Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, Erez; Berkum, Nynke L. van; Williams, Louise; Imakaev, Maxim; Ragoczy, Tobias; Telling, Agnes; Amit, Ido; Lajoie, Bryan R.; Sabo, Peter J.; Dorschner, Michael O.; Sandstrom, Richard; Bernstein, B; Bender, Michael A.; Groudine, Mark; Gnirke, Andreas; Stamatoyannopoulos, J; Mirny, Leonid A.; Lander, Eric S.; Dekker, Job

doi:10.1126/science.1181369

Cited by 7,837 publications

(10,118 citation statements)

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“…[10], see Methods for details) and mutual ranks of gene co-expression rates (provided by COXPRESdb[11]). We controlled the effect of transcription factors on co-expression using transcription control similarity (TCS, see Methods for details) [12], and used 6,084 genes with both TF annotation (from ITFP[13]) and co-expression information for analyses.…”

Section: Resultsmentioning

confidence: 99%

“…One of the well-known models for such structure is open and closed chromatin [10,12]. Under an assumption that sequence-neighboring genes have a similar chromatin structure, N. Batada et al found that these genes have higher co-expression rates than separate ones [12].…”

Section: Resultsmentioning

confidence: 99%

“…GSE18199 [10]. Both observed interactions (OH) and Pearson correlation of them (PC) were used in our analyses.…”

Section: Methodsmentioning

confidence: 99%

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Human transcriptional interactome of chromatin contribute to gene co-expression

Dong

Chen

et al. 2010

BMC Genomics

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BackgroundTranscriptional interactome of chromatin is one of the important mechanisms in gene transcription regulation. By chromatin conformation capture and 3D FISH experiments, several chromatin interactions cases among sequence-distant genes or even inter-chromatin genes were reported. However, on genomics level, there is still little evidence to support these mechanisms. Recently based on Hi-C experiment, a genome-wide picture of chromatin interactions in human cells was presented. It provides a useful material for analysing whether the mechanism of transcriptional interactome is common.ResultsThe main work here is to demonstrate whether the effects of transcriptional interactome on gene co-expression exist on genomic level. While controlling the effects of transcription factors control similarities (TCS), we tested the correlation between Hi-C interaction and the mutual ranks of gene co-expression rates (provided by COXPRESdb) of intra-chromatin gene pairs. We used 6,084 genes with both TF annotation and co-expression information, and matched them into 273,458 pairs with similar Hi-C interaction ranks in different cell types. The results illustrate that co-expression is strongly associated with chromatin interaction. Further analysis using GO annotation reveals potential correlation between gene function similarity, Hi-C interaction and their co-expression.ConclusionsAccording to the results in this research, the intra-chromatin interactome may have relation to gene function and associate with co-expression. This study provides evidence for illustrating the effect of transcriptional interactome on transcription regulation.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Human transcriptional interactome of chromatin contribute to gene co-expression

Dong

Chen

et al. 2010

BMC Genomics

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“…The improper coordination of chromosome condensation and segregation during the cell cycle can lead to important structural abnormalities and result in cell death or diseases such as cancer (Valton & Dekker, 2016). In recent years, major advances in imaging and chromosome conformation capture approaches (Dekker et al , 2002; Lieberman‐Aiden et al , 2009; 3C, Hi‐C) have complemented earlier work by describing at an unprecedented resolution the multiple hierarchical layers of genome organization. A variety of remarkable 3D chromosomal structures have been described in a number of species, including in unicellular organisms such as bacteria and yeasts.…”

Section: Introductionmentioning

confidence: 99%

“…To explore new chromosomal structural features over the cell cycle progression, we analyzed the internal folding and overall organization of S. cerevisiae genome over 15 synchronized time points and the role of cohesin and condensin using Hi‐C (Dekker et al , 2002; Lieberman‐Aiden et al , 2009). This analysis provides a broad overview and in‐depth insight on SMC‐dependent structural transitions resulting in chromosome individualization and segregation, including a potential role for a condensin‐dependent loop in contributing to the segregation of the rDNA cluster.…”

Section: Introductionmentioning

confidence: 99%

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

et al. 2017

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Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome‐wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher‐order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions. During replication, cohesion establishment promotes numerous long‐range intra‐chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle. Formation of a condensin‐dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin‐mediated forces may also directly facilitate segregation. This work therefore comprehensively recapitulates cell cycle‐dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division.

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Introduction and Historical Overview of DNA Sequencing

Nelson

Snyder

Gardner

et al. 2011

CP Molecular Biology

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The process of DNA sequencing has made tremendous strides in throughput, improved accuracy, ease of production, and lowered cost. As the practice of DNA sequencing has improved, so has the downstream data analysis with sophisticated databases and bioinformatics tools. Together, these advances have enlarged the number of applications upon which DNA sequencing can be brought to bear. This introductory unit provides a description of DNA sequencing with a focus on current and "NextGen" (second and third generation) automated technologies and applications. Supplement 96 Figure 7.0.2 General strategy for DNA sequencing.To sequence a fragment of DNA, a set of radiolabeled single-stranded oligonucleotides is generated in four separate reactions. In each of the four reactions, the oligonucleotides have one fixed end and one end that terminates sequentially at each A, T, G, or C, respectively. The products of each reaction are fractionated by electrophoresis on adjacent lanes of a high-resolution polyacrylamide gel. After autoradiography, the DNA sequence can be "read" directly from the gel.

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Cited by 7,837 publications

References 35 publications

Human transcriptional interactome of chromatin contribute to gene co-expression

Human transcriptional interactome of chromatin contribute to gene co-expression

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

Introduction and Historical Overview of DNA Sequencing

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