Method to Watch |
Featured
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Research Briefing |
Genome architecture mapping detects transcriptionally active, multiway chromatin contacts
Genome architecture mapping (GAM) enables understanding of 3D genome structure in the nucleus. We directly compared multiplex-GAM and Hi-C data and found that local chromatin interactions were generally detected by both methods, but active genomic regions rich in enhancers that established higher-order contacts were preferentially detected by GAM.
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Article
| Open Access
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
Multiplex-genome architecture mapping (multiplex-GAM) enables rapid, unbiased, ligation-free mapping of genome-wide chromatin interactions.
- Robert A. Beagrie
- , Christoph J. Thieme
- & Ana Pombo
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News & Views |
Mapping beads on strings
DiMeLo-seq leverages immunotethered DNA methyltransferases with long-read sequencing to map the locations of chromatin proteins in their natural context.
- Kami Ahmad
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Method to Watch |
Greater detail in the nucleus
Probing spatially organized DNA and its interacting elements in single cells will deepen our understanding of cell-type-specific gene regulation.
- Lei Tang
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Research Highlight |
Mapping genome structures in single cells
Researchers develop single-cell SPRITE to detect higher-order 3D genome structures in single cells.
- Lei Tang
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Article |
DeepC: predicting 3D genome folding using megabase-scale transfer learning
DeepC uses transfer learning-based deep neural networks for predicting genome folding from megabase-scale DNA sequence.
- Ron Schwessinger
- , Matthew Gosden
- & Jim R. Hughes
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Article |
Predicting 3D genome folding from DNA sequence with Akita
Akita enables three-dimensional genome folding predictions from DNA sequence using a convolutional neural network.
- Geoff Fudenberg
- , David R. Kelley
- & Katherine S. Pollard
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Article |
3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing
OligoFISSEQ combines Oligopaints with fluorescence in situ sequencing to enable the 3D mapping of many regions across the genome in human cells to interrogate genome organization at improved genomic resolution. OligoFISSEQ is compatible with immunochemistry and OligoSTORM for super-resolution imaging.
- Huy Q. Nguyen
- , Shyamtanu Chattoraj
- & C.-ting Wu
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Research Highlight |
Radial genome organization
Sequencing gradually digested chromatin along the nuclear radius enables the mapping of radial organization of chromatin in human cells.
- Lei Tang
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Article |
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
Single-nucleus methyl-3C sequencing jointly interrogates 3D chromatin organization and DNA methylation in human cells, and these joint measurements more accurately distinguish different cell types than either unimodal method.
- Dong-Sung Lee
- , Chongyuan Luo
- & Joseph R. Ecker
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Brief Communication |
HiChIRP reveals RNA-associated chromosome conformation
HiChIRP combines a modified chromosome conformation capture protocol with enrichment of RNA-associated chromosome conformation to visualize genome-wide looping linked to an RNA of interest.
- Maxwell R. Mumbach
- , Jeffrey M. Granja
- & Howard Y. Chang
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Research Highlight |
Variability in genome structure
Comparisons of genome organization in many individual cells with high-throughput FISH show extensive variation.
- Nicole Rusk
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Research Highlight |
Diploid genome in 3D
Dip-C, a descendent of the 3C method, reveals 3D genome structures of single diploid human cells.
- Lei Tang
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Article |
Trac-looping measures genome structure and chromatin accessibility
Insertion of a bivalent linker between two regions of interest allows chromatin contacts to be probed without proximity ligation.
- Binbin Lai
- , Qingsong Tang
- & Keji Zhao
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Research Highlight |
Polymer model predicts chromatin folding
3C-based methods and polymer modeling indentify the impact of structural variants.
- Lei Tang
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Research Highlights |
Seeing DNA
DNA and chromatin structures can be visualized in situ with electron tomography.
- Zachary J Lapin
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Research Highlights |
Native chromosome conformation
Isolation of nuclei in an isotonic buffer retains chromosome loops and allows the probing of intrinsic loop conformation.
- Nicole Rusk
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Technology Feature |
Genomics in 3D and 4D
DNA folding shapes gene expression. Emerging techniques promise to reveal the intricacies of this architectural language of chromosomes.
- Vivien Marx
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Methods in Brief |
Imaging chromosome organization
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Article |
UMI-4C for quantitative and targeted chromosomal contact profiling
UMI-4C is a rapid, simplified barcoding approach to targeted chromatin conformation capture that produces high-complexity libraries from low sample input, is easily multiplexed and gives a quantitative, statistically defined readout.
- Omer Schwartzman
- , Zohar Mukamel
- & Amos Tanay
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Research Highlights |
Retraining an editor as a mapmaker
A sequence-specific labeling system based on CRISPR/Cas9 enables simultaneous imaging of multiple chromosomal sites in live cells.
- Michael Eisenstein
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Perspective |
Genome-wide footprinting: ready for prime time?
The Perspective by Sung, Baek and Hager discusses consensus, remaining issues and hurdles for genomic footprinting.
- Myong-Hee Sung
- , Songjoon Baek
- & Gordon L Hager
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Perspective |
Genomic footprinting
This Perspective by Vierstra and Stamatoyannopoulos discusses the prospects and challenges of genomic footprinting applied to complex genomes.
- Jeff Vierstra
- & John A Stamatoyannopoulos
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Analysis |
Analysis of computational footprinting methods for DNase sequencing experiments
This comparison of ten computational methods for detecting transcription factor binding sites in DNase hypersensitive regions in the genome determines which methods work consistently well, how DNase-seq experimental artifacts should be corrected for and which score is best for ranking methods.
- Eduardo G Gusmao
- , Manuel Allhoff
- & Ivan G Costa
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Method to Watch |
Unraveling nuclear architecture
New approaches are needed to see the dynamics of 3D chromatin structure at high resolution and throughput.
- Nicole Rusk
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Research Highlights |
A single cell's open chromatin
Increasing the sensitivity of DNase-seq allows chromatin accessibility to be profiled from very low numbers of cells.
- Nicole Rusk
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Methods in Brief |
Mapping accessible chromatin in single cells
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Methods in Brief |
Chromatin accessibility in single cells
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Research Highlights |
Transcription factors without footprints
A tool to find specific footprint signatures on DNA shows that regulatory proteins with short residency time do not leave footprints.
- Nicole Rusk
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Brief Communication |
3D genome reconstruction from chromosomal contacts
ShRec3D (shortest-path reconstruction in 3D) converts sparse chromosome contact maps into spatial distances followed by 3D reconstruction.
- Annick Lesne
- , Julien Riposo
- & Julien Mozziconacci
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Methods in Brief |
Cell type–specific ChIP
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Article |
Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH
By separately sequencing and mapping smaller and larger DNase I fragments from the same DNase I digestion experiment, the approach allows simultaneous profiling of transcription factor footprints relative to nucleosome occupancy.
- Jeff Vierstra
- , Hao Wang
- & John A Stamatoyannopoulos
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Research Highlights |
Finding function in the folds
Single-cell modeling of chromosomal organization could help scientists untangle how genomic organization informs function and vice versa.
- Michael Eisenstein
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Brief Communication |
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Segway, a method using dynamic Bayesian network techniques, segments a genome and produces functional labels defined by histone modifications, transcription-factor binding, locations of open chromatin and other genome-wide functional data.
- Michael M Hoffman
- , Orion J Buske
- & William Stafford Noble
From genome structure to function