scholarly journals Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding

2022 ◽  
Author(s):  
Michel Planat ◽  
Marcelo M. Amaral ◽  
Fang Fang ◽  
David Chester ◽  
Raymond Aschheim ◽  
...  
Keyword(s):  
Dna Binding ◽  
Leucine Zipper ◽  
Cell Type ◽  
Finitely Generated ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
Finitely Generated Groups ◽  
Optimal Functioning ◽  
Dna Binding Motifs ◽  
Syntactical Rule

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.

scholarly journals Group Theory of Syntactical Freedom in DNA Transcription and Genome Decoding

2021 ◽  
Author(s):  
Michel Planat ◽  
Marcelo Amaral ◽  
Fang Fang ◽  
David Chester ◽  
Raymond Aschheim ◽  
...  
Keyword(s):  
Dna Binding ◽  
Leucine Zipper ◽  
Cell Type ◽  
Finitely Generated ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
Finitely Generated Groups ◽  
Optimal Functioning ◽  
Dna Binding Motifs ◽  
Syntactical Rule

Transcription factors (TFs) are proteins that recognize specific DNA fragments in order to decode the genome and ensure its optimal functioning. TFs work at the local and global scales by specifying cell type, cell growth and death, cell migration, organization and timely tasks. We investigate the structure of DNA-binding motifs with the theory of finitely generated groups. The DNA ‘word’ in the binding domain -the motif- may be seen as the generator of a finitely generated group Fdna on four letters, the bases A, T, G and C. It is shown that, most of the time, the DNA-binding motifs have subgroup structure close to free groups of rank three or less, a property that we call ‘syntactical freedom’. Such a property is associated to the aperiodicity of the motif when it is seen as a substitution sequence. Examples are provided for the major families of TFs such as leucine zipper factors, zinc finger factors, homeo-domain factors, etc. We also discuss the exceptions to the existence of such a DNA syntactical rule and their functional role. This includes the TATA box in the promoter region of some genes, the single nucleotide markers (SNP) and the motifs of some genes of ubiquitous role in transcription and regulation.

scholarly journals The Type III Effector HsvG of the Gall-Forming Pantoea agglomerans Mediates Expression of the Host Gene HSVGT

2012 ◽  
Vol 25 (2) ◽  
pp. 231-240 ◽  
Author(s):  
Gal Nissan ◽  
Shulamit Manulis-Sasson ◽  
Laura Chalupowicz ◽  
Doron Teper ◽  
Adva Yeheskel ◽  
...  
Keyword(s):  
Amino Acids ◽  
Transcription Factor ◽  
Dna Binding ◽  
Leucine Zipper ◽  
Pantoea Agglomerans ◽  
In Planta ◽  
Binding Motifs ◽  
Type Iii Effector ◽  
Type Iii ◽  
Dna Binding Motifs

The type III effector HsvG of the gall-forming Pantoea agglomerans pv. gypsophilae is a DNA-binding protein that is imported to the host nucleus and involved in host specificity. The DNA-binding region of HsvG was delineated to 266 amino acids located within a secondary structure region near the N-terminus of the protein but did not display any homology to canonical DNA-binding motifs. A binding site selection procedure was used to isolate a target gene of HsvG, named HSVGT, in Gypsophila paniculata. HSVGT is a predicted acidic protein of the DnaJ family with 244 amino acids. It harbors characteristic conserved motifs of a eukaryotic transcription factor, including a bipartite nuclear localization signal, zinc finger, and leucine zipper DNA-binding motifs. Quantitative real-time polymerase chain reaction analysis demonstrated that HSVGT transcription is specifically induced in planta within 2 h after inoculation with the wild-type P. agglomerans pv. gypsophilae compared with the hsvG mutant. Induction of HSVGT reached a peak of sixfold at 4 h after inoculation and progressively declined thereafter. Gel-shift assay demonstrated that HsvG binds to the HSVGT promoter, indicating that HSVGT is a direct target of HsvG. Our results support the hypothesis that HsvG functions as a transcription factor in gypsophila.

scholarly journals Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice

Planta ◽  
2021 ◽  
Vol 253 (2) ◽  
Author(s):  
Joung Sug Kim ◽  
SongHwa Chae ◽  
Kyong Mi Jun ◽  
Gang-Seob Lee ◽  
Jong-Seong Jeon ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Binding ◽  
Gene Networks ◽  
Upstream Region ◽  
Transcriptional Level ◽  
Cis Elements ◽  
Promoter Regions ◽  
Entire Genome ◽  
Binding Motifs ◽  
Dna Binding Motifs

Abstract Main conclusion The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Abstract Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5′ upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

The orientation and spacing of core DNA-binding motifs dictate selective transcriptional responses to three nuclear receptors

Cell ◽  
1991 ◽  
Vol 65 (7) ◽  
pp. 1267-1279 ◽  
Author(s):  
Anders M. Näär ◽  
Jean-Marle Boutin ◽  
Steven M. Lipkin ◽  
Victor C. Yu ◽  
Jeffrey M. Holloway ◽  
...  
Keyword(s):  
Dna Binding ◽  
Nuclear Receptors ◽  
Transcriptional Responses ◽  
Binding Motifs ◽  
Dna Binding Motifs

ChemInform Abstract: Novel Class of DNA Binding Motifs Based on Bistetrahydrofuran and Bisfuran Skeleton with Long Alkyl Chains

ChemInform ◽  
2010 ◽  
Vol 32 (47) ◽  
pp. no-no
Author(s):  
Shigeki Sasaki ◽  
Takayuki Shibata ◽  
Hidemine Torigoe ◽  
Yosinori Shibata ◽  
Minoru Maeda
Keyword(s):  
Dna Binding ◽  
Binding Motifs ◽  
Alkyl Chains ◽  
Dna Binding Motifs

scholarly journals Improvement of  29 DNA polymerase amplification performance by fusion of DNA binding motifs

2010 ◽  
Vol 107 (38) ◽  
pp. 16506-16511 ◽  
Author(s):  
M. de Vega ◽  
J. M. Lazaro ◽  
M. Mencia ◽  
L. Blanco ◽  
M. Salas
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Binding Motifs ◽  
Dna Binding Motifs

scholarly journals A serine/proline-rich protein is fused to HRX in t(4;11) acute leukemias

Blood ◽  
1993 ◽  
Vol 81 (5) ◽  
pp. 1124-1131 ◽  
Author(s):  
J Morrissey ◽  
DC Tkachuk ◽  
A Milatovich ◽  
U Francke ◽  
M Link ◽  
...  
Keyword(s):  
Amino Acids ◽  
Dna Binding ◽  
Chromosome Band ◽  
Binding Motif ◽  
Significant Similarity ◽  
Acute Leukemias ◽  
Binding Motifs ◽  
Consensus Sequences ◽  
Charged Amino Acids ◽  
Dna Binding Motifs

Translocations involving chromosome band 11q23 in acute leukemias have recently been shown to involve the HRX gene that codes for a protein with significant similarity to Drosophila trithorax. HRX gene alterations are consistently observed in t(4;11) (q21;q23)-carrying leukemias and cell lines by Southern blot analyses and are accompanied by HRX transcripts of anomalous size on Northern blots. HRX-homologous cDNAs were isolated from a library prepared from t(4;11)-carrying acute leukemia cells. cDNAs representative of transcription products from the derivative 11 chromosome were shown to contain HRX sequences fused to sequences derived from chromosome band 4q21. Fragments of the latter were used to clone and analyze cDNAs for wild-type 4q21 transcripts that predicted a 140-Kd basic protein (named FEL) that is rich in prolines, serines, and charged amino acids. FEL contains guanosine triphosphate-binding and nuclear localization consensus sequences and uses one of two possible 5' exons encoding the first 12 or 5 amino acids. After t(4;11) translocations, 913 C-terminal amino acids of FEL are fused in frame to the N-terminal portion of HRX containing its minor groove DNA binding motifs. These features are similar to predicted t(11;19) fusion proteins, suggesting that HRX consistently contributes a novel DNA-binding motif to at least two different chimeric proteins in acute leukemias.

scholarly journals Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Colin T. Waters ◽  
Stephen S. Gisselbrecht ◽  
Yuliya A. Sytnikova ◽  
Tiziana M. Cafarelli ◽  
David E. Hill ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Enhancer Activity ◽  
Epistatic Interactions ◽  
Binding Motifs ◽  
Transcriptional Enhancers ◽  
Significant Challenge ◽  
Dna Binding Sites ◽  
Dna Binding Motifs ◽  
Quantitative Changes

AbstractUnderstanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers. We measure quantitative changes in enhancer activity and discover a range of epistatic interactions among the motifs, both synergistic and alleviating. We find that understanding the regulatory consequences of TF binding motifs requires that they be investigated in combination across enhancer contexts.

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