The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

AbstractMADS-box transcription factors are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of molecular domestication of these elements, which by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

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

Genome Biology ◽

10.1186/s13059-021-02574-x ◽

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

Bioinformatics ◽

10.1093/bioinformatics/btu643 ◽

2014 ◽

Vol 31 (2) ◽

pp. 178-186 ◽

Cited By ~ 49

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

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The GLI gene encodes a nuclear protein which binds specific sequences in the human genome

Molecular and Cellular Biology ◽

10.1128/mcb.10.2.634-642.1990 ◽

1990 ◽

Vol 10 (2) ◽

pp. 634-642

Author(s):

K W Kinzler ◽

B Vogelstein

Keyword(s):

Zinc Finger ◽

Base Pair ◽

Binding Sites ◽

Protein Product ◽

Variable Number ◽

Binding Motifs ◽

Dna Binding Motifs ◽

Pair Sequence ◽

Polymerase Chain

The GLI gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the GLI gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three GLI binding sites were identified by using a novel procedure in which total human DNA was bound to a GLI recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The GLI protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify GLI binding sites should be applicable to the characterization of other zinc finger proteins.

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The GLI gene encodes a nuclear protein which binds specific sequences in the human genome.

Molecular and Cellular Biology ◽

10.1128/mcb.10.2.634 ◽

1990 ◽

Vol 10 (2) ◽

pp. 634-642 ◽

Cited By ~ 311

Author(s):

K W Kinzler ◽

B Vogelstein

Keyword(s):

Zinc Finger ◽

Base Pair ◽

Binding Sites ◽

Protein Product ◽

Variable Number ◽

Binding Motifs ◽

Dna Binding Motifs ◽

Pair Sequence ◽

Polymerase Chain

The GLI gene is amplified in a subset of human tumors and encodes a protein product with five zinc finger DNA-binding motifs. In this study, we show that the GLI gene product has a predominantly nuclear localization and binds DNA in a sequence-specific fashion. Three GLI binding sites were identified by using a novel procedure in which total human DNA was bound to a GLI recombinant fusion protein, and the polymerase chain reaction was used to amplify and recover the bound sequences. The GLI protein protected a 23- to 24-base region within all three binding sites, and the protected region in each case included the 9-base-pair sequence 5'-GACCACCCA-3'. One of the binding sites was contained within a 63-base-pair repeat of the variable number of tandem repeat type, whereas the other two sites were represented once in the genome. The approach used here to identify GLI binding sites should be applicable to the characterization of other zinc finger proteins.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.675815 ◽

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.

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

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340040402 ◽

1988 ◽

Vol 4 (4) ◽

pp. 229-239 ◽

Cited By ~ 22

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

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

Planta ◽

10.1007/s00425-021-03572-w ◽

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.

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