↓ Skip to main content

Nuclear Bodies and Noncoding RNAs

Overview of attention for book
Cover of 'Nuclear Bodies and Noncoding RNAs'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization
  3. Altmetric Badge
    Chapter 2 Super-Resolution Imaging of Nuclear Bodies by STED Microscopy.
  4. Altmetric Badge
    Chapter 3 High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale.
  5. Altmetric Badge
    Chapter 4 Time-Lapse Imaging of Nuclear Bodies
  6. Altmetric Badge
    Chapter 5 Visualization of Nucleic Acids with Synthetic Exciton-Controlled Fluorescent Oligonucleotide Probes
  7. Altmetric Badge
    Chapter 6 Live CLEM Imaging to Analyze Nuclear Structures at High Resolution
  8. Altmetric Badge
    Chapter 7 Ultrastructural Analysis of Nuclear Bodies Using Electron Microscopy
  9. Altmetric Badge
    Chapter 8 Analyses of Nuclear Proteins and Nucleic Acid Structures Using Atomic Force Microscopy.
  10. Altmetric Badge
    Chapter 9 Genome-Wide Co-Localization Screening of Nuclear Body Components Using a Fluorescently Tagged FLJ cDNA Clone Library.
  11. Altmetric Badge
    Chapter 10 Purification of Specific Chromatin Regions Using Oligonucleotides: Capture Hybridization Analysis of RNA Targets (CHART).
  12. Altmetric Badge
    Chapter 11 RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin.
  13. Altmetric Badge
    Chapter 12 In Situ Dissection of RNA Functional Subunits by Domain-Specific Chromatin Isolation by RNA Purification (dChIRP).
  14. Altmetric Badge
    Chapter 13 Extracting, Enriching, and Identifying Nuclear Body Sub-Complexes Using Label-Based Quantitative Mass Spectrometry.
  15. Altmetric Badge
    Chapter 14 Studying RNA-Binding Protein Interactions with Target mRNAs in Eukaryotic Cells: Native Ribonucleoprotein Immunoprecipitation (RIP) Assays
  16. Altmetric Badge
    Chapter 15 Cross-Linking and Immunoprecipitation of Nuclear RNA-Binding Proteins
  17. Altmetric Badge
    Chapter 16 Purification of Noncoding RNA and Bound Proteins Using FLAG Peptide-Conjugated Antisense-Oligonucleotides.
  18. Altmetric Badge
    Chapter 17 MMCT-Mediated Chromosome Engineering Technique Applicable to Functional Analysis of lncRNA and Nuclear Dynamics
  19. Altmetric Badge
    Chapter 18 Reconstitution of Nucleocytoplasmic Transport Using Digitonin-Permeabilized Cells
  20. Altmetric Badge
    Chapter 19 Genome-Wide Analysis of Long Noncoding RNA Turnover.
  21. Altmetric Badge
    Chapter 20 Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modified DNA Antisense Oligonucleotides.
  22. Altmetric Badge
    Chapter 21 siRNA Screening of Nuclear Proteins
Attention for Chapter 3: High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale.
Altmetric Badge

Mentioned by

twitter
1 tweeter

Citations

dimensions_citation
4 Dimensions

Readers on

mendeley
58 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Chapter title
High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale.
Chapter number 3
Book title
Nuclear Bodies and Noncoding RNAs
Published in
Methods in molecular biology, January 2015
DOI 10.1007/978-1-4939-2253-6_3
Pubmed ID
Book ISBNs
978-1-4939-2252-9, 978-1-4939-2253-6
Authors

Luca Giorgetti, Tristan Piolot, Edith Heard

Abstract

Characterizing the three-dimensional organization of chromosomes is a fundamental goal in molecular biology and will be critical to understand how gene expression is regulated by distal regulatory sequences such as enhancers. Chromosome conformation capture (3C) techniques have recently revealed that the interactions between regulatory elements appear to occur in the context of topologically associating domains (TADs), each spanning few hundreds kilobases, within which the chromatin fiber preferentially interacts. However, 3C-based data represent average interaction probabilities of the chromatin fiber over millions of cells. To understand how variable chromatin conformation is within each TAD, one needs to employ single-cell techniques such as 3D DNA FISH. Given the small size of TADs however (typically <1 Mb), classical DNA FISH design needs to be adapted to achieve high genomic and spatial resolution. Here, we describe a high-resolution 3D DNA FISH approach we recently developed, based on a combination of short plasmid probes and computational correction of optical aberrations. We describe probe design and generation and the 3D DNA FISH procedure. We further discuss how to optimize microscope settings and to implement calibration-bead-assisted computational corrections in order to achieve 50 nm resolution in two-color distance measurements between probes that can be as close as 50 kb along the genome.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 58 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 3 5%
China 1 2%
Italy 1 2%
United States 1 2%
Unknown 52 90%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 22 38%
Researcher 11 19%
Student > Master 10 17%
Student > Bachelor 4 7%
Student > Doctoral Student 2 3%
Other 4 7%
Unknown 5 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 22 38%
Biochemistry, Genetics and Molecular Biology 21 36%
Chemistry 2 3%
Medicine and Dentistry 2 3%
Immunology and Microbiology 1 2%
Other 2 3%
Unknown 8 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 04 January 2015.
All research outputs
#3,799,183
of 4,691,600 outputs
Outputs from Methods in molecular biology
#2,172
of 3,382 outputs
Outputs of similar age
#122,562
of 155,993 outputs
Outputs of similar age from Methods in molecular biology
#267
of 401 outputs
Altmetric has tracked 4,691,600 research outputs across all sources so far. This one is in the 3rd percentile – i.e., 3% of other outputs scored the same or lower than it.
So far Altmetric has tracked 3,382 research outputs from this source. They receive a mean Attention Score of 1.4. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 155,993 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 401 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.