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Transcriptional control of gene expression

Section edited by Jean-Francois Beaulieu

This section will consider submissions that focus on the analysis of gene expression levels and patterns, transcription mechanisms and the regulation of transcription.

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  1. Hexaploid wheat is an important cereal crop that has been targeted to enhance grain micronutrient content including zinc (Zn) and iron (Fe). In this direction, modulating the expression of plant transporters i...

    Authors: Shivani Sharma, Gazaldeep Kaur, Anil Kumar, Varsha Meena, Jaspreet Kaur and Ajay Kumar Pandey
    Citation: BMC Molecular Biology 2019 20:22
    Content type: Research article Published on:

  4. With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene e...

    Authors: Md. Sabbir Hossain, Rasel Ahmed, Md. Samiul Haque, Md. Monjurul Alam and Md. Shahidul Islam
    Citation: BMC Molecular Biology 2019 20:13
    Content type: Research article Published on:

  5. The underlying mechanisms by which probiotic lactic acid bacteria (LAB) enhance the health of the consumer have not been fully elucidated. Verification of probiotic modes of action can be achieved by using sin...

    Authors: Winschau F. Van Zyl, Leon M. T. Dicks and Shelly M. Deane
    Citation: BMC Molecular Biology 2019 20:10
    Content type: Methodology article Published on:

  6. Myocyte enhancer factor 2A (MEF2A) plays an important role in cell proliferation, differentiation and survival. Functional deletion or mutation in MEF2A predisposes individuals to cardiovascular disease mainly...

    Authors: Yujuan Xiong, Lin Wang, Wenyi Jiang, Lihua Pang, Weihua Liu, Aiqun Li, Yun Zhong, Wenchao Ou, Benrong Liu and Shi-ming Liu
    Citation: BMC Molecular Biology 2019 20:8
    Content type: Research article Published on:

  7. A major cause of phytoplankton mortality is predation by zooplankton. Strategies to avoid grazers have probably played a major role in the evolution of phytoplankton and impacted bloom dynamics and trophic ene...

    Authors: Sara Harðardóttir, Sylke Wohlrab, Ditte Marie Hjort, Bernd Krock, Torkel Gissel Nielsen, Uwe John and Nina Lundholm
    Citation: BMC Molecular Biology 2019 20:7
    Content type: Research article Published on:

  8. Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this ins...

    Authors: Satnam Singh, Mridula Gupta, Suneet Pandher, Gurmeet Kaur, Neha Goel, Pankaj Rathore and Subba Reddy Palli
    Citation: BMC Molecular Biology 2019 20:6
    Content type: Research article Published on:

  9. Recently different forms of nanographene were proposed as the material with high anticancer potential. However, the mechanism of the suppressive activity of the graphene on cancer development remains unclear. ...

    Authors: Maciej Szmidt, Adrian Stankiewicz, Kaja Urbańska, Sławomir Jaworski, Marta Kutwin, Mateusz Wierzbicki, Marta Grodzik, Beata Burzyńska, Monika Góra, André Chwalibog and Ewa Sawosz
    Citation: BMC Molecular Biology 2019 20:2
    Content type: Research article Published on:

  10. MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs ar...

    Authors: Berna I. G. Kappeler, Luciana C. A. Regitano, Mirele D. Poleti, Aline S. M. Cesar, Gabriel C. M. Moreira, Gustavo Gasparin and Luiz L. Coutinho
    Citation: BMC Molecular Biology 2019 20:1
    Content type: Research article Published on:

  11. NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as w...

    Authors: Leiah M. Luoma and Fred B. Berry
    Citation: BMC Molecular Biology 2018 19:14
    Content type: Research article Published on:

  12. Ischemia–reperfusion injury has been proven to induce organ dysfunction and death, although the mechanism is not fully understood. Long non-coding RNAs (lncRNAs) have drawn wide attention with their important ...

    Authors: Lin Lin, Zhengfei Yang, Guanghui Zheng, Yongxun Zhuansun, Yue Wang, Jianguo Li, Rui Chen and Wanchun Tang
    Citation: BMC Molecular Biology 2018 19:11
    Content type: Research article Published on:

  13. 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
    Citation: BMC Molecular Biology 2018 19:10
    Content type: Research article Published on:

  14. 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
    Citation: BMC Molecular Biology 2018 19:9
    Content type: Research article Published on:

  15. 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
    Citation: BMC Molecular Biology 2018 19:8
    Content type: Research article Published on:

  16. 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
    Citation: BMC Molecular Biology 2018 19:7
    Content type: Methodology article Published on:

  18. 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
    Citation: BMC Molecular Biology 2018 19:4
    Content type: Research article Published on:

  19. 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
    Citation: BMC Molecular Biology 2018 19:2
    Content type: Methodology article Published on:

  20. 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
    Citation: BMC Molecular Biology 2017 18:22
    Content type: Methodology article Published on:

  22. 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
    Citation: BMC Molecular Biology 2017 18:18
    Content type: Research article Published on:

  23. 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
    Citation: BMC Molecular Biology 2017 18:17
    Content type: Research article Published on:

  25. 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
    Citation: BMC Molecular Biology 2017 18:15
    Content type: Research article Published on:

  26. 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
    Citation: BMC Molecular Biology 2017 18:14
    Content type: Research article Published on:

  27. 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
    Citation: BMC Molecular Biology 2017 18:12
    Content type: Research article Published on:

  28. 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
    Citation: BMC Molecular Biology 2017 18:10
    Content type: Research article Published on:

  29. 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
    Citation: BMC Molecular Biology 2017 18:9
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Molecular Biology 2017 18:11

  30. 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
    Citation: BMC Molecular Biology 2017 18:6
    Content type: Research article Published on:

  31. 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
    Citation: BMC Molecular Biology 2017 18:5
    Content type: Research article Published on:

  32. 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
    Citation: BMC Molecular Biology 2017 18:4
    Content type: Research article Published on:

  33. 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
    Citation: BMC Molecular Biology 2017 18:2
    Content type: Research article Published on:

  36. 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
    Citation: BMC Molecular Biology 2016 17:16
    Content type: Research article Published on:

  37. 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
    Citation: BMC Molecular Biology 2016 17:15
    Content type: Research Article Published on:

  40. 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
    Citation: BMC Molecular Biology 2016 17:6
    Content type: Research article Published on:

  43. 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
    Citation: BMC Molecular Biology 2015 16:23
    Content type: Research article Published on:

  44. 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
    Citation: BMC Molecular Biology 2015 16:22
    Content type: Research article Published on:

  46. 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
    Citation: BMC Molecular Biology 2015 16:20
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Molecular Biology 2016 17:2

  47. 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
    Citation: BMC Molecular Biology 2015 16:15
    Content type: Research article Published on:

  48. 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
    Citation: BMC Molecular Biology 2015 16:13
    Content type: Research article Published on:

  49. 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
    Citation: BMC Molecular Biology 2014 15:23
    Content type: Research article Published on:

  50. 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
    Citation: BMC Molecular Biology 2014 15:24
    Content type: Research article Published on:

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