Journal articles: 'Promoter Recognition'

1

Fickett, James W., and Artemis G. Hatzigeorgiou. "Eukaryotic Promoter Recognition." Genome Research 7, no. 9 (September 1, 1997): 861–78. http://dx.doi.org/10.1101/gr.7.9.861.

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2

Mao, Steve. "Mechanism of promoter recognition." Science 362, no. 6421 (December 20, 2018): 1372.11–1374. http://dx.doi.org/10.1126/science.362.6421.1372-k.

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3

Shen, Li, Xiaogeng Feng, Yuan Yuan, Xudong Luo, Thomas P. Hatch, Kelly T. Hughes, Jun S. Liu, and You-xun Zhang. "Selective Promoter Recognition by Chlamydial σ28 Holoenzyme." Journal of Bacteriology 188, no. 21 (August 25, 2006): 7364–77. http://dx.doi.org/10.1128/jb.01014-06.

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ABSTRACT The σ transcription factor confers the promoter recognition specificity of RNA polymerase (RNAP) in eubacteria. Chlamydia trachomatis has three known sigma factors, σ66, σ54, and σ28. We developed two methods to facilitate the characterization of promoter sequences recognized by C. trachomatis σ28 (σ28 Ct). One involved the arabinose-induced expression of plasmid-encoded σ28 Ct in a strain of Escherichia coli defective in the σ28 structural gene, fliA. The second was an analysis of transcription in vitro with a hybrid holoenzyme reconstituted with E. coli RNAP core and recombinant σ28 Ct. These approaches were used to investigate the interactions of σ28 Ct with the σ28 Ct-dependent hctB promoter and selected E. coli σ28 (σ28 Ec)-dependent promoters, in parallel, compared with the promoter recognition properties of σ28 EC. Our results indicate that RNAP containing σ28 Ct has at least three characteristics: (i) it is capable of recognizing some but not all σ28 EC-dependent promoters; (ii) it can distinguish different promoter structures, preferentially activating promoters with upstream AT-rich sequences; and (iii) it possesses a greater flexibility than σ28 EC in recognizing variants with different spacing lengths separating the −35 and −10 elements of the core promoter.

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4

Bajic, V. B., S. H. Seah, A. Chong, G. Zhang, J. L. Y. Koh, and V. Brusic. "Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters." Bioinformatics 18, no. 1 (January 1, 2002): 198–99. http://dx.doi.org/10.1093/bioinformatics/18.1.198.

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5

BUSBY, S. "Promoter structure, promoter recognition, and transcription activation in prokaryotes." Cell 79, no. 5 (December 1994): 743–46. http://dx.doi.org/10.1016/0092-8674(94)90063-9.

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6

Brunner, M., and H. Bujard. "Promoter recognition and promoter strength in the Escherichia coli system." EMBO Journal 6, no. 10 (October 1987): 3139–44. http://dx.doi.org/10.1002/j.1460-2075.1987.tb02624.x.

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7

Deng, Wensheng, Barbora Malecová, Thomas Oelgeschläger, and Stefan G. E. Roberts. "TFIIB Recognition Elements Control the TFIIA-NC2 Axis in Transcriptional Regulation." Molecular and Cellular Biology 29, no. 6 (December 29, 2008): 1389–400. http://dx.doi.org/10.1128/mcb.01346-08.

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ABSTRACT TFIIB recognizes DNA sequence-specific motifs that can flank the TATA elements of the promoters of protein-encoding genes. The TFIIB recognition elements (BREu and BREd) can have positive or negative effects on transcription in a promoter context-dependent manner. Here we show that the BREs direct the selective recruitment of TFIIA and NC2 to the promoter. We find that TFIIA preferentially associates with BRE-containing promoters while NC2 is recruited to promoters that lack consensus BREs. The functional relevance of the BRE-dependent recruitment of TFIIA and NC2 was determined by small interfering RNA-mediated knockdown of TFIIA and NC2, both of which elicited BRE-dependent effects on transcription. Our results confirm the established functional reciprocity of TFIIA and NC2. However, our findings show that TFIIA assembly at BRE-containing promoters results in reduced transcriptional activity, while NC2 acts as a positive factor at promoters that lack functional BREs. Taken together, our results provide a basis for the selective recruitment of TFIIA and NC2 to the promoter and give new insights into the functional relationship between core promoter elements and general transcription factor activity.

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8

Hutchinson, Gordon. "International workshop tackles promoter recognition problem." Trends in Genetics 12, no. 4 (April 1996): 159. http://dx.doi.org/10.1016/0168-9525(96)30021-8.

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9

Lukashin, A. V., V. V. Anshelevich, B. R. Amirikyan, A. I. Gragerov, and M. D. Frank-Kamenetskii. "Neural Network Models for Promoter Recognition." Journal of Biomolecular Structure and Dynamics 6, no. 6 (June 1989): 1123–33. http://dx.doi.org/10.1080/07391102.1989.10506540.

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10

Wang, Lei, Yuli Guo, and Jay D. Gralla. "Regulation of Sigma 54-Dependent Transcription by Core Promoter Sequences: Role of −12 Region Nucleotides." Journal of Bacteriology 181, no. 24 (December 15, 1999): 7558–65. http://dx.doi.org/10.1128/jb.181.24.7558-7565.1999.

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ABSTRACT The tetranucleotide core recognition sequence (TTGC) of the sigma 54 promoter −12 recognition element was altered by random substitution. The resulting promoter mutants were characterized in vivo and in vitro. Deregulated promoters were identified, implying that this core element can mediate the response to enhancer-binding proteins. These promoters had in common a substitution at position −12 (consensus C), indicating its importance for keeping basal transcription in check. In another screen, nonfunctional promoters were identified. Their analysis indicated that positions −13 (consensus G) and −15 (consensus T) are important to maintain minimal promoter function. In vitro studies showed that the −13 and −15 positions contribute to closed-complex formation, whereas the −12 position has a stronger effect on recognition of the fork junction intermediate created during open-complex formation. Overall the data indicate that the −12 region core contains specific subsequences that direct the diverse RNA polymerase interactions required both to produce RNA and to restrict this RNA synthesis in the absence of activation.

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11

Koo, B. M., V. A. Rhodius, G. Nonaka, P. L. deHaseth, and C. A. Gross. "Reduced capacity of alternative s to melt promoters ensures stringent promoter recognition." Genes & Development 23, no. 20 (October 15, 2009): 2426–36. http://dx.doi.org/10.1101/gad.1843709.

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12

Miroslavova, Nora S., and Stephen J. W. Busby. "Investigations of the modular structure of bacterial promoters." Biochemical Society Symposia 73 (January 1, 2006): 1–10. http://dx.doi.org/10.1042/bss0730001.

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Bacterial RNA polymerase holoenzyme carries different determinants that contact different promoter DNA sequence elements. These contacts are essential for the recognition of promoters prior to transcript initiation. Here, we have investigated how active promoters can be built from different combinations of elements. Our results show that the contribution of different contacts to promoter activity is critically dependent on the overall promoter context, and that certain combinations of contacts can hinder transcription initiation.

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13

Brodolin, Konstantin L., Vasily M. Studitsky, and Andrei D. Mirzabekov. "Conformational changes inE.coliRNA polymerase during promoter recognition." Nucleic Acids Research 21, no. 24 (1993): 5748–53. http://dx.doi.org/10.1093/nar/21.24.5748.

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14

Ohler, U., S. Harbeck, H. Niemann, E. Noth, and M. G. Reese. "Interpolated markov chains for eukaryotic promoter recognition." Bioinformatics 15, no. 5 (May 1, 1999): 362–69. http://dx.doi.org/10.1093/bioinformatics/15.5.362.

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15

Bhuiyan, Tanja, and H. Th Marc Timmers. "Promoter Recognition: Putting TFIID on the Spot." Trends in Cell Biology 29, no. 9 (September 2019): 752–63. http://dx.doi.org/10.1016/j.tcb.2019.06.004.

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16

Bajic, V. B., A. Chong, Seng Hong Seah, and V. Brusic. "An intelligent system for vertebrate promoter recognition." IEEE Intelligent Systems 17, no. 4 (July 2002): 64–70. http://dx.doi.org/10.1109/mis.2002.1024754.

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17

Auble, David T., and Pieter L. DeHaseth. "Promoter recognition by Escherichia coli RNA polymerase." Journal of Molecular Biology 202, no. 3 (August 1988): 471–82. http://dx.doi.org/10.1016/0022-2836(88)90279-3.

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18

Ayers, Deborah G., David T. Auble, and Pieter L. deHaseth. "Promoter recognition by Escherichia coli RNA polymerase." Journal of Molecular Biology 207, no. 4 (June 1989): 749–56. http://dx.doi.org/10.1016/0022-2836(89)90241-6.

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19

Müller, Ferenc, and Làszlò Tora. "The multicoloured world of promoter recognition complexes." EMBO Journal 23, no. 1 (December 18, 2003): 2–8. http://dx.doi.org/10.1038/sj.emboj.7600027.

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20

Römer, Patrick, Simone Hahn, Tina Jordan, Tina Strauß, Ulla Bonas, and Thomas Lahaye. "Plant Pathogen Recognition Mediated by Promoter Activation of the Pepper Bs3 Resistance Gene." Science 318, no. 5850 (October 26, 2007): 645–48. http://dx.doi.org/10.1126/science.1144958.

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Plant disease resistance (R) proteins recognize matching pathogen avirulence proteins. Alleles of the pepper R gene Bs3 mediate recognition of the Xanthomonas campestris pv. vesicatoria (Xcv) type III effector protein AvrBs3 and its deletion derivative AvrBs3Δrep16. Pepper Bs3 and its allelic variant Bs3-E encode flavin monooxygenases with a previously unknown structure and are transcriptionally activated by the Xcv effector proteins AvrBs3 and AvrBs3Δrep16, respectively. We found that recognition specificity resides in the Bs3 and Bs3-E promoters and is determined by binding of AvrBs3 or AvrBs3Δrep16 to a defined promoter region. Our data suggest a recognition mechanism in which the Avr protein binds and activates the promoter of the cognate R gene.

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21

SOROKIN, ANATOLY A., ALEXANDR A. OSYPOV, TIMUR R. DZHELYADIN, PETR M. BESKARAVAINY, and SVETLANA G. KAMZOLOVA. "ELECTROSTATIC PROPERTIES OF PROMOTER RECOGNIZED BYE. COLIRNA POLYMERASE Eσ70." Journal of Bioinformatics and Computational Biology 04, no. 02 (April 2006): 455–67. http://dx.doi.org/10.1142/s0219720006002077.

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A comparative analysis of electrostatic patterns for 359 σ70-specific promoters and 359 nonpromoter regions on electrostatic map of Escherichia coli genome was carried out. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile which correlate with promoter sequences. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which differ for different promoter groups and may be involved as signal elements in differential recognition of various promoters by the enzyme. Some specific electrostatic elements which are responsible for modulating promoter activities due to ADP-ribosylation of RNA polymerase α-subunit were found in far upstream regions of T4 phage early promoters and E. coli ribosomal promoters.

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22

Stawicki, Scott Stevenson, and C. Cheng Kao. "Spatial Perturbations within an RNA Promoter Specifically Recognized by a Viral RNA-Dependent RNA Polymerase (RdRp) Reveal That RdRp Can Adjust Its Promoter Binding Sites." Journal of Virology 73, no. 1 (January 1, 1999): 198–204. http://dx.doi.org/10.1128/jvi.73.1.198-204.1999.

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ABSTRACT RNA synthesis during viral replication requires specific recognition of RNA promoters by the viral RNA-dependent RNA polymerase (RdRp). Four nucleotides (−17, −14, −13, and −11) within the brome mosaic virus (BMV) subgenomic core promoter are required for RNA synthesis by the BMV RdRp (R. W. Siegel et al., Proc. Natl. Acad. Sci. USA 94:11238–11243, 1997). The spatial requirements for these four nucleotides and the initiation (+1) cytidylate were examined in RNAs containing nucleotide insertions and deletions within the BMV subgenomic core promoter. Spatial perturbations between nucleotides −17 and −11 resulted in decreased RNA synthesis in vitro. However, synthesis was still dependent on the key nucleotides identified in the wild-type core promoter and the initiation cytidylate. In contrast, changes between nucleotides −11 and +1 had a less severe effect on RNA synthesis but resulted in RNA products initiated at alternative locations in addition to the +1 cytidylate. The results suggest a degree of flexibility in the recognition of the subgenomic promoter by the BMV RdRp and are compared with functional regions in other DNA and RNA promoters.

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23

Ross, Wilma, Sarah E. Aiyar, Julia Salomon, and Richard L. Gourse. "Escherichia coli Promoters with UP Elements of Different Strengths: Modular Structure of Bacterial Promoters." Journal of Bacteriology 180, no. 20 (October 15, 1998): 5375–83. http://dx.doi.org/10.1128/jb.180.20.5375-5383.1998.

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ABSTRACT The α subunit of Escherichia coli RNA polymerase (RNAP) participates in promoter recognition through specific interactions with UP element DNA, a region upstream of the recognition hexamers for the ς subunit (the −10 and −35 hexamers). UP elements have been described in only a small number of promoters, including the rRNA promoter rrnB P1, where the sequence has a very large (30- to 70-fold) effect on promoter activity. Here, we analyzed the effects of upstream sequences from several additional E. coli promoters (rrnD P1, rrnB P2, λp R, lac, merT, and RNA II). The relative effects of different upstream sequences were compared in the context of their own core promoters or as hybrids to thelac core promoter. Different upstream sequences had different effects, increasing transcription from 1.5- to ∼90-fold, and several had the properties of UP elements: they increased transcription in vitro in the absence of accessory protein factors, and transcription stimulation required the C-terminal domain of the RNAP α subunit. The effects of the upstream sequences correlated generally with their degree of similarity to an UP element consensus sequence derived previously. Protection of upstream sequences by RNAP in footprinting experiments occurred in all cases and was thus not a reliable indicator of UP element strength. These data support a modular view of bacterial promoters in which activity reflects the composite effects of RNAP interactions with appropriately spaced recognition elements (−10, −35, and UP elements), each of which contributes to activity depending on its similarity to the consensus.

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24

Vulliémoz, Diane, and Laurent Roux. "Given the Opportunity, the Sendai Virus RNA-Dependent RNA Polymerase Could as Well Enter Its Template Internally." Journal of Virology 76, no. 16 (August 15, 2002): 7987–95. http://dx.doi.org/10.1128/jvi.76.16.7987-7995.2002.

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ABSTRACT The negative-stranded RNA viral genome is an RNA-protein complex of helicoidal symmetry, resistant to nonionic detergent and high salt, in which the RNA is protected from RNase digestion. The 15,384 nucleotides of the Sendai virus genome are bound to 2,564 subunits of the N protein, each interacting with six nucleotides so tightly that the bases are poorly accessible to soluble reagents. With such a uniform structure, the question of template recognition by the viral RNA polymerase has been raised. In a previous study, the N-phase context has been proposed to be crucial for this recognition, a notion referring to the importance of the position in which the nucleotides interact with the N protein. The N-phase context ruled out the role of the template 3′-OH congruence, a feature resulting from the obedience to the rule of six that implies the precise interaction of the last six 3′-OH nucleotides with the last N protein. The N-phase context then allows prediction of the recognition by the RNA polymerase of a replication promoter sequence even if internally positioned, a promoter which normally lies at the template extremity. In this study, with template minireplicons bearing tandem replication promoters separated by intervening sequences, we present data that indeed show that initiation of RNA synthesis takes place at the internal promoter. This internal initiation can best be interpreted as the result of the polymerase entering the template at the internal promoter. In this way, the data are consistent with the importance of the N-phase context in template recognition. Moreover, by introducing between the two promoters a stretch of 10 A residues which represent a barrier for RNA synthesis, we found that the ability of the RNA polymerase to cross this barrier depends on the type of replication promoter, strong or weak, that the RNA polymerase starts on, a sign that the RNA polymerase may be somehow imprinted in its activity by the nature of the promoter on which it starts synthesis.

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25

Gaal, Tamas, Wilma Ross, Shawn T. Estrem, Lam H. Nguyen, Richard R. Burgess, and Richard L. Gourse. "Promoter recognition and discrimination by EsigmaS RNA polymerase." Molecular Microbiology 42, no. 4 (November 2001): 939–54. http://dx.doi.org/10.1046/j.1365-2958.2001.02703.x.

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26

Knudsen, S. "Promoter2.0: for the recognition of PolII promoter sequences." Bioinformatics 15, no. 5 (May 1, 1999): 356–61. http://dx.doi.org/10.1093/bioinformatics/15.5.356.

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27

D'Alessio, J. A., R. Ng, H. Willenbring, and R. Tjian. "Core promoter recognition complex changes accompany liver development." Proceedings of the National Academy of Sciences 108, no. 10 (February 22, 2011): 3906–11. http://dx.doi.org/10.1073/pnas.1100640108.

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28

Matsunaga, Michio, and Judith A. Jaehning. "Intrinsic Promoter Recognition by a “Core” RNA Polymerase." Journal of Biological Chemistry 279, no. 43 (September 1, 2004): 44239–42. http://dx.doi.org/10.1074/jbc.c400384200.

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29

Gordon, L., A. Ya Chervonenkis, A. J. Gammerman, I. A. Shahmuradov, and V. V. Solovyev. "Sequence alignment kernel for recognition of promoter regions." Bioinformatics 19, no. 15 (October 10, 2003): 1964–71. http://dx.doi.org/10.1093/bioinformatics/btg265.

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30

Christensen, Lisa Lystbæk, and Jytte Josephsen. "The Methyltransferase from the LlaDII Restriction-Modification System Influences the Level of Expression of Its Own Gene." Journal of Bacteriology 186, no. 2 (January 15, 2004): 287–95. http://dx.doi.org/10.1128/jb.186.2.287-295.2004.

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ABSTRACT The type II restriction-modification (R-M) system LlaDII isolated from Lactococcus lactis contains two tandemly arranged genes, llaDIIR and llaDIIM, encoding a restriction endonuclease (REase) and a methyltransferase (MTase), respectively. Interestingly, two LlaDII recognition sites are present in the llaDIIM promoter region, suggesting that they may influence the activity of the promoter through methylation status. In this study, separate promoters for llaDIIR and llaDIIM were identified, and the regulation of the two genes at the transcriptional level was investigated. DNA fragments containing the putative promoters were cloned in a promoter probe vector and tested for activity in the presence and absence of the active MTase. The level of expression of the MTase was 5- to 10-fold higher than the level of expression of the REase. The results also showed that the presence of M.LlaDII reduced the in vivo expression of the llaDIIM promoter (P llaDIIM ) up to 1,000-fold, whereas the activity of the llaDIIR promoter (P llaDIIR ) was not affected. Based on site-specific mutations it was shown that both of the LlaDII recognition sites within P llaDIIM are required to obtain complete repression of transcriptional activity. No regulation was found for llaDIIR, which appears to be constitutively expressed.

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31

Eggers, Christian H., Melissa J. Caimano, and Justin D. Radolf. "Analysis of Promoter Elements Involved in the Transcriptional Initiation of RpoS-Dependent Borrelia burgdorferi Genes." Journal of Bacteriology 186, no. 21 (November 1, 2004): 7390–402. http://dx.doi.org/10.1128/jb.186.21.7390-7402.2004.

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ABSTRACT Borrelia burgdorferi, the causative agent of Lyme disease, encodes an RpoS ortholog (RpoSBb) that controls the temperature-inducible differential expression of at least some of the spirochete's lipoprotein genes, including ospC and dbpBA. To begin to dissect the determinants of RpoSBb recognition of, and selectivity for, its dependent promoters, we linked a green fluorescent protein reporter to the promoter regions of several B. burgdorferi genes with well-characterized expression patterns. Consistent with the expression patterns of the native genes/proteins in B. burgdorferi strain 297, we found that expression of the ospC, dbpBA, and ospF reporters in the spirochete was RpoSBb dependent, while the ospE and flaB reporters were RpoSBb independent. To compare promoter recognition by RpoSBb with that of the prototype RpoS (RpoSEc), we also introduced our panel of constructs into Escherichia coli. In this surrogate, maximal expression from the ospC, dbpBA, and ospF promoters clearly required RpoS, although in the absence of RpoSEc the ospF promoter was weakly recognized by another E. coli sigma factor. Furthermore, RpoSBb under the control of an inducible promoter was able to complement an E. coli rpoS mutant, although RpoSEc and RpoSBb each initiated greater activity from their own dependent promoters than they did from those of the heterologous sigma factor. Genetic analysis of the ospC promoter demonstrated that (i) the T(−14) in the presumptive −10 region plays an important role in sigma factor recognition in both organisms but is not as critical for transcriptional initiation by RpoSBb as it is for RpoSEc; (ii) the nucleotide at the −15 position determines RpoS or σ70 selectivity in E. coli but does not serve the same function in B. burgdorferi; and (iii) the 110-bp region upstream of the core promoter is not required for RpoSEc- or RpoSBb-dependent activity in E. coli but is required for maximal expression from this promoter in B. burgdorferi. Taken together, the results of our studies suggest that the B. burgdorferi and E. coli RpoS proteins are able to catalyze transcription from RpoS-dependent promoters of either organism, but at least some of the nucleotide elements involved in transcriptional initiation and sigma factor selection in B. burgdorferi play a different role than has been described for E. coli.

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32

Schornack, Sebastian, Kristin Peter, Ulla Bonas, and Thomas Lahaye. "Expression Levels of avrBs3-Like Genes Affect Recognition Specificity in Tomato Bs4- But Not in Pepper Bs3-Mediated Perception." Molecular Plant-Microbe Interactions® 18, no. 11 (November 2005): 1215–25. http://dx.doi.org/10.1094/mpmi-18-1215.

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The tomato Bs4 disease resistance gene mediates recognition of avrBs4-expressing strains of the bacterial spot pathogen Xanthomonas campestris pv. vesicatoria to give a hypersensitive response (HR). Here, we present the characterization of the Bs4 promoter and its application for lowlevel expression of bacterial type III effector proteins in planta. Real-time polymerase chain reaction showed that Bs4 is constitutively expressed at low levels and that transcript abundance does not change significantly upon infection with avrBs4-containing xanthomonads. A 302-bp promoter fragment was found to be sufficient to promote Bs4 gene function. Previous studies have shown that high, constitutive in planta expression of avrBs3 (AvrBs3 and AvrBs4 proteins are 96.6% identical) via the Cauliflower mosaic virus 35S (35S) promoter triggers a Bs4-dependent HR whereas X. campestris pv. vesicatoria-mediated delivery of AvrBs3 into the plant cytoplasm does not. Here, we demonstrate that, when expressed under control of the weak Bs4 promoter, avrBs3 does not trigger a Bs4-dependent HR whereas avrBs4 does. In contrast, the pepper Bs3 gene, which mediates recognition of AvrBs3- but not AvrBs4- delivering xanthomonads, retains its recognition specificity even if avrBs4 was expressed in planta from the strong 35S promoter. Importantly, Bs4 promoter-driven expression of hax3, hax4 (two recently isolated avrBs3-like genes), avrBs3, and avrBs4 resulted in identical reactions as observed upon infection with X. campestris pv. vesicatoria strains that express the respective avr gene, suggesting that the protein levels expressed under control of the Bs4 promoter are similar to those that are translocated by the bacterial type III secretion system.

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33

Mans, Ruud M. W., and Dagmar Knebel-Mörsdorf. "In Vitro Transcription of pe38/Polyhedrin Hybrid Promoters Reveals Sequences Essential for Recognition by the Baculovirus-Induced RNA Polymerase and for the Strength of Very Late Viral Promoters." Journal of Virology 72, no. 4 (April 1, 1998): 2991–98. http://dx.doi.org/10.1128/jvi.72.4.2991-2998.1998.

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ABSTRACT In vitro transcription was used to analyze the promoter specificity of the α-amanitin-resistant RNA polymerase that is induced late during infection of Autographa californica multicapsid nuclear polyhedrosis virus. By modifying the preparation of crude nuclear extracts, we have established an assay that permits differentiation between weak late and strong very late viral promoters. The virus-induced RNA polymerase initiates at a TAAG sequence motif in both late and very late promoters. Based on the sensitivity of our in vitro transcription system, we have investigated the sequences responsible for a functional TAAG motif and their putative role with respect to the strength of very late promoters. By constructing hybrid promoters between the early pe38 and the very late polyhedrin promoters, we demonstrated that the replacement of 7 nucleotides upstream of the nonfunctional TAAG sequences in the pe38 promoter with the corresponding sequences of the polyhedrin promoter was sufficient for recognition by the virus-induced RNA polymerase. The strength of the very late polyhedrin promoter was established after replacing the 5′ untranslated sequences of the pe38 promoter by those of the polyhedrin promoter in addition to the 7 nucleotides upstream of the TAAG motif.

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34

Tsukihashi, Yoshihiro, Tsuyoshi Miyake, Masashi Kawaichi, and Tetsuro Kokubo. "Impaired Core Promoter Recognition Caused by Novel Yeast TAF145 Mutations Can Be Restored by Creating a Canonical TATA Element within the Promoter Region of the TUB2Gene." Molecular and Cellular Biology 20, no. 7 (April 1, 2000): 2385–99. http://dx.doi.org/10.1128/mcb.20.7.2385-2399.2000.

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ABSTRACT The general transcription factor TFIID, which is composed of TATA-binding protein (TBP) and an array of TBP-associated factors (TAFs), has been shown to play a crucial role in recognition of the core promoters of eukaryotic genes. We isolated Saccharomyces cerevisiae yeast TAF145 (yTAF145) temperature-sensitive mutants in which transcription of a specific subset of genes was impaired at restrictive temperatures. The set of genes affected in these mutants overlapped with but was not identical to the set of genes affected by a previously reportedyTAF145 mutant (W.-C. Shen and M. R. Green, Cell 90:615–624, 1997). To identify sequences which rendered transcription yTAF145 dependent, we conducted deletion analysis of theTUB2 promoter using a novel mini-CLN2 hybrid gene reporter system. The results showed that the yTAF145mutations we isolated impaired core promoter recognition but did not affect activation by any of the transcriptional activators we tested. These observations are consistent with the reported yTAF145 dependence of the CLN2 core promoter in the mutant isolated by Shen and Green, although the CLN2 core promoter functioned normally in the mutants we report here. These results suggest that different promoters require different yTAF145 functions for efficient transcription. Interestingly, insertion of a canonical TATA element into the TATA-less TUB2 promoter rescued impaired transcription in the yTAF145 mutants we studied. It therefore appears that strong binding of TBP to the core promoter can alleviate the requirement for at least one yTAF145 function.

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35

Rooney, R. J., P. Raychaudhuri, and J. R. Nevins. "E4F and ATF, two transcription factors that recognize the same site, can be distinguished both physically and functionally: a role for E4F in E1A trans activation." Molecular and Cellular Biology 10, no. 10 (October 1990): 5138–49. http://dx.doi.org/10.1128/mcb.10.10.5138-5149.1990.

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Previous experiments have identified an element in the adenovirus E4 promoter that is critical for E1A-dependent trans activation and that can confer inducibility to a heterologous promoter. This DNA element is a recognition site for multiple nuclear factors, including ATF, which is likely a family of DNA-binding factors with similar DNA recognition properties. However, ATF activity was found not to be altered in any demonstrable way as a result of adenovirus infection. In contrast, another factor that recognizes this element, termed E4F, was found at only very low levels in uninfected cells but was increased markedly upon adenovirus infection, as measured in DNA-binding assays. Although both the ATF activity and the E4F activity recognized and bound to the same two sites in the E4 promoter, they differed in their sequence recognition of these sites. Furthermore, E4F bound only to a small subset of the ATF recognition sites; for instance, E4F did not recognize the ATF sites in the E2 or E3 promoters. Various E4F and ATF binding sites were inserted into an expression vector and tested by cotransfection assays for responsiveness to E1A. We found that a sequence capable of binding E4F could confer E1A inducibility. In contrast, a sequence that could bind ATF but not E4F did not confer E1A inducibility. We also found that E4F formed a stable complex with the E4 promoter, whereas the ATF DNA complex was unstable and rapidly dissociated. We conclude that the DNA-binding specificity of E4F as well as the alterations in DNA-binding activity of E4F closely correlates with E1A stimulation of the E4 promoter.

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Rooney, R. J., P. Raychaudhuri, and J. R. Nevins. "E4F and ATF, two transcription factors that recognize the same site, can be distinguished both physically and functionally: a role for E4F in E1A trans activation." Molecular and Cellular Biology 10, no. 10 (October 1990): 5138–49. http://dx.doi.org/10.1128/mcb.10.10.5138.

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Previous experiments have identified an element in the adenovirus E4 promoter that is critical for E1A-dependent trans activation and that can confer inducibility to a heterologous promoter. This DNA element is a recognition site for multiple nuclear factors, including ATF, which is likely a family of DNA-binding factors with similar DNA recognition properties. However, ATF activity was found not to be altered in any demonstrable way as a result of adenovirus infection. In contrast, another factor that recognizes this element, termed E4F, was found at only very low levels in uninfected cells but was increased markedly upon adenovirus infection, as measured in DNA-binding assays. Although both the ATF activity and the E4F activity recognized and bound to the same two sites in the E4 promoter, they differed in their sequence recognition of these sites. Furthermore, E4F bound only to a small subset of the ATF recognition sites; for instance, E4F did not recognize the ATF sites in the E2 or E3 promoters. Various E4F and ATF binding sites were inserted into an expression vector and tested by cotransfection assays for responsiveness to E1A. We found that a sequence capable of binding E4F could confer E1A inducibility. In contrast, a sequence that could bind ATF but not E4F did not confer E1A inducibility. We also found that E4F formed a stable complex with the E4 promoter, whereas the ATF DNA complex was unstable and rapidly dissociated. We conclude that the DNA-binding specificity of E4F as well as the alterations in DNA-binding activity of E4F closely correlates with E1A stimulation of the E4 promoter.

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Zamudio-Ochoa, Angelica, Yaroslav I. Morozov, Azadeh Sarfallah, Michael Anikin, and Dmitry Temiakov. "Mechanisms of mitochondrial promoter recognition in humans and other mammalian species." Nucleic Acids Research 50, no. 5 (February 22, 2022): 2765–81. http://dx.doi.org/10.1093/nar/gkac103.

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Abstract Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.

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Sanfaçon, Hélène. "Regulation of mRNA formation in plants: lessons from the cauliflower mosaic virus transcription signals." Canadian Journal of Botany 70, no. 5 (May 1, 1992): 885–99. http://dx.doi.org/10.1139/b92-113.

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The cauliflower mosaic virus (CaMV) transcription signals are common tools of plant molecular biologists. In this article, the transcription signals are discussed in light of the life cycle of CaMV, a plant pararetrovirus. Production of mature 35S RNA, the terminally redundant genomic RNA, is regulated by the 35S promoter, a very strong promoter, and by the polyadenylation signal that is present twice on the RNA but recognized only at its 3′ end. Dissection of the promoter has identified several organ-specific elements acting in concert to express the 35S RNA in most plant cells. Studies on the polyadenylation signal have revealed upstream elements inducing recognition of the AATAAA sequence and have led to the proposal that the conditional recognition of this signal is dependent on its distance from the promoter. Comparison of the CaMV signals with other plant signals allows speculation on the plant transcriptional machinery and on some striking resemblances and differences to the animal and yeast systems. Finally, potential applications of this knowledge will be described such as the construction of hybrid plant promoters or polyadenylation signals using the 35S minimal elements. Key words: cauliflower mosaic virus, 35S promoter, polyadenylation signal, 35S RNA, transcription, retroviruses.

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Schmitt-Ney, M., W. Doppler, R. K. Ball, and B. Groner. "Beta-casein gene promoter activity is regulated by the hormone-mediated relief of transcriptional repression and a mammary-gland-specific nuclear factor." Molecular and Cellular Biology 11, no. 7 (July 1991): 3745–55. http://dx.doi.org/10.1128/mcb.11.7.3745-3755.1991.

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Transcription from the beta-casein milk protein gene promoter is induced by the synergistic action of glucocorticoid and prolactin hormones in the murine mammary epithelial cell line, HC11. We analyzed the binding of nuclear proteins to the promoter and determined their binding sites. Site-directed mutagenesis was used to determine the function of nuclear factor binding. During lactogenic hormone induction of HC11 cells, the binding of two nuclear factors increased. The binding of two other nuclear factors, present in uninduced cells, decreased. The basal activity of the promoter could be increased to and above the level of the induced wild-type promoter when the recognition sequences of the negatively regulated factors were mutated. This suggests that the beta-casein promoter is regulated by the relief of the repression of transcription. An essential tissue-specific factor was also found in nuclear extracts from the mammary glands of mice. Mutation of its recognition sequence in the beta-casein promoter led to the abolition of the induction of transcription by lactogenic hormones. The DNA sequences recognized by all five of these nuclear factors are conserved in the promoters of different casein genes from several species, confirming their importance in the regulation of milk protein gene transcription.

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Schmitt-Ney, M., W. Doppler, R. K. Ball, and B. Groner. "Beta-casein gene promoter activity is regulated by the hormone-mediated relief of transcriptional repression and a mammary-gland-specific nuclear factor." Molecular and Cellular Biology 11, no. 7 (July 1991): 3745–55. http://dx.doi.org/10.1128/mcb.11.7.3745.

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Transcription from the beta-casein milk protein gene promoter is induced by the synergistic action of glucocorticoid and prolactin hormones in the murine mammary epithelial cell line, HC11. We analyzed the binding of nuclear proteins to the promoter and determined their binding sites. Site-directed mutagenesis was used to determine the function of nuclear factor binding. During lactogenic hormone induction of HC11 cells, the binding of two nuclear factors increased. The binding of two other nuclear factors, present in uninduced cells, decreased. The basal activity of the promoter could be increased to and above the level of the induced wild-type promoter when the recognition sequences of the negatively regulated factors were mutated. This suggests that the beta-casein promoter is regulated by the relief of the repression of transcription. An essential tissue-specific factor was also found in nuclear extracts from the mammary glands of mice. Mutation of its recognition sequence in the beta-casein promoter led to the abolition of the induction of transcription by lactogenic hormones. The DNA sequences recognized by all five of these nuclear factors are conserved in the promoters of different casein genes from several species, confirming their importance in the regulation of milk protein gene transcription.

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Pupov, Danil, Daria Esyunina, Andrey Feklistov, and Andrey Kulbachinskiy. "Single-strand promoter traps for bacterial RNA polymerase." Biochemical Journal 452, no. 2 (May 10, 2013): 241–48. http://dx.doi.org/10.1042/bj20130069.

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Besides canonical double-strand DNA promoters, multisubunit RNAPs (RNA polymerases) recognize a number of specific single-strand DNA and RNA templates, resulting in synthesis of various types of RNA transcripts. The general recognition principles and the mechanisms of transcription initiation on these templates are not fully understood. To investigate further the molecular mechanisms underlying the transcription of single-strand templates by bacterial RNAP, we selected high-affinity single-strand DNA aptamers that are specifically bound by RNAP holoenzyme, and characterized a novel class of aptamer-based transcription templates. The aptamer templates have a hairpin structure that mimics the upstream part of the open promoter bubble with accordingly placed specific promoter elements. The affinity of the RNAP holoenzyme to such DNA structures probably underlies its promoter-melting activity. Depending on the template structure, the aptamer templates can direct synthesis of productive RNA transcripts or effectively trap RNAP in the process of abortive synthesis, involving DNA scrunching, and competitively inhibit promoter recognition. The aptamer templates provide a novel tool for structure–function studies of transcription initiation by bacterial RNAP and its inhibition.

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Amaya, Edward, Anastasia Khvorova, and Patrick J. Piggot. "Analysis of Promoter Recognition In Vivo Directed by ςF of Bacillus subtilis by Using Random-Sequence Oligonucleotides." Journal of Bacteriology 183, no. 12 (June 15, 2001): 3623–30. http://dx.doi.org/10.1128/jb.183.12.3623-3630.2001.

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ABSTRACT Formation of spores from vegetative bacteria by Bacillus subtilis is a primitive system of cell differentiation. Critical to spore formation is the action of a series of sporulation-specific RNA polymerase ς factors. Of these, ςF is the first to become active. Few genes have been identified that are transcribed by RNA polymerase containing ςF (E-ςF), and only two genes of known function are exclusively under the control of E-ςF, spoIIR and spoIIQ. In order to investigate the features of promoters that are recognized by E-ςF, we studied the effects of randomizing sequences for the −10 and −35 regions of the promoter for spoIIQ. The randomized promoter regions were cloned in front of a promoterless copy of lacZ in a vector designed for insertion by double crossover of single copies of the promoter-lacZ fusions into the amyE region of the B. subtilischromosome. This system made it possible to test for transcription oflacZ by E-ςF in vivo. The results indicate a weak ςF-specific −10 consensus, GG/tNNANNNT, of which the ANNNT portion is common to all sporulation-associated ς factors, as well as to ςA. There was a rather stronger −35 consensus, GTATA/T, of which GNATA is also recognized by other sporulation-associated ς factors. The looseness of the ςF promoter requirement contrasts with the strict requirement for ςA-directed promoters ofB. subtilis. It suggests that additional, unknown, parameters may help determine the specificity of promoter recognition by E-ςF in vivo.

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Klauck, Hugo André, Gabriel Dall’Alba, Scheila de Avila e Silva, and Ana Paula Longaray Delamare. "Prediction and Recognition of Gram-Negative Bacterial Promoter Sequences: An Analysis of Available Web Tools." Journal of Biotechnology Research, no. 67 (July 2, 2020): 90–97. http://dx.doi.org/10.32861/jbr.67.90.97.

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Many computational methods aim to improve the prediction and recognition of transcription elements in prokaryotes. Despite this, the natural features of those elements make their prediction and recognition remain as an open field of research. In this paper, we compared the open-access tools BacPP, BPROM, bTSSfinder, CNNPromoter_b, iPro70-PseZNC, NNPP2, PePPer, and PromPredict. First, we listed the overall functionalities of each tool and the resources available on their web pages. Later, we carried out a comparison of prediction results using 206 intergenic regions. When evaluating the prediction using intergenic regions containing a single promoter within each, NNPP2 and BacPP obtained >90% correct predictions, with NNPP2 obtaining the highest values of match between predicted promoter location and location indicated by RegulonDB. Overall, many discrepancies were observed among the results. They may be explained by the differences in the methodologies that each tool applies for promoter prediction, not excluding the natural features of promoters as a factor as well. In any case, the results highlight the necessity to continue the efforts to improve promoter prediction, perhaps combining multiple approaches. Through said efforts, some of the challenges of the postgenomic era may be tackled as well.

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Potamias, George, and Alexandros Kanterakis. "Feature Selection for the Promoter Recognition and Prediction Problem." International Journal of Data Warehousing and Mining 3, no. 3 (July 2007): 60–78. http://dx.doi.org/10.4018/jdwm.2007070105.

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Kondrakhin, Y. V., A. E. Kel, N. A. Kolchanov, A. G. Romashchenko, and L. Milanesi. "Eukaryotic promoter recognition by binding sites for transcription factors." Bioinformatics 11, no. 5 (1995): 477–88. http://dx.doi.org/10.1093/bioinformatics/11.5.477.

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Werner, T. "The state of the art of mammalian promoter recognition." Briefings in Bioinformatics 4, no. 1 (January 1, 2003): 22–30. http://dx.doi.org/10.1093/bib/4.1.22.

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Yan, Yi-Yong, Jing Lin, Tian-Miao Ou, Jia-Heng Tan, Ding Li, Lian-Quan Gu, and Zhi-Shu Huang. "Selective recognition of oncogene promoter G-quadruplexes by Mg2+." Biochemical and Biophysical Research Communications 402, no. 4 (November 2010): 614–18. http://dx.doi.org/10.1016/j.bbrc.2010.10.065.

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Lee, Dong-Hoon, Naum Gershenzon, Malavika Gupta, Ilya P. Ioshikhes, Danny Reinberg, and Brian A. Lewis. "Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1." Molecular and Cellular Biology 25, no. 21 (November 1, 2005): 9674–86. http://dx.doi.org/10.1128/mcb.25.21.9674-9686.2005.

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ABSTRACT Downstream elements are a newly appreciated class of core promoter elements of RNA polymerase II-transcribed genes. The downstream core element (DCE) was discovered in the human β-globin promoter, and its sequence composition is distinct from that of the downstream promoter element (DPE). We show here that the DCE is a bona fide core promoter element present in a large number of promoters and with high incidence in promoters containing a TATA motif. Database analysis indicates that the DCE is found in diverse promoters, supporting its functional relevance in a variety of promoter contexts. The DCE consists of three subelements, and DCE function is recapitulated in a TFIID-dependent manner. Subelement 3 can function independently of the other two and shows a TFIID requirement as well. UV photo-cross-linking results demonstrate that TAF1/TAFII250 interacts with the DCE subelement DNA in a sequence-dependent manner. These data show that downstream elements consist of at least two types, those of the DPE class and those of the DCE class; they function via different DNA sequences and interact with different transcription activation factors. Finally, these data argue that TFIID is, in fact, a core promoter recognition complex.

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Rani, T. Sobha, and Raju S. Bapi. "Analysis of n-Gram based Promoter Recognition Methods and Application to Whole Genome Promoter Prediction." In Silico Biology 9, no. 1,2 (2009): S1—S16. http://dx.doi.org/10.3233/isb-2009-0388.

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Kamzolova, S. G., V. S. Sivozhelezov, A. A. Sorokin, T. R. Dzhelyadin, N. N. Ivanova, and R. V. Polozov. "RNA Polymerase—Promoter Recognition. Specific Features of Electrostatic Potential of “Early” T4 Phage DNA Promoters." Journal of Biomolecular Structure and Dynamics 18, no. 3 (December 2000): 325–34. http://dx.doi.org/10.1080/07391102.2000.10506669.

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Journal articles on the topic 'Promoter Recognition'

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