Interaction of Maize Chromatin-Associated HMG Proteins with Mononucleosomes: Role of Core and Linker Histones

2003 ◽  
Vol 384 (7) ◽  
pp. 1019-1027 ◽  
Author(s):  
J. Lichota ◽  
K. D. Grasser
Keyword(s):  
Dna Binding ◽  
High Mobility ◽  
Micrococcal Nuclease ◽  
Hmg Proteins ◽  
Binding Motifs ◽  
Linker Histones ◽  
Dna Binding Motifs ◽  
Core Histones ◽  
Hmgb Proteins ◽  
Nucleosome Binding

AbstractTwo groups of plant chromatin-associated high mobility group (HMG) proteins, namely the HMGA family, typically containing four A/T-hook DNA-binding motifs, and the HMGB family, containing a single HMG-box DNA-binding domain, have been identified. We have examined the interaction of recombinant maize HMGA and five different HMGB proteins with mononucleosomes (containing approx. 165 bp of DNA) purified from micrococcal nuclease-digested maize chromatin. The HMGB proteins interacted with the nucleosomes independent of the presence of the linker histone H1, while the binding of HMGA in the presence of H1 differed from that observed in the absence of H1. HMGA and the HMGB proteins bound H1-containing nucleosome particles with similar affinity. The plant HMG proteins could also bind nucleosomes that were briefly treated with trypsin (removing the N-terminal domains of the core histones), suggesting that the histone N-termini are dispensable for HMG protein binding. In the presence of untreated nucleosomes and trypsinised nucleosomes, HMGB1 could be chemically crosslinked with a core histone, which indicates that the trypsin-resistant part of the histones within the nucleosome is the main interaction partner of HMGB1 rather than the histone N-termini. In conclusion, these results indicate that specific nucleosome binding of the plant HMGB proteins requires simultaneous DNA and histone contacts.

scholarly journals The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis

2020 ◽  
Vol 21 (10) ◽  
pp. 3710 ◽  
Author(s):  
Linjia Su ◽  
Zifang Deng ◽  
Fenfei Leng
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Dna Binding ◽  
High Mobility ◽  
High Mobility Group ◽  
Current Evidence ◽  
High Mobility Group Protein ◽  
Binding Motifs ◽  
Dna Binding Motifs ◽  
Group Protein

The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three “AT-hook” DNA-binding motifs and a negatively charged C-terminal motif. It is a multifunctional nuclear protein directly linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Biochemical and biophysical studies showed that HMGA2 is an intrinsically disordered protein (IDP) and could form homodimers in aqueous buffer solution. The “AT-hook” DNA-binding motifs specifically bind to the minor groove of AT-rich DNA sequences and induce DNA-bending. HMGA2 plays an important role in adipogenesis most likely through stimulating the proliferative expansion of preadipocytes and also through regulating the expression of transcriptional factor Peroxisome proliferator-activated receptor γ (PPARγ) at the clonal expansion step from preadipocytes to adipocytes. Current evidence suggests that a main function of HMGA2 is to maintain stemness and renewal capacity of stem cells by which HMGA2 binds to chromosome and lock chromosome into a specific state, to allow the human embryonic stem cells to maintain their stem cell potency. Due to the importance of HMGA2 in adipogenesis and tumorigenesis, HMGA2 is considered a potential therapeutic target for anticancer and anti-obesity drugs. Efforts are taken to identify inhibitors targeting HMGA2.

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 Macronuclei and micronuclei in Tetrahymena thermophila contain high-mobility-group-like chromosomal proteins containing a highly conserved eleven-amino-acid putative DNA-binding sequence.

1991 ◽  
Vol 11 (1) ◽  
pp. 166-174 ◽  
Author(s):  
I G Schulman ◽  
T Wang ◽  
M Wu ◽  
J Bowen ◽  
R G Cook ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Tetrahymena Thermophila ◽  
High Mobility ◽  
Amino Acid Sequences ◽  
High Mobility Group ◽  
Binding Motif ◽  
Hmg Proteins ◽  
Chromosomal Proteins ◽  
Conserved Sequence

HMG (high-mobility-group protein) B and HMG C are abundant nonhistone chromosomal proteins isolated from Tetrahymena thermophila macronuclei with solubilities, molecular weights, and amino acid compositions like those of vertebrate HMG proteins. Genomic clones encoding each of these proteins have been sequenced. Both are single-copy genes that encode single polyadenylated messages whose amounts are 10 to 15 times greater in growing cells than in starved, nongrowing cells. The derived amino acid sequences of HMG B and HMG C contain a highly conserved sequence, the HMG 1 box, found in vertebrate HMGs 1 and 2, and we speculate that this sequence may represent a novel, previously unrecognized DNA-binding motif in this class of chromosomal proteins. Like HMGs 1 and 2, HMGs B and C contain a high percentage of aromatic amino acids. However, the Tetrahymena HMGs are small, are associated with nucleosome core particles, and can be specifically extracted from macronuclei by elutive intercalation, properties associated with vertebrate HMGs 14 and 17, not HMGs 1 and 2. Thus, it appears that these Tetrahymena proteins have features in common with both of the major subgroups of higher eucaryotic HMG proteins. Surprisingly, a linker histone found exclusively in transcriptionally inactive micronuclei also has several HMG-like characteristics, including the ability to be specifically extracted from nuclei by elutive intercalation and the presence of the HMG 1 box. This finding suggests that at least in T. thermophila, proteins with HMG-like properties are not restricted to regions of transcriptionally active chromatin.

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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