High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale

2014 ◽  
pp. 37-53 ◽  
Author(s):  
Luca Giorgetti ◽  
Tristan Piolot ◽  
Edith Heard
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Optical Aberrations

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.

scholarly journals Adaptive optics enhanced all-optical photoacoustic tomography

2021 ◽  
Author(s):  
Jakub Czuchnowski ◽  
Robert Prevedel
Keyword(s):  
High Resolution ◽  
Image Quality ◽  
Adaptive Optics ◽  
Photoacoustic Signal ◽  
Photoacoustic Tomography ◽  
Optical Aberrations ◽  
Fabry Perot ◽  
Mammalian Tissues ◽  
All Optical

AbstractAll-optical ultrasound detection bears a number of unique advantages for photoacoustic tomography, including the ability for high resolution sampling of the acoustic field and its compatibility with a wide variety of other optical modalities. However, optical schemes based on miniaturized cavities are sensitive to optical aberrations as well as manufacturing-induced cavity imperfections which degrade sensor sensitivity and deteriorate photoacoustic image quality. Here we present an experimental method based on adaptive optics that is capable of enhancing the overall sensitivity of Fabry-Pérot based photoacoustic sensors. We experimentally observe clear improvements in photoacoustic signal detection as well as overall image quality after photoacoustic tomography reconstructions when applied to mammalian tissues in vivo.

scholarly journals A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Suhn Kyong Rhie ◽  
Andrew A. Perez ◽  
Fides D. Lay ◽  
Shannon Schreiner ◽  
Jiani Shi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
High Resolution ◽  
Cancer Cells ◽  
Chromatin Structure ◽  
Cancer Biology ◽  
Ctcf Binding ◽  
Chromatin Interaction ◽  
Prostate Cancer Cells ◽  
Cancer Transcriptome

Abstract To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation.

A high-resolution analysis of chromatin structure alongp53 sequences

1996 ◽  
Vol 17 (4) ◽  
pp. 192-201 ◽  
Author(s):  
Silvia Tornaletti ◽  
Steven Bates ◽  
Gerd P. Pfeifer
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
High Resolution Analysis ◽  
Resolution Analysis

scholarly journals High-resolution cryo-EM reconstructions in the presence of substantial aberrations

2019 ◽  
Author(s):  
Raquel Bromberg ◽  
Yirui Guo ◽  
Dominika Borek ◽  
Zbyszek Otwinowski
Keyword(s):  
High Resolution ◽  
Single Particle ◽  
Analytical Formula ◽  
Information Loss ◽  
Optical Aberrations ◽  
Shift Method ◽  
Single Particle Reconstruction ◽  
Beam Image ◽  
The Cost ◽  
Particle Reconstruction

The beam-image shift method accelerates data acquisition in cryo-EM single particle reconstruction (cryo-EM SPR) by fast repositioning of the imaging area, but at the cost of more severe and complex optical aberrations.We analyze here how uncorrected anti-symmetric aberrations, such as coma and trefoil, affect cryo-EM SPR results, and then infer an analytical formula quantifying information loss due to their presence that explains why Fourier-shell coefficient (FSC)-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. We validate our analysis with reference-based aberration refinement for two cryo-EM SPR datasets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and obtained 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively.Our results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher-order aberrations and address inconsistent guidelines regarding the level of aberrations acceptable in cryo-EM SPR experiments.

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 Human immunoglobulin kappa gene enhancer: chromatin structure analysis at high resolution.

1987 ◽  
Vol 7 (1) ◽  
pp. 15-25 ◽  
Author(s):  
J M Gimble ◽  
E E Max
Keyword(s):  
High Resolution ◽  
B Cell ◽  
Chromatin Structure ◽  
Genomic Sequence ◽  
Dimethyl Sulfate ◽  
Dnase I ◽  
Homologous Region ◽  
Immunoglobulin Kappa ◽  
Gene Enhancer

The murine immunoglobulin kappa gene enhancer has previously been found to coincide with a region of altered chromatin structure reflected in a DNase I hypersensitivity site detectable on Southern blots of B-cell DNA. We examined the chromatin structure of the homologous region of human DNA using the high-resolution electroblotting method originally developed for genomic sequence analysis by G. Church and W. Gilbert (Proc. Natl. Acad. Sci. USA 81:1991-1995, 1984). Analysis of DNA isolated from cells treated in vivo with dimethyl sulfate revealed two B-cell-specific sites of enhanced guanine methylation. Both sites are located within perfect inverted repeats theoretically capable of forming cruciform structures; one of these repeats overlaps an enhancer core sequence. No enhancement or protection of guanine methylation was observed within sequences similar to sites of altered methylation previously described in the immunoglobulin heavy-chain enhancer. Treatment of isolated nuclei with DNase I or a variety of restriction endonucleases defined a B-cell-specific approximately 0.25-kilobase region of enhanced nuclease susceptibility similar to that observed in the murine kappa enhancer. The 130-base-pair DNA segment that shows high sequence conservation between human, mouse, and rabbit DNAs lies at the 5' end of the nuclease-susceptible region.

scholarly journals High-Resolution Structural Analysis of Chromatin at Specific Loci: Saccharomyces cerevisiae Silent Mating-Type Locus HMRa

1999 ◽  
Vol 19 (12) ◽  
pp. 7944-7950 ◽  
Author(s):  
Anish Ravindra ◽  
Kerstin Weiss ◽  
Robert T. Simpson
Keyword(s):  
High Resolution ◽  
Mating Type ◽  
Chromatin Structure ◽  
Micrococcal Nuclease ◽  
Histone H4 ◽  
Type Locus ◽  
Amino Terminal ◽  
Regulator Protein ◽  
Chromosome Iii ◽  
Nuclease Mapping

ABSTRACT Genetic and biochemical evidence implicates chromatin structure in the silencing of the two quiescent mating-type loci near the telomeres of chromosome III in yeast. With high-resolution micrococcal nuclease mapping, we show that the HMRa locus has 12 precisely positioned nucleosomes spanning the distance between the E and I silencer elements. The nucleosomes are arranged in pairs with very short linkers; the pairs are separated from one another by longer linkers of ∼20 bp. Both the basic amino-terminal region of histone H4 and the silent information regulator protein Sir3p are necessary for the organized repressive chromatin structure of the silent locus. Compared to HMRa, only small differences in the availability of the TATA box are present for the promoter in the cassette at the active MATa locus. Features of the chromatin structure of this silent locus compared to the previously studied HMLα locus suggest differences in the mechanisms of silencing and may relate to donor selection during mating-type interconversion.

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