional elongation. TRIM28 was shown to sta...

Authors: Heeyoun Bunch and Stuart K Calderwood

Analysis artefacts of the INS-IGF2 fusion transcript

In gene expression analysis, overlapping genes, splice variants, and fusion transcripts are potential sources of data analysis artefacts, depending on how the observed intensity is assigned to one, or more gen...

Authors: Rasmus Wernersson, Thomas Frogne, Claude Rescan, Lena Hansson, Christine Bruun, Mads Grønborg, Jan Nygaard Jensen and Ole Dragsbæk Madsen

SIRT6 protein deacetylase interacts with MYH DNA glycosylase, APE1 endonuclease, and Rad9–Rad1–Hus1 checkpoint clamp

SIRT6, a member of the NAD⁺-dependent histone/protein deacetylase family, regulates genomic stability, metabolism, and lifespan. MYH glycosylase and APE1 are two base excision repair (BER) enzymes involved in mut...

Authors: Bor-Jang Hwang, Jin Jin, Ying Gao, Guoli Shi, Amrita Madabushi, Austin Yan, Xin Guan, Michal Zalzman, Satoshi Nakajima, Li Lan and A-Lien Lu