Program in Gene Function and Expression,
Department of Biochemistry and Molecular Pharmacology,
Department of Systems Biology,
Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology
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Capturing chromosome conformation.
Science (New York, N.Y.) Feb, 2002 | Pubmed ID: 11847345
A closer look at long-range chromosomal interactions.
Trends in biochemical sciences Jun, 2003 | Pubmed ID: 12826398
A mechanical basis for chromosome function.
Proceedings of the National Academy of Sciences of the United States of America Aug, 2004 | Pubmed ID: 15299144
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.
Molecular cell Feb, 2005 | Pubmed ID: 15694345
The three 'C' s of chromosome conformation capture: controls, controls, controls.
Nature methods Jan, 2006 | Pubmed ID: 16369547
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications.
Proceedings of the National Academy of Sciences of the United States of America Aug, 2006 | Pubmed ID: 16891414
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.
Genome research Oct, 2006 | Pubmed ID: 16954542
Mapping networks of physical interactions between genomic elements using 5C technology.
Nature protocols , 2007 | Pubmed ID: 17446898
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature Jun, 2007 | Pubmed ID: 17571346
GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p.
Genome biology , 2007 | Pubmed ID: 17577398
Quantitative analysis of chromosome conformation capture assays (3C-qPCR).
Nature protocols , 2007 | Pubmed ID: 17641637
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex.
Nature cell biology Oct, 2007 | Pubmed ID: 17828248
Mapping chromatin interactions by chromosome conformation capture.
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] May, 2006 | Pubmed ID: 18265379
Chromosome conformation capture carbon copy technology.
Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.] Oct, 2007 | Pubmed ID: 18265398
A mechanism for Ikaros regulation of human globin gene switching.
British journal of haematology May, 2008 | Pubmed ID: 18318763
Gene regulation in the third dimension.
Science (New York, N.Y.) Mar, 2008 | Pubmed ID: 18369139
Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction.
The Journal of biological chemistry Dec, 2008 | Pubmed ID: 18930918
Long-range chromosomal interactions and gene regulation.
Molecular bioSystems Nov, 2008 | Pubmed ID: 18931780
Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C).
Methods in molecular biology (Clifton, N.J.) , 2009 | Pubmed ID: 18951182
Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery.
Genes & development Apr, 2009 | Pubmed ID: 19390086
Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions.
PLoS genetics May, 2009 | Pubmed ID: 19424429
Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization.
EMBO reports Jul, 2009 | Pubmed ID: 19525922
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening.
PLoS genetics Jun, 2009 | Pubmed ID: 19543368
Determining spatial chromatin organization of large genomic regions using 5C technology.
Methods in molecular biology (Clifton, N.J.) , 2009 | Pubmed ID: 19588094
My5C: web tools for chromosome conformation capture studies.
Nature methods Oct, 2009 | Pubmed ID: 19789528
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science (New York, N.Y.) Oct, 2009 | Pubmed ID: 19815776
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
Nucleic acids research Jul, 2010 | Pubmed ID: 20360044
Integrating one-dimensional and three-dimensional maps of genomes.
Journal of cell science Jun, 2010 | Pubmed ID: 20519580
Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2010 | Pubmed ID: 20616024
Mediator and cohesin connect gene expression and chromatin architecture.
Nature Sep, 2010 | Pubmed ID: 20720539
Genomics tools for unraveling chromosome architecture.
Nature biotechnology Oct, 2010 | Pubmed ID: 20944601
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.
Nature structural & molecular biology Jan, 2011 | Pubmed ID: 21131981
Sister cohesion and structural axis components mediate homolog bias of meiotic recombination.
Cell Dec, 2010 | Pubmed ID: 21145459
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.
Nature Apr, 2011 | Pubmed ID: 21423168
Chromatin globules: a common motif of higher order chromosome structure?
Current opinion in cell biology Jun, 2011 | Pubmed ID: 21489772
Translocation mapping exposes the risky lifestyle of B cells.
Cell Sep, 2011 | Pubmed ID: 21962501
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.
Molecular cell Oct, 2011 | Pubmed ID: 22017872
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.
Nature methods Dec, 2011 | Pubmed ID: 22037702
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.
Nature methods Dec, 2011 | Pubmed ID: 22037705
THE STRUCTURE AND FUNCTION OF CHROMATIN AND CHROMOSOMES.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing , 2012 | Pubmed ID: 22174298
Evidence for transcript networks composed of chimeric RNAs in human cells.
PloS one , 2012 | Pubmed ID: 22238572
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.
Cell Mar, 2012 | Pubmed ID: 22341456
Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Nature May, 2012 | Pubmed ID: 22495304
The context of gene expression regulation.
F1000 biology reports , 2012 | Pubmed ID: 22500194
MORC family ATPases required for heterochromatin condensation and gene silencing.
Science (New York, N.Y.) Jun, 2012 | Pubmed ID: 22555433
CTCF and cohesin help neurons raise their self-awareness.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2012 | Pubmed ID: 22615386
Hi-C: a comprehensive technique to capture the conformation of genomes.
Methods (San Diego, Calif.) Nov, 2012 | Pubmed ID: 22652625
An encyclopedia of mouse DNA elements (Mouse ENCODE).
Genome biology Aug, 2012 | Pubmed ID: 22889292
Analysis of long-range chromatin interactions using Chromosome Conformation Capture.
Methods (San Diego, Calif.) Nov, 2012 | Pubmed ID: 22903059
HiTC: exploration of high-throughput 'C' experiments.
Bioinformatics (Oxford, England) Nov, 2012 | Pubmed ID: 22923296
Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Nature methods Oct, 2012 | Pubmed ID: 22941365
The accessible chromatin landscape of the human genome.
Nature Sep, 2012 | Pubmed ID: 22955617
The long-range interaction landscape of gene promoters.
Nature Sep, 2012 | Pubmed ID: 22955621
From cells to chromatin: capturing snapshots of genome organization with 5C technology.
Methods (San Diego, Calif.) Nov, 2012 | Pubmed ID: 23137922
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.
Genome research Feb, 2013 | Pubmed ID: 23152449
3C-based technologies to study the shape of the genome.
Methods (San Diego, Calif.) Nov, 2012 | Pubmed ID: 23199640
The hierarchy of the 3D genome.
Molecular cell Mar, 2013 | Pubmed ID: 23473598
Nuclear biology: what's been most surprising?
Cell Mar, 2013 | Pubmed ID: 23616995
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
Nature reviews. Genetics Jun, 2013 | Pubmed ID: 23657480
Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Cell Jun, 2013 | Pubmed ID: 23706625
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Genome research Dec, 2013 | Pubmed ID: 24002784
Organization of the mitotic chromosome.
Science (New York, N.Y.) Nov, 2013 | Pubmed ID: 24200812
Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny.
Genes & development Nov, 2013 | Pubmed ID: 24240234
High-throughput genome scaffolding from in vivo DNA interaction frequency.
Nature biotechnology Dec, 2013 | Pubmed ID: 24270850
Defining functional DNA elements in the human genome.
Proceedings of the National Academy of Sciences of the United States of America Apr, 2014 | Pubmed ID: 24753594
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.
Cell May, 2014 | Pubmed ID: 24813616
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Proceedings of the National Academy of Sciences of the United States of America Aug, 2014 | Pubmed ID: 25275169
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.
Nature Dec, 2014 | Pubmed ID: 25307058
Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture.
Epigenetics & chromatin , 2014 | Pubmed ID: 25435919
The Hitchhiker's guide to Hi-C analysis: practical guidelines.
Methods (San Diego, Calif.) Jan, 2015 | Pubmed ID: 25448293
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Genome research Apr, 2015 | Pubmed ID: 25677180
Condensin-driven remodelling of X chromosome topology during dosage compensation.
Nature Jul, 2015 | Pubmed ID: 26030525
Chromosome Conformation Capture (3C) in Budding Yeast.
Cold Spring Harbor protocols Jun, 2015 | Pubmed ID: 26034304
Randomized ligation control for chromosome conformation capture.
Cold Spring Harbor protocols Jun, 2015 | Pubmed ID: 26034305
Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast.
Cold Spring Harbor protocols Jun, 2015 | Pubmed ID: 26034306
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.
Cell Jul, 2015 | Pubmed ID: 26119342
Hi-C in Budding Yeast.
Cold Spring Harbor protocols Jul, 2015 | Pubmed ID: 26134906
Measuring Chromatin Structure in Budding Yeast.
Cold Spring Harbor protocols Jul, 2015 | Pubmed ID: 26134912
The yeast genome undergoes significant topological reorganization in quiescence.
Nucleic acids research Sep, 2015 | Pubmed ID: 26202961
Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis.
Genes & development Aug, 2015 | Pubmed ID: 26253537
Structural and functional diversity of Topologically Associating Domains.
FEBS letters Oct, 2015 | Pubmed ID: 26348399
Genome-wide maps of nuclear lamina interactions in single human cells.
Cell Sep, 2015 | Pubmed ID: 26365489
Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.
Genome biology Sep, 2015 | Pubmed ID: 26415882
Long-Range Chromatin Interactions.
Cold Spring Harbor perspectives in biology Oct, 2015 | Pubmed ID: 26430217
High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.
Molecular cell Oct, 2015 | Pubmed ID: 26431028
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Genome biology , 2015 | Pubmed ID: 26619908
The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.
Cell reports Dec, 2015 | Pubmed ID: 26655901
Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.
American journal of human genetics Jan, 2016 | Pubmed ID: 26748519
Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire.
Cell reports Feb, 2016 | Pubmed ID: 26804913
Activation of proto-oncogenes by disruption of chromosome neighborhoods.
Science (New York, N.Y.) Mar, 2016 | Pubmed ID: 26940867
The 3D Genome as Moderator of Chromosomal Communication.
Cell Mar, 2016 | Pubmed ID: 26967279
TAD disruption as oncogenic driver.
Current opinion in genetics & development Feb, 2016 | Pubmed ID: 27111891
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.
Cell stem cell May, 2016 | Pubmed ID: 27152443
Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma.
American journal of respiratory and critical care medicine Dec, 2016 | Pubmed ID: 27367781
SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.
Genome research Sep, 2016 | Pubmed ID: 27435934
Structural organization of the inactive X chromosome in the mouse.
Nature Jul, 2016 | Pubmed ID: 27437574
RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.
Biochimica et biophysica acta Nov, 2016 | Pubmed ID: 27514584
Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2016 | Pubmed ID: 27791029
Mapping the 3D genome: Aiming for consilience.
Nature reviews. Molecular cell biology Nov, 2016 | Pubmed ID: 27869158
CTCF-mediated topological boundaries during development foster appropriate gene regulation.
Genes & development 12, 2016 | Pubmed ID: 28087711
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.
Molecular cell Feb, 2017 | Pubmed ID: 28157505
Epigenetic characteristics of the mitotic chromosome in 1D and 3D.
Critical reviews in biochemistry and molecular biology Apr, 2017 | Pubmed ID: 28228067
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.
Methods (San Diego, Calif.) Jul, 2017 | Pubmed ID: 28435001
Shelterin components mediate genome reorganization in response to replication stress.
Proceedings of the National Academy of Sciences of the United States of America May, 2017 | Pubmed ID: 28490498
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Cell May, 2017 | Pubmed ID: 28525758
SMC complexes differentially compact mitotic chromosomes according to genomic context.
Nature cell biology Sep, 2017 | Pubmed ID: 28825700
The 4D nucleome project.
Nature 09, 2017 | Pubmed ID: 28905911
The cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.
Genes & development Nov, 2017 | Pubmed ID: 29273679
A pathway for mitotic chromosome formation.
Science (New York, N.Y.) Feb, 2018 | Pubmed ID: 29348367
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.
Nature methods Jun, 2018 | Pubmed ID: 29735996
CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.
Cell Jun, 2018 | Pubmed ID: 29958106
Integrative detection and analysis of structural variation in cancer genomes.
Nature genetics Oct, 2018 | Pubmed ID: 30202056
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.
Nature genetics Dec, 2018 | Pubmed ID: 30374068
Higher-Order Organization Principles of Pre-translational mRNPs.
Molecular cell Nov, 2018 | Pubmed ID: 30415953
The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome.
Nature communications Jan, 2019 | Pubmed ID: 30604745
CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.
Genome research Feb, 2019 | Pubmed ID: 30655336
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
Cell Mar, 2019 | Pubmed ID: 30799036
Measuring the reproducibility and quality of Hi-C data.
Genome biology Mar, 2019 | Pubmed ID: 30890172
Heterochromatin drives compartmentalization of inverted and conventional nuclei.
Nature Jun, 2019 | Pubmed ID: 31168090
Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.
Stem cell reports Jul, 2019 | Pubmed ID: 31231024
Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei.
Nature Aug, 2019 | Pubmed ID: 31375785
Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
Cell stem cell Nov, 2019 | Pubmed ID: 31495782
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.
Nature communications Oct, 2019 | Pubmed ID: 31582744
Highly structured homolog pairing reflects functional organization of the Drosophila genome.
Nature communications Oct, 2019 | Pubmed ID: 31582763
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.
Nature cell biology Nov, 2019 | Pubmed ID: 31685986
Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.
Molecular cell Jan, 2020 | Pubmed ID: 31704182
SPEN integrates transcriptional and epigenetic control of X-inactivation.
Nature 02, 2020 | Pubmed ID: 32025035
Ultrastructural Details of Mammalian Chromosome Architecture.
Molecular cell May, 2020 | Pubmed ID: 32213324
Mechanisms and Functions of Chromosome Compartmentalization.
Trends in biochemical sciences May, 2020 | Pubmed ID: 32311333
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature Jul, 2020 | Pubmed ID: 32728249
Large domains of heterochromatin direct the formation of short mitotic chromosome loops.
eLife Sep, 2020 | Pubmed ID: 32915140
Multi-contact 3C reveals that the human genome during interphase is largely not entangled.
Nature structural & molecular biology Dec, 2020 | Pubmed ID: 32929283
Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain.
The EMBO journal Nov, 2020 | Pubmed ID: 32935369
Detecting chromatin interactions between and along sister chromatids with SisterC.
Nature methods Oct, 2020 | Pubmed ID: 32968250
Is Involved in Corneal Stroma Development by Regulating Neural Crest Migration.
International journal of molecular sciences Oct, 2020 | Pubmed ID: 33096935
Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML.
JCI insight Feb, 2021 | Pubmed ID: 33351783
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
Nature genetics Mar, 2021 | Pubmed ID: 33574602
Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.
Nature genetics May, 2021 | Pubmed ID: 33927399
Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.
Genome biology and evolution Jun, 2021 | Pubmed ID: 33964136
Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture.
Current protocols Jul, 2021 | Pubmed ID: 34286910
Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.
eLife Aug, 2021 | Pubmed ID: 34406118
Systematic evaluation of chromosome conformation capture assays.
Nature methods Sep, 2021 | Pubmed ID: 34480151
Symbiodinium microadriaticum (coral microalgal endosymbiont).
Trends in genetics : TIG Nov, 2021 | Pubmed ID: 34518054
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.
Cold Spring Harbor perspectives in biology Jul, 2022 | Pubmed ID: 34518339
Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.
Nature communications Oct, 2021 | Pubmed ID: 34716321
Spatial organization of transcribed eukaryotic genes.
Nature cell biology Mar, 2022 | Pubmed ID: 35177821
Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.
Scientific reports Mar, 2022 | Pubmed ID: 35304523
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Nature May, 2022 | Pubmed ID: 35474001
Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis.
BMC biology May, 2022 | Pubmed ID: 35549698
CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.
Nature cell biology Oct, 2022 | Pubmed ID: 36202971
Regulation of the mitotic chromosome folding machines.
The Biochemical journal Oct, 2022 | Pubmed ID: 36268993
A cohesin traffic pattern genetically linked to gene regulation.
Nature structural & molecular biology Dec, 2022 | Pubmed ID: 36482254
Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
Nature structural & molecular biology Jan, 2023 | Pubmed ID: 36550219
Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Nature structural & molecular biology Jan, 2023 | Pubmed ID: 36564591
Nynke L. van Berkum*,1,
Erez Lieberman-Aiden*,2,3,4,5,
Louise Williams*,2,
Maxim Imakaev6,
Andreas Gnirke2,
Leonid A. Mirny3,6,
Job Dekker1,
Eric S. Lander2,7,8
1Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,
2, Broad Institute of Harvard and Massachusetts Institute of Technology,
3Division of Health Sciences and Technology, Massachusetts Institute of Technology,
4Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University ,
5Department of Applied Mathematics, Harvard University ,
6Department of Physics, Massachusetts Institute of Technology,
7Department of Systems Biology, Harvard Medical School,
8Department of Biology, Massachusetts Institute of Technology
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