scholarly journals Chromatin structure shapes the search process of transcription factors

2016 ◽  
Author(s):  
Neslihan Avcu ◽  
Nacho Molina
Keyword(s):  
Transcription Factors ◽  
High Resolution ◽  
Diffusion Process ◽  
Protein Interactions ◽  
Chromatin Structure ◽  
3D Structure ◽  
Regulatory Proteins ◽  
Local Concentration ◽  
Multi Scale ◽  
First Time

The diffusion of regulatory proteins within the nucleus plays a crucial role in the dynamics of transcriptional regulation. The standard model assumes a 3D plus ID diffusion process: regulatory proteins either move freely in solution or slide on DNA. This model however does not considered the 3D structure of chromatin. Here we proposed a multi-scale stochastic model that integrates, for the first time, high-resolution information on chromatin structure as well as DNA-protein interactions. The dynamics of transcription factors was modeled as a slide plus jump diffusion process on a chromatin network based on pair-wise contact maps obtained from high-resolution Hi-C experiments. Our model allowed us to uncover the effects of chromatin structure on transcription factor occupancy profiles and target search times. Finally, we showed that binding sites clustered on few topological associated domains leading to a higher local concentration of transcription factors which could reflect an optimal strategy to efficiently use limited transcriptional resources.

scholarly journals Construction of yeast one-hybrid library and screening of transcription factors regulating LhMYBSPLATTER expression in Asiatic hybrid lilies (Lilium spp.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuwei Cao ◽  
Mengmeng Bi ◽  
Panpan Yang ◽  
Meng Song ◽  
Guoren He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Theoretical Basis ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Proteins ◽  
Biosynthesis Pathway ◽  
Temporal Expression ◽  
Anthocyanin Pigmentation ◽  
Cdna Insert ◽  
R2r3 Myb ◽  
First Time

Abstract Background Anthocyanins, which belong to flavonoids, are widely colored among red-purple pigments in the Asiatic hybrid lilies (Lilium spp.). Transcription factor (TF) LhMYBSPLATTER (formerly known as LhMYB12-Lat), identified as the major kernel protein, regulating the anthocyanin biosynthesis pathway in ‘Tiny Padhye’ of Tango Series cultivars, which the pigmentation density is high in the lower half of tepals and this patterning is of exceptional ornamental value. However, the research on mechanism of regulating the spatial and temporal expression differences of LhMYBSPLATTER, which belongs to the R2R3-MYB subfamily, is still not well established. To explore the molecular mechanism of directly related regulatory proteins of LhMYBSPLATTER in the anthocyanin pigmentation, the yeast one-hybrid (Y1H) cDNA library was constructed and characterized. Results In this study, we describe a yeast one-hybrid library to screen transcription factors that regulate LhMYBSPLATTER gene expression in Lilium, with the library recombinant efficiency of over 98%. The lengths of inserted fragments ranged from 400 to 2000 bp, and the library capacity reached 1.6 × 106 CFU of cDNA insert, which is suitable to fulfill subsequent screening. Finally, seven prey proteins, including BTF3, MYB4, IAA6-like, ERF4, ARR1, ERF WIN1-like, and ERF061 were screened by the recombinant bait plasmid and verified by interaction with the LhMYBSPLATTER promoter. Among them, ERFs, AUX/IAA, and BTF3 may participate in the negative regulation of the anthocyanin biosynthesis pathway in Lilium. Conclusion A yeast one-hybrid library of lily was successfully constructed in the tepals for the first time. Seven candidate TFs of LhMYBSPLATTER were screened, which may provide a theoretical basis for the study of floral pigmentation.

scholarly journals Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes

2018 ◽  
Author(s):  
Langyu Gu ◽  
Canwei Xia
Keyword(s):  
Transcription Factors ◽  
Cluster Expansion ◽  
Expression Patterns ◽  
3D Structure ◽  
Teleost Fishes ◽  
Duplicated Genes ◽  
Specific Expression ◽  
Forkhead Transcription Factors ◽  
Apolipoprotein D ◽  
First Time

AbstractBackgroundGene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attentions considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the ligand (e.g., pheromone and hormone)-transporter genes, apolipoprotein D (ApoD) genes in a cluster, specific to teleost fishes.ResultsThe single ApoD gene in the ancestor expands in two clusters with a dynamic evolutionary pattern in teleost fishes. Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, evolutionary rate detection and breakpoint detection, orthologous genes show conserved expression patterns. Lineage-specific duplicated genes that are under positive selection evolved specific and even new expression profiles. Different duplicates show high tissue-specific expression patterns (e.g., skin, eye, anal fin pigmentation patterns, gonads, gills, spleen and lower pharyngeal jaw). Cluster analyses based on protein 3D structure comparisons, especially the four loops at the opening side, show segregation patterns with different duplicates. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes, and they are located next to the breakpoints of genome rearrangements.ConclusionsHere, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both protein and expression levels after duplication. Evidence from different aspects, i.e. abnormal expression induced disease in human, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, highly specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes that are under positive selection, and their locations next to breakpoints of genome rearrangement, suggests the potential advantageous roles of ApoD genes in teleost fishes. Cluster expansion of ApoD genes specific to teleost fishes thus provides an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.

scholarly journals Construction of Yeast One-hybrid Library and Screening of Transcription Factors Regulating LhMYB12-Lat Expression in Asiatic Hybrid Lilies (Lilium spp.)

2021 ◽  
Author(s):  
Yuwei Cao ◽  
Mengmeng Bi ◽  
Panpan Yang ◽  
Meng Song ◽  
Guoren He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Theoretical Basis ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Proteins ◽  
Biosynthesis Pathway ◽  
Temporal Expression ◽  
Anthocyanin Pigmentation ◽  
Cdna Insert ◽  
R2r3 Myb ◽  
First Time

Abstract Background: Anthocyanins, which belong to flavonoids, are widely colored among red-purple pigments in the Asiatic hybrid lilies (Lilium spp.). Transcription factor (TFs) LhMYB12-Lat, identified as the major kernel protein, regulating the anthocyanin biosynthesis pathway in ‘Tiny Padhye’ of Tango series cultivars, which the pigmentation density is high in the lower half of tepals and this patterning is of exceptional ornamental value. However, the research on mechanism of regulating the spatial and temporal expression differences of LhMYB12-Lat, which belongs to the R2R3-MYB subfamily, is still not well established. To explore the molecular mechanism of directly related regulatory proteins of LhMYB12-Lat in the anthocyanin pigmentation, the yeast one-hybrid (Y1H) cDNA library was constructed and characterized. Results: In this study, we describe a yeast one-hybrid library to screen transcription factors that regulate LhMYB12-Lat gene expression in Lilium, with the library recombinant efficiency of over 98%. The lengths of inserted fragments ranged from 400-2000 bp, and the library capacity reached 1.6 × 106 CFU of cDNA insert, which is suitable to fulfill subsequent screening. Finally, seven prey proteins, including BTF3, MYB4, IAA6-like, ERF4, ARR1, ERF WIN1-like, and ERF061 were screened by the recombinant bait plasmid and verified by interaction with the LhMYB12-Lat promoter. Among them, ERF, AUX/IAA, and BTF3 may participate in the negative regulation of the anthocyanin biosynthesis pathway in Lilium.Conclusion: A yeast one-hybrid library of lily was successfully constructed in the tepals for the first time. Seven candidate TFs of LhMYB12-Lat were screened, which may provide a theoretical basis for the study of floral pigmentation.

scholarly journals Plant Transcription Factors Involved in Drought and Associated Stresses

2021 ◽  
Vol 22 (11) ◽  
pp. 5662
Author(s):  
Maria Hrmova ◽  
Syed Sarfraz Hussain
Keyword(s):  
Transcription Factors ◽  
Stress Tolerance ◽  
Protein Interactions ◽  
Dna Sequences ◽  
Leucine Zipper ◽  
Plant Stress ◽  
3D Structure ◽  
Post Translational Modification ◽  
Basic Leucine Zipper ◽  
The Impact

Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants—this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.

scholarly journals A novel registration method for high resolution remote sensing images based on JSEG and NMI

2015 ◽  
Vol 12 (1) ◽  
pp. 289-306 ◽  
Author(s):  
Chao Wang ◽  
Aiye Shi ◽  
Xin Wang ◽  
Fengchen Huang ◽  
Hui Liu
Keyword(s):  
Remote Sensing ◽  
High Resolution ◽  
Image Registration ◽  
Control Point ◽  
Remote Sensing Images ◽  
Registration Method ◽  
Multi Scale ◽  
Feature Point Extraction ◽  
First Time ◽  
Selection Of

When traditional multi-scale analysis tools are applied to high resolution remote sensing image registration, difficulties and limitations are common in selection of directional sub-bands and distribution optimization of control point pairs etc. Aiming at this issue, a novel registration method based on JSEG and NMI is proposed in this paper. It is the method that incorporates the multi-scale segmentation method (JSEG) into image registration for the first time and proposes an adaptive feature point extraction method on the basis of blocking strategy. Then, NMI is adopted to obtain a set of control point pairs. Finally, the image registration is realized by virtue of Delaunay triangle local transform mapping functions. In accordance with experiments on high resolution remote sensing images collected by different sensors, it is found that the method can not only extract feature points accurately but also ensure reasonable distribution of control point pairs. Meanwhile, compared with traditional multi-scale tools-based methods, the method has relatively high accuracy and robustness.

scholarly journals The high-resolution structure of cell membranes revealed by in situ cryo-electron tomography

2021 ◽  
Author(s):  
Guanfang Zhao ◽  
Sihang Cheng ◽  
Yang Yu ◽  
Tianyi Zou ◽  
Huili Wang ◽  
...  
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Interactions ◽  
Cell Membranes ◽  
Electron Tomography ◽  
3D Structure ◽  
Structure Characterization ◽  
Cryo Electron Tomography

As the structural unit of life, cell is defined by the membrane system. The cell membrane separates the internal and external environment of the cell, and the endomembrane system defines the organelles to perform different functions1-3. However, lack of tools to in situ observe membrane proteins at a molecular resolution has limited our understanding of membrane organization and membrane protein interactions. Here we characterize the high-resolution 3D structure of human red blood cell (hRBC) membranes and the membrane proteins for the first time in situ by cryo-electron tomography (CryoET)4-7. By analyzing tomograms, we have obtained the first fine three-dimensional (3D) structure of hRBC membranes and found the asymmetrical distribution of membrane proteins on both sides of the membranes. We found that the membrane proteins are mainly located on the cytoplasmic side of hRBC membranes, with protein sizes ranging from 6nm to 8nm, in contrast to the ectoplasmic side with basically no proteins. Quantitative analysis of the density of hRBC membrane proteins shows that the membranes with higher protein occupancy have less phospholipid, making the membranes more rigid. Meanwhile, we obtained the channel protein-like structures by preliminary analysis of the membrane protein. Our results represent the first in situ structure characterization of the cell membranes and membrane proteins through cryoET and opens the door for understanding the biological functions of cell membranes in their physiological environments.

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

NMR spectroscopy in the conformational analysis of peptides: an overview

2020 ◽  
Vol 27 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Nmr Spectroscopy ◽  
Protein Interactions ◽  
3D Structure ◽  
Theoretical Background ◽  
Triple Resonance ◽  
Protein Protein Interactions ◽  
Nmr Studies ◽  
Conformational Preferences ◽  
Dynamic Perspective ◽  
Nmr Methods

Background: NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. Objective: This review provides a toolkit to investigate peptide conformational properties by NMR. Methods: Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through Pubmed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. Results: The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. Conclusion: NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

Ground state molecular parameters of phosphine, PH3, from the simultaneous analysis of the high-resolution infrared, microwave and submillimeterwave spectra

1985 ◽  
Vol 50 (11) ◽  
pp. 2480-2492 ◽  
Author(s):  
Soňa Přádná ◽  
Dušan Papoušek ◽  
Jyrki Kauppinen ◽  
Sergei P. Belov ◽  
Andrei F. Krupnov ◽  
...  
Keyword(s):  
Fourier Transform ◽  
High Resolution ◽  
Ground State ◽  
Unitary Transformation ◽  
Point Of View ◽  
Acoustic Detection ◽  
Molecular Parameters ◽  
Microwave Spectrometer ◽  
Fourier Transform Spectra ◽  
First Time

Fourier transform spectra of the ν2 band of PH3 have been remeasured with 0.0045 cm-1 resolution. Ground state combination differences from these data have been fitted simultaneously with the microwave and submillimeterwave data to determine the ground state spectroscopical parameters of PH3 including the parameters of the Δk = ± 3n interactions. The correlation between the latter parameters has been discussed from the point of view of the existence of two equivalent effective rotational operators which are related by a unitary transformation. The ΔJ = 0, +1, ΔK = 0 (A1 ↔ A2, E ↔ E) rotational transitions in the ν2 and ν4 states have been measured for the first time by using a microwave spectrometer and a radiofrequency spectrometer with acoustic detection.

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