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Loop extrusion

Loop extrusion is a major mechanism of nuclear organization. It is a dynamic process in which structural maintenance of chromosomes (SMC) protein complexes progressively grow loops of DNA or chromatin. In this process, SMC complexes, such as condensin or cohesin, bind to DNA/chromatin, use ATP-driven motor activity to reel in DNA, and as a result…

Key components, Biological function & Background

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Key components

NIPBLWAPLCell cycleTranscriptional regulationMitosis
23 related topics

Biological function

Cell divisionCentromereEnhancerPromoterV(D)J recombination
7 related topics

Background

DNA repairHi-C
2 related topics

Evidence for loop extrusion

Sister chromatids
1 related topics

Topics to explore

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Overview

Background

Key components

Evidence for loop extrusion

Biological function

Theoretical models of loop extrusion

Advanced semantic analysis

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Map overview Semantic statistics

Loop extrusion

Nodes50
Edges49
Triples135
Avg. degree1.96
Density0.04
Components1

How this topic connects Entity context

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Loop extrusion

Top relations

related to Biological function · 26
Loop extrusion → As, Cell, Condensin, CTCF, CTCF-dependent, DNA, During, Enhancer, Generally, II, In, Loop, Mitosis, Neurons, Protocadherin, Protocadherins, SMC, T-cell, TAD, TADs
related to Roadblocks of loop extrusion · 23
Loop extrusion → Additionally, As, CTCF, DNA, Extruding, For, Furthermore, However, Loop, MCM, Other, R-loops, Replication, RNA, SA2, SCC1, Some, TADs, The, The C-terminal DNA-binding
related to Modifications and factors for loading/unloading · 20
Loop extrusion → Acetylation, CTCF-bound, DNA, ESCO1, ESCO2, In, Mau2, NIPBL, NSE2, PDS5, Post-translational, SCC2, SCC4, Similarly, SMC, SMC5/6, SUMOylation, The, The SMC, WAPL
related to SMC proteins · 17
Loop extrusion → At, ATP, ATPase, Cohesin, Cycles, Despite, DNA, During, Loop, SMC, SMC1, SMC3, SMC5/6, The, These, Two SMC, Unlike
related to Theoretical models of loop extrusion · 15
Loop extrusion → Bound, Cohesin, CTCF, Extrusion Barriers, II, In, LEF, LEF Translocation, LEF-LEF, LEFs, RNA, Stochastic Binding, These, Unbinding, When LEFs
related to Key components · 8
Loop extrusion → ATP-dependent, DNA, NIPBL/MAU2, Road-blocks, SMC, The, Unloaders, WAPL
related to background · 6
Loop extrusion → At, DNA, For, Hi-C, Loop, The
related to Molecular mechanism · 6
Loop extrusion → Brownian-ratchet, DNA-loop, DNA-pumping, DNA-segment, SMC, The
related to Evidence for the biological role of loop extrusion · 5
Loop extrusion → Depletion, II, In, Most, TADs
is a · 2
Loop extrusion → key mechanism that organizes DNA into loops, major mechanism of nuclear organization

Important terminology Word statistics

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Important terminology

cohesin extrusion loop dna smc chromatin ctcf condensin loops role found lefs proteins process complexes key extruding mechanism loading evidence

Entity relationships Subject–Predicate–Object triples

SubjectPredicateObjectConfidenceSrc
Loop extrusionis amajor mechanism of nuclear organization0.90text
Loop extrusionis akey mechanism that organizes DNA into loops0.90text
ESCO1instance ofAcetylation of cohesin by enzymes0.80text
ESCO2 stabilizes chromatin loopsinstance ofAcetylation of cohesin by enzymes0.80text
particularly at CTCF-bound sitesinstance ofAcetylation of cohesin by enzymes0.80text
CTCF or RNA polymerase II can act as obstaclesinstance ofBound proteins0.80text
stalling or halting LEF motion.Since the exact modalities of LEF dynamics remain uncertaininstance ofBound proteins0.80text
these models provide a flexible framework to explore different hypothetical behaviors of LEFs.In these modelsinstance ofBound proteins0.80text
the statistics of LEFs are characterized by two key physical parametersinstance ofBound proteins0.80text
Loop extrusionrelated to backgroundThe0.60section
Loop extrusionrelated to backgroundDNA0.60section
Loop extrusionrelated to backgroundAt0.60section

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