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6355 result(s) for 'general transcription factors vs specific' within BMC Genomics

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  1. The endothelial compartment, comprising arterial, venous and lymphatic cell types, is established prenatally in association with rapid phenotypic and functional changes. The molecular mechanisms underpinning t...

    Authors: Jihoon E Joo, Ursula Hiden, Luciana Lassance, Lavinia Gordon, David J Martino, Gernot Desoye and Richard Saffery
    Citation: BMC Genomics 2013 14:475
    Content type: Research article Published on:

  2. Recent studies have shown that some pseudogenes are transcribed and contribute to cancer when dysregulated. In particular, pseudogene transcripts can function as competing endogenous RNAs (ceRNAs). The high si...

    Authors: Joshua D Welch, Jeanette Baran-Gale, Charles M Perou, Praveen Sethupathy and Jan F Prins
    Citation: BMC Genomics 2015 16:113
    Content type: Research article Published on:

  3. Plant response mechanisms to heat and drought stresses have been considered in strategies for generating stress tolerant genotypes, but with limited success. Here, we analyzed the transcriptome and improved to...

    Authors: José A. Casaretto, Ashraf El-kereamy, Bin Zeng, Suzy M. Stiegelmeyer, Xi Chen, Yong-Mei Bi and Steven J. Rothstein
    Citation: BMC Genomics 2016 17:312
    Content type: Research article Published on:

  4. Transcription start sites (TSSs) with pronounced and phased nucleosome arrays downstream and nucleosome-depleted regions upstream of TSSs are observed in various species.

    Authors: Yoichiro Nakatani, Cecilia C. Mello, Shin-ichi Hashimoto, Atsuko Shimada, Ryohei Nakamura, Tatsuya Tsukahara, Wei Qu, Jun Yoshimura, Yutaka Suzuki, Sumio Sugano, Hiroyuki Takeda, Andrew Fire and Shinichi Morishita
    Citation: BMC Genomics 2015 16:978
    Content type: Research article Published on:

  5. Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo t...

    Authors: Amandeep Mittal, Inderjit Singh Yadav, Naresh Kumar Arora, Rajbir Singh Boora, Meenakshi Mittal, Parwinder Kaur, William Erskine, Parveen Chhuneja, Manav Indra Singh Gill and Kuldeep Singh
    Citation: BMC Genomics 2020 21:484
    Content type: Research article Published on:

  6. Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations...

    Authors: Eli M. S. Gendron, Xue Qing, Joseph L. Sevigny, Hongmei Li, Zhiyin Liu, Mark Blaxter, Thomas O. Powers, W. Kelly Thomas and Dorota L. Porazinska
    Citation: BMC Genomics 2024 25:615
    Content type: Research Published on:

  7. Plants synthesize metabolites to adapt to a continuously changing environment. Metabolite biosynthesis often occurs in response to the tissue-specific combinatorial developmental cues that are transcriptionall...

    Authors: Xiaoyang Gao, Qixuan Su, Jing Li, Wenjing Yang, Baolin Yao, Jiawei Guo, Shengying Li and Changning Liu
    Citation: BMC Genomics 2022 23(Suppl 1):559
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  8. Poplar (Populus cathayana)and willow (Salix rehderiana) are important fast-growing trees in China. Grafting plays an important role in improving plant stress resistance and construction of ornamental plants. It i...

    Authors: Le Yang, Yao Chen, Xuejiao Liu, Sheng Zhang and Qingquan Han
    Citation: BMC Genomics 2023 24:676
    Content type: Research Published on:

  9. Flowering at the right time is a very important factor affecting the stable annual yield of longan. However, a lack of knowledge of the regulatory mechanism and key genes of longan flowering restricts healthy ...

    Authors: Dengwei Jue, Zhexin Li, Wenlin Zhang, Jianmin Tang, Ting Xie, Xuelian Sang and Qigao Guo
    Citation: BMC Genomics 2024 25:308
    Content type: Research Published on:

  10. Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is ...

    Authors: Victoria V Mironova, Nadezda A Omelyanchuk, Daniil S Wiebe and Victor G Levitsky
    Citation: BMC Genomics 2014 15(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  11. Solanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nemato...

    Authors: Paolo Bagnaresi, Tea Sala, Tiziana Irdani, Cristina Scotto, Antonella Lamontanara, Massimiliano Beretta, Giuseppe Leonardo Rotino, Sara Sestili, Luigi Cattivelli and Emidio Sabatini
    Citation: BMC Genomics 2013 14:540
    Content type: Research article Published on:

  12. Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into ...

    Authors: Yu-Feng Huang, Chun-Chin Huang, Yu-Cheng Liu, Yen-Jen Oyang and Chien-Kang Huang
    Citation: BMC Genomics 2009 10(Suppl 3):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  13. Long noncoding RNAs (lncRNAs) have emerged as an important class of transcriptional regulators in cellular processes. The past decades have witnessed great progress in lncRNA studies in a variety of organisms....

    Authors: Longsheng Xing, Yu Xi, Xi Qiao, Cong Huang, Qiang Wu, Nianwan Yang, Jianyang Guo, Wanxue Liu, Wei Fan, Fanghao Wan and Wanqiang Qian
    Citation: BMC Genomics 2021 22:4
    Content type: Research article Published on:

  14. The parasitoid wasp, Trichogramma dendrolimi, can enter diapause at the prepupal stage. Thus, diapause is an efficient preservation method during the mass production of T. dendrolimi. Previous studies on diapause...

    Authors: Xue Zhang, Wenmei Du, Junjie Zhang, Zhen Zou and Changchun Ruan
    Citation: BMC Genomics 2020 21:864
    Content type: Research article Published on:

  15. Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, ...

    Authors: Huaibing Yao, Zhihua Dou, Zhongkai Zhao, Xiaorui Liang, Haitao Yue, Wanpeng Ma, Zhanqiang Su, Yuzhuo Wang, Zelin Hao, Hui Yan, Zhuangyuan Wu, Liang Wang, Gangliang Chen and Jie Yang
    Citation: BMC Genomics 2023 24:660
    Content type: Research Published on:

  16. Leishmania parasites cause a diverse spectrum of diseases in humans ranging from spontaneously healing skin lesions (e.g., L. major) to life-threatening visceral diseases (e.g., L. infantum). The high conservatio...

    Authors: Annie Rochette, Frédéric Raymond, Jean-Michel Ubeda, Martin Smith, Nadine Messier, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Marc Ouellette and Barbara Papadopoulou
    Citation: BMC Genomics 2008 9:255
    Content type: Research article Published on:

  17. Blue mold is a globally important and economically impactful postharvest disease of apples caused by multiple Penicillium spp. There are currently four postharvest fungicides registered for blue mold control, and...

    Authors: Franz J. Lichtner, Verneta L. Gaskins, Kerik D. Cox and Wayne M. Jurick II
    Citation: BMC Genomics 2020 21:574
    Content type: Research article Published on:

  20. Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data i...

    Authors: Nathalia M. V. Flórez-Zapata, M. Humberto Reyes-Valdés and Octavio Martínez
    Citation: BMC Genomics 2016 17:490
    Content type: Research article Published on:

  21. Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we...

    Authors: Ali Moumeni, Kouji Satoh, Ramiah Venuprasad, Rachid Serraj, Arvind Kumar, Hei Leung and Shoshi Kikuchi
    Citation: BMC Genomics 2015 16:1110
    Content type: Research article Published on:

  22. The molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional r...

    Authors: Flavia Bossi, Jue Fan, Jun Xiao, Lilyana Chandra, Max Shen, Yanniv Dorone, Doris Wagner and Seung Y. Rhee
    Citation: BMC Genomics 2017 18:480
    Content type: Research article Published on:

  23. Hericium erinaceus, a rare edible and medicine fungus, is widely used in the food and medical field. Polysaccharides from H. erinaceus are the main bioactive compound that exert high bioactive value in the medica...

    Authors: Ming Gong, Henan Zhang, Di Wu, Zhong Zhang, Jinsong Zhang, Dapeng Bao and Yan Yang
    Citation: BMC Genomics 2021 22:160
    Content type: Research article Published on:

  24. Alternative splicing (AS) of genes is an efficient means of generating variation in protein structure and function. AS variation has been observed between tissues, cell types, and different treatments in non-w...

    Authors: Hua Bao, Eryang Li, Shawn D Mansfield, Quentin CB Cronk, Yousry A El-Kassaby and Carl J Douglas
    Citation: BMC Genomics 2013 14:359
    Content type: Research article Published on:

  25. The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathoge...

    Authors: Audrey M. V. Ah-Fong, Kyoung Su Kim and Howard S. Judelson
    Citation: BMC Genomics 2017 18:198
    Content type: Research article Published on:

  26. Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increas...

    Authors: Xiao-Qing Huang, Xiao-Hong Lu, Man-Hong Sun, Rong-Jun Guo, Anne D. van Diepeningen and Shi-Dong Li
    Citation: BMC Genomics 2019 20:570
    Content type: Research article Published on:

  27. Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering ro...

    Authors: Sovanna Tan, Frédéric Debellé, Pascal Gamas, Florian Frugier and Mathias Brault
    Citation: BMC Genomics 2019 20:373
    Content type: Research article Published on:

  28. The intestinal epithelium plays a critical role in nutrient absorption and innate immune defense. Recent studies showed that metabolic stress pathways, in particular the integrated stress response (ISR), contr...

    Authors: Jessica Tsalikis, Qun Pan, Ivan Tattoli, Charles Maisonneuve, Benjamin J. Blencowe, Dana J. Philpott and Stephen E. Girardin
    Citation: BMC Genomics 2016 17:680
    Content type: Research article Published on:

  30. The transcription regulator PhoP has been shown to be important for Y. pestis survival in macrophages and under various in vitro stresses. However, the mechanism by which PhoP promotes bacterial intracellular sur...

    Authors: Yingli Li, He Gao, Long Qin, Bei Li, Yanping Han, Zhaobiao Guo, Yajun Song, Junhui Zhai, Zongmin Du, Xiaoyi Wang, Dongsheng Zhou and Ruifu Yang
    Citation: BMC Genomics 2008 9:143
    Content type: Research article Published on:

  31. Snakes exhibit extreme intestinal regeneration following months-long fasts that involves unparalleled increases in metabolism, function, and tissue growth, but the specific molecular control of this process is...

    Authors: Aundrea K. Westfall, Blair W. Perry, Abu H. M. Kamal, Nicole R. Hales, Jarren C. Kay, Madhab Sapkota, Drew R. Schield, Mark W. Pellegrino, Stephen M. Secor, Saiful M. Chowdhury and Todd A. Castoe
    Citation: BMC Genomics 2022 23:6
    Content type: Research article Published on:

  32. Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the ...

    Authors: Ning Chen, Hao Zhang, En Zang, Zhi-Xia Liu, Ya-Fei Lan, Wei-Li Hao, Shan He, Xing Fan, Gen-Lou Sun and Yi-Ling Wang
    Citation: BMC Genomics 2022 23:466
    Content type: Research Published on:

  33. Eukaryotic genomes are replicated during S phase according to a temporal program. Several determinants control the timing of origin firing, including the chromatin environment and epigenetic modifications. How...

    Authors: Ignacio Soriano, Esther C Morafraile, Enrique Vázquez, Francisco Antequera and Mónica Segurado
    Citation: BMC Genomics 2014 15:791
    Content type: Research article Published on:

  34. Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis...

    Authors: Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xingchu Yan and Xinxin Geng
    Citation: BMC Genomics 2019 20:456
    Content type: Research article Published on:

  35. Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a nov...

    Authors: Ruben Pio, David Blanco, Maria Jose Pajares, Elena Aibar, Olga Durany, Teresa Ezponda, Jackeline Agorreta, Javier Gomez-Roman, Miguel Angel Anton, Angel Rubio, Maria D Lozano, Jose M López-Picazo, Francesc Subirada, Tamara Maes and Luis M Montuenga
    Citation: BMC Genomics 2010 11:352
    Content type: Methodology article Published on:

  37. The endometrium is a heterogeneous tissue composed of luminal epithelial (LE), glandular epithelial (GE), and stromal cells (ST), experiencing progesterone regulated dynamic changes during the estrous cycle. I...

    Authors: Gonçalo Pereira, Yongzhi Guo, Elisabete Silva, Claudia Bevilacqua, Gilles Charpigny, Luís Lopes-da-Costa and Patrice Humblot
    Citation: BMC Genomics 2022 23:82
    Content type: Research Published on:

  38. Short-read high-throughput DNA sequencing technologies provide new tools to answer biological questions. However, high cost and low throughput limit their widespread use, particularly in organisms with smaller...

    Authors: Philippe Lefrançois, Ghia M Euskirchen, Raymond K Auerbach, Joel Rozowsky, Theodore Gibson, Christopher M Yellman, Mark Gerstein and Michael Snyder
    Citation: BMC Genomics 2009 10:37
    Content type: Methodology article Published on:

  39. Epulopiscium sp. type B, a large intestinal bacterial symbiont of the surgeonfish Naso tonganus, does not reproduce by binary fission. Instead, it forms multiple intracellular offspring using a process with morph...

    Authors: David A Miller, Garret Suen, Kendall D Clements and Esther R Angert
    Citation: BMC Genomics 2012 13:265
    Content type: Research article Published on:

  40. Bovine tuberculosis is an enduring disease of cattle that has significant repercussions for human health. The advent of high-throughput functional genomics technologies has facilitated large-scale analyses of ...

    Authors: Kieran G Meade, Eamonn Gormley, Mairéad B Doyle, Tara Fitzsimons, Cliona O'Farrelly, Eamon Costello, Joseph Keane, Yingdong Zhao and David E MacHugh
    Citation: BMC Genomics 2007 8:400
    Content type: Research article Published on:

  41. Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways...

    Authors: Ronald B. Walter, Mikki Boswell, Jordan Chang, William T. Boswell, Yuan Lu, Kaela Navarro, Sean M. Walter, Dylan J. Walter, Raquel Salinas and Markita Savage
    Citation: BMC Genomics 2018 19:355
    Content type: Research article Published on:

  42. Symbiosis is central to ecosystems and has been an important driving force of the diversity of life. Close and long-term interactions are known to develop cooperative molecular mechanisms between the symbiotic...

    Authors: Mieko Kono, Yoshiaki Kon, Yoshihito Ohmura, Yoko Satta and Yohey Terai
    Citation: BMC Genomics 2020 21:671
    Content type: Research article Published on:

  43. Seed oil accumulates primarily as triacylglycerol (TAG). While the biochemical pathway for TAG biosynthesis is known, its regulation remains unclear. Previous research identified microsomal diacylglycerol acyl...

    Authors: Nirmala Sharma, Maureen Anderson, Arvind Kumar, Yan Zhang, E Michael Giblin, Suzanne R Abrams, L Irina Zaharia, David C Taylor and Pierre R Fobert
    Citation: BMC Genomics 2008 9:619
    Content type: Research article Published on:

  44. Efforts to elucidate the function of enhancers in vivo are underway but their vast numbers alongside differing enhancer architectures make it difficult to determine their impact on gene activity. By systematic...

    Authors: Siddharth Sethi, Ilya E. Vorontsov, Ivan V. Kulakovskiy, Simon Greenaway, John Williams, Vsevolod J. Makeev, Steve D. M. Brown, Michelle M. Simon and Ann-Marie Mallon
    Citation: BMC Genomics 2020 21:754
    Content type: Research article Published on:

  45. Nutritional strategies can decrease saturated fatty acids (SFAs) and increase health beneficial fatty acids (FAs) in bovine milk. The pathways/genes involved in these processes are not properly defined. Next-g...

    Authors: Eveline M. Ibeagha-Awemu, Ran Li, Adolf A. Ammah, Pier-Luc Dudemaine, Nathalie Bissonnette, Chaouki Benchaar and Xin Zhao
    Citation: BMC Genomics 2016 17:104
    Content type: Research article Published on:

  46. As in other eukaryotes, plant mitogen-activated protein kinase (MAPK) cascades are composed of three classes of hierarchically organized protein kinases, namely MAPKKKs, MAPKKs, and MAPKs. These modules rapidl...

    Authors: Marie-Claude Nicole, Louis-Philippe Hamel, Marie-Josée Morency, Nathalie Beaudoin, Brian E Ellis and Armand Séguin
    Citation: BMC Genomics 2006 7:223
    Content type: Research article Published on:

  47. Plasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of t...

    Authors: Lia Chappell, Philipp Ross, Lindsey Orchard, Timothy J. Russell, Thomas D. Otto, Matthew Berriman, Julian C. Rayner and Manuel Llinás
    Citation: BMC Genomics 2020 21:395
    Content type: Research article Published on:

  48. DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is ex...

    Authors: Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand and Marcos J. Araúzo-Bravo
    Citation: BMC Genomics 2017 18:964
    Content type: Research Article Published on:

  49. Isoflavonoids are a class of specialized metabolites found predominantly in legumes. They play a role in signaling for symbiosis with nitrogen-fixing bacteria and inhibiting pathogen infection.

    Authors: Mehran Dastmalchi, Patrick Chapman, Jaeju Yu, Ryan S. Austin and Sangeeta Dhaubhadel
    Citation: BMC Genomics 2017 18:70
    Content type: Research article Published on:

  50. Mouse fetuses up to 16 day of embryonic development and nude (Foxn1- deficient) mice are examples of animals that undergo regenerative (scar-free) skin healing. The expression of transcription factor Foxn1 in ...

    Authors: Anna Kur-Piotrowska, Marta Kopcewicz, Leslie P. Kozak, Pawel Sachadyn, Anna Grabowska and Barbara Gawronska-Kozak
    Citation: BMC Genomics 2017 18:56
    Content type: Research Article Published on:

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