Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding “EF hands” are related by charge and sequence reversal

1988 ◽  
Vol 4 (4) ◽  
pp. 229-239 ◽  
Author(s):  
Jane S. Richardson ◽  
David C. Richardson
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Lap Joints ◽  
Ion Binding ◽  
Binding Motifs ◽  
Dna Binding Motifs ◽  
Ef Hands ◽  
Ion Binding Sites

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.

scholarly journals LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis

2014 ◽  
Vol 31 (2) ◽  
pp. 178-186 ◽  
Author(s):  
Sha He ◽  
Hai Zhang ◽  
Haihua Liu ◽  
Hao Zhu
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Base Pairing ◽  
Binding Motifs ◽  
Dna Binding Motifs ◽  
Hoogsteen Base Pairing

scholarly journals Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content

2021 ◽  
Vol 12 ◽  
Author(s):  
Inna A. Suvorova ◽  
Mikhail S. Gelfand
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Sites ◽  
Dna Interaction ◽  
Orthologous Genes ◽  
Binding Motifs ◽  
Bacterial Transcription ◽  
Alternating Direction ◽  
Dna Binding Motifs ◽  
General Protein

The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYW3–4RYGRAMC and TGRAACAN1–2TGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. We identified trends in site positioning relative to the translational gene start, and show that TFs in 94 orthologous groups bind tandem sites with 18–22 nucleotides between their centers. We predict protein–DNA contacts via the correlation analysis of nucleotides in binding sites and amino acids of the DNA-binding domain of TFs, and show that the majority of interacting positions and predicted contacts are similar for both types of motifs and conform well both to available experimental data and to general protein–DNA interaction trends.

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.

scholarly journals Transcription Factor–DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources

2016 ◽  
Vol 2016 (11) ◽  
pp. pdb.top080622 ◽  
Author(s):  
Joshua L. Schipper ◽  
Raluca M. Gordân
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Dna Binding ◽  
Binding Motifs ◽  
Dna Binding Motifs

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

Field-dependent aluminum-27 NMR studies of the transferrins: an approach for the study of metal ion binding sites in larger proteins

1993 ◽  
Vol 115 (21) ◽  
pp. 9750-9753 ◽  
Author(s):  
James M. Aramini ◽  
Markus W. Germann ◽  
Hans J. Vogel
Keyword(s):  
Binding Sites ◽  
Metal Ion ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Nmr Studies ◽  
Field Dependent ◽  
Ion Binding Sites ◽  
Metal Ion Binding Sites

scholarly journals Synthesis and Photoregulated Metal Coordination of Azobenzene Polymer Having Ion Binding Sites

1991 ◽  
Vol 23 (2) ◽  
pp. 127-134 ◽  
Author(s):  
Masato Nanasawa ◽  
Takahiro Nishiyama ◽  
Hiroyoshi Kamogawa
Keyword(s):  
Binding Sites ◽  
Metal Coordination ◽  
Ion Binding ◽  
Azobenzene Polymer ◽  
Ion Binding Sites

Characterization of the Ferrous Ion Binding Sites of Apple 1-Aminocyclopropane-1-carboxylate Oxidase by Site-Directed Mutagenesis

1996 ◽  
Vol 225 (3) ◽  
pp. 697-700 ◽  
Author(s):  
Jei-Fu Shaw ◽  
Yun-Shan Chou ◽  
Rey-Chang Chang ◽  
Shang Fa Yang
Keyword(s):  
Binding Sites ◽  
Site Directed Mutagenesis ◽  
Ferrous Ion ◽  
Directed Mutagenesis ◽  
Ion Binding ◽  
Ion Binding Sites
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