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 Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Dave W Anderson ◽  
Alesia N McKeown ◽  
Joseph W Thornton
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Sites ◽  
Steroid Hormone Receptor ◽  
Biological Processes ◽  
Epistatic Interactions ◽  
Dna Binding Sites ◽  
Evolutionary Paths ◽  
Historical Transition ◽  
Transcription Factor Proteins

Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.

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 Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

2021 ◽  
Vol 49 (7) ◽  
pp. 3856-3875
Author(s):  
Marina Kulik ◽  
Melissa Bothe ◽  
Gözde Kibar ◽  
Alisa Fuchs ◽  
Stefanie Schöne ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Dna Binding ◽  
Receptor Binding ◽  
Binding Sites ◽  
Specific Gene ◽  
Functional Diversification ◽  
Enhancer Activity ◽  
Sequence Composition

Abstract The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

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 Analysis of two distinct single-stranded DNA binding sites on the recA nucleoprotein filament.

1993 ◽  
Vol 268 (30) ◽  
pp. 22525-22530
Author(s):  
A Zlotnick ◽  
R.S. Mitchell ◽  
R.K. Steed ◽  
S.L. Brenner
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Single Stranded Dna ◽  
Dna Binding Sites
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