Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers

AbstractThe interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

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Finding protein-binding sites in DNA sequences: the next generation

Trends in Biochemical Sciences ◽

10.1016/s0968-0004(97)01006-2 ◽

1997 ◽

Vol 22 (3) ◽

pp. 103-104 ◽

Cited By ~ 30

Author(s):

K French

Keyword(s):

Protein Binding ◽

Dna Sequences ◽

Binding Sites ◽

Next Generation ◽

Protein Binding Sites

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Structure of the coat protein-binding domain of the scaffolding protein from a double-stranded DNA virus11Edited by M. Summers

Journal of Molecular Biology ◽

10.1006/jmbi.2000.3620 ◽

2000 ◽

Vol 297 (5) ◽

pp. 1195-1202 ◽

Cited By ~ 52

Author(s):

Yahong Sun ◽

Matthew H. Parker ◽

Peter Weigele ◽

Sherwood Casjens ◽

Peter E. Prevelige Jr ◽

...

Keyword(s):

Coat Protein ◽

Protein Binding ◽

Binding Domain ◽

Scaffolding Protein ◽

Double Stranded Dna

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Electron microscopy of Achlya deoxyribonucleic acid sequence organization

Molecular and Cellular Biology ◽

10.1128/mcb.1.2.136-143.1981 ◽

1981 ◽

Vol 1 (2) ◽

pp. 136-143

Author(s):

M Pellegrini ◽

W E Timberlake ◽

R B Goldberg

Keyword(s):

Dna Sequences ◽

Deoxyribonucleic Acid ◽

Microscopic Analysis ◽

Single Copy ◽

Electron Microscopic ◽

Sequence Organization ◽

Double Stranded Dna ◽

Copy Dna ◽

Gene 32 ◽

Single Copy Dna

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.

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Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1620749114 ◽

2017 ◽

Vol 114 (29) ◽

pp. E5995-E6004 ◽

Cited By ~ 66

Author(s):

Yan O. Zubo ◽

Ivory Clabaugh Blakley ◽

Maria V. Yamburenko ◽

Jennifer M. Worthen ◽

Ian H. Street ◽

...

Keyword(s):

Protein Binding ◽

Binding Sites ◽

Growth And Development ◽

Abiotic Factors ◽

Physiological Responses ◽

Physiological Role ◽

Primary Response ◽

Type B ◽

Protein Binding Microarrays

The plant hormone cytokinin affects a diverse array of growth and development processes and responses to the environment. How a signaling molecule mediates such a diverse array of outputs and how these response pathways are integrated with other inputs remain fundamental questions in plant biology. To this end, we characterized the transcriptional network initiated by the type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) that mediate the cytokinin primary response, making use of chromatin immunoprecipitation sequencing (ChIP-seq), protein-binding microarrays, and transcriptomic approaches. By ectopic overexpression of ARR10, Arabidopsis lines hypersensitive to cytokinin were generated and used to clarify the role of cytokinin in regulation of various physiological responses. ChIP-seq was used to identify the cytokinin-dependent targets for ARR10, thereby defining a crucial link between the cytokinin primary-response pathway and the transcriptional changes that mediate physiological responses to this phytohormone. Binding of ARR10 was induced by cytokinin with binding sites enriched toward the transcriptional start sites for both induced and repressed genes. Three type-B ARR DNA-binding motifs, determined by use of protein-binding microarrays, were enriched at ARR10 binding sites, confirming their physiological relevance. WUSCHEL was identified as a direct target of ARR10, with its cytokinin-enhanced expression resulting in enhanced shooting in tissue culture. Results from our analyses shed light on the physiological role of the type-B ARRs in regulating the cytokinin response, mechanism of type-B ARR activation, and basis by which cytokinin regulates diverse aspects of growth and development as well as responses to biotic and abiotic factors.

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Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2

Nucleic Acids Research ◽

10.1093/nar/gkaa067 ◽

2020 ◽

Vol 48 (7) ◽

pp. 3869-3887 ◽

Cited By ~ 1

Author(s):

Linlin Hou ◽

Yuanjie Wei ◽

Yingying Lin ◽

Xiwei Wang ◽

Yiwei Lai ◽

...

Keyword(s):

Dna Sequences ◽

Target Genes ◽

Rna Binding ◽

Rna Binding Proteins ◽

High Mobility ◽

Binding Motif ◽

Dna And Rna ◽

Somatic Cell Reprogramming ◽

Double Stranded Dna

Abstract Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate that the transcription factor Sox2 is able to directly bind RNA in vitro as well as in mouse and human cells. Sox2 targets RNA via a 60-amino-acid RNA binding motif (RBM) positioned C-terminally of the DNA binding high mobility group (HMG) box. Sox2 can associate with RNA and DNA simultaneously to form ternary RNA/Sox2/DNA complexes. Deletion of the RBM does not affect selection of target genes but mitigates binding to pluripotency related transcripts, switches exon usage and impairs the reprogramming of somatic cells to a pluripotent state. Our findings designate Sox2 as a multi-functional factor that associates with RNA whilst binding to cognate DNA sequences, suggesting that it may co-transcriptionally regulate RNA metabolism during somatic cell reprogramming.

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Protein-binding microarrays: probing disease markers at the interface of proteomics and genomics

Trends in Molecular Medicine ◽

10.1016/j.molmed.2009.06.004 ◽

2009 ◽

Vol 15 (8) ◽

pp. 352-358 ◽

Cited By ~ 12

Author(s):

Jan Kerschgens ◽

Tanja Egener-Kuhn ◽

Nicolas Mermod

Keyword(s):

Protein Binding ◽

Disease Markers ◽

Protein Binding Microarrays

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Integrated approach for the identification of human hepatocyte nuclear factor 4α target genes using protein binding microarrays

Hepatology ◽

10.1002/hep.23357 ◽

2009 ◽

Vol 51 (2) ◽

pp. 642-653 ◽

Cited By ~ 105

Author(s):

Eugene Bolotin ◽

Hailing Liao ◽

Tuong Chi Ta ◽

Chuhu Yang ◽

Wendy Hwang-Verslues ◽

...

Keyword(s):

Protein Binding ◽

Target Genes ◽

Integrated Approach ◽

Human Hepatocyte ◽

Nuclear Factor ◽

Hepatocyte Nuclear Factor ◽

Hepatocyte Nuclear Factor 4Α ◽

Protein Binding Microarrays

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Heterogeneous nuclear ribonucleoprotein D0B is a sequence-specificDNA-binding protein

Biochemical Journal ◽

10.1042/bj3380417 ◽

1999 ◽

Vol 338 (2) ◽

pp. 417-425 ◽

Cited By ~ 21

Author(s):

Mate TOLNAY ◽

Lyudmila A. VERESHCHAGINA ◽

George C. TSOKOS

Keyword(s):

Dna Sequences ◽

Rna Binding ◽

Binding Protein ◽

Double Helix ◽

Physiological Role ◽

Single Stranded Dna ◽

Heterogeneous Nuclear Ribonucleoprotein ◽

Double Stranded Dna ◽

Nuclear Ribonucleoprotein

Complement receptor 2 (CR2) is important in the regulation of the B lymphocyte response; the regulation of its expression is therefore of central importance. We recently reported that a 42 kDa heterogeneous nuclear ribonucleoprotein (hnRNP) is involved in the transcriptional regulation of the human CR2 gene [Tolnay, Lambris and Tsokos (1997) J. Immunol. 159, 5492–5501]. We cloned the cDNA encoding this protein and found it to be identical with hnRNP D0B, a sequence-specific RNA-binding protein. By using a set of mutated oligonucleotides, we demonstrated that the recombinant hnRNP D0B displays sequence specificity for double-stranded oligonucleotide defined by the CR2 promoter. We conducted electrophoretic mobility-shift assays to estimate the apparent Kd of hnRNP D0B for the double-stranded DNA motif and found it to be 59 nM. Interestingly, hnRNP D0B displayed affinities of 28 and 18 nM for the sense and anti-sense strands of the CR2 promoter-defined oligonucleotide respectively. The significantly greater binding affinity of hnRNP D0B for single-stranded DNA than for double-stranded DNA suggests that the protein might melt the double helix. The intranuclear concentration of sequence-specific protein was estimated to be 250–400 nM, indicating that the protein binds to the CR2 promoter in vivo. Co-precipitation of a complex formed in vivo between hnRNP D0B and the TATA-binding protein demonstrates that hnRNP D0B interacts with the basal transcription apparatus. Our results suggest a new physiological role for hnRNP D0B that involves binding to double- and single-stranded DNA sequences in a specific manner and functioning as a transcription factor.

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