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lncRNA and gene looping: what's the connection?

Shibayama Y, Fanucchi S, Magagula L, Mhlanga MM - Transcription (2014)

Bottom Line: Recent functional studies have unveiled the significant role chromatin topology plays in gene regulation.Several lines of evidence suggest genes access necessary factors for transcription by forming chromatin loops.A clearer picture of the players involved in chromatin organization, including lncRNA, is emerging.

View Article: PubMed Central - PubMed

Affiliation: a Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research; Pretoria, Gauteng, South Africa.

ABSTRACT
Recent functional studies have unveiled the significant role chromatin topology plays in gene regulation. Several lines of evidence suggest genes access necessary factors for transcription by forming chromatin loops. A clearer picture of the players involved in chromatin organization, including lncRNA, is emerging.

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Figure 2. Topological domains and multigene complexes. (A) Chromosomes are organized into subchromosomal domains, referred to as TADs. CTCF, a sequence-specific DNA-binding protein, binds to consensus sites (CS) that frequently flank genes.24 At CS sites, the multiprotein cohesin ‘ring-like’ complex (including the Smc1-Smc3 heterodimer, Rad21 and Scc3/SA1/SA2) is loaded onto chromatin by Nipbl. The mediator complex may also be recruited to CTCF and/or cohesin occupied chromatin to stabilize loop topology, and regulate transcription initiation and elongation.21 (B) Enhancer-promoter and promoter-promoter interactions in a single multigene complex. eRNA may possibly hold together the entire multigene complex.
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Figure 2: Figure 2. Topological domains and multigene complexes. (A) Chromosomes are organized into subchromosomal domains, referred to as TADs. CTCF, a sequence-specific DNA-binding protein, binds to consensus sites (CS) that frequently flank genes.24 At CS sites, the multiprotein cohesin ‘ring-like’ complex (including the Smc1-Smc3 heterodimer, Rad21 and Scc3/SA1/SA2) is loaded onto chromatin by Nipbl. The mediator complex may also be recruited to CTCF and/or cohesin occupied chromatin to stabilize loop topology, and regulate transcription initiation and elongation.21 (B) Enhancer-promoter and promoter-promoter interactions in a single multigene complex. eRNA may possibly hold together the entire multigene complex.

Mentions: High-throughput chromosome conformation capture in Drosophila, mouse and human cells have suggested that genomes are segregated into discrete megabase-sized local domains termed “topologically associating domains” or “topological domains” (TADs) (Fig. 2A).26-28 The highly stable and invariant nature of these domains suggests that they are a pervasive and intrinsic mechanism of chromatin organization within genomes. A characteristic feature of TADs is the enrichment of intra-domain chromatin contacts.26 FISH results confirm a spatial distinction between domains and contact arrangements within domains, as loci within a single domain are closer in nuclear space than those in different domains despite having similar genomic distances from one another.26,28 TADS therefore may provide a layer of structural regulation governing the principle of long-range chromatin contact.


lncRNA and gene looping: what's the connection?

Shibayama Y, Fanucchi S, Magagula L, Mhlanga MM - Transcription (2014)

Figure 2. Topological domains and multigene complexes. (A) Chromosomes are organized into subchromosomal domains, referred to as TADs. CTCF, a sequence-specific DNA-binding protein, binds to consensus sites (CS) that frequently flank genes.24 At CS sites, the multiprotein cohesin ‘ring-like’ complex (including the Smc1-Smc3 heterodimer, Rad21 and Scc3/SA1/SA2) is loaded onto chromatin by Nipbl. The mediator complex may also be recruited to CTCF and/or cohesin occupied chromatin to stabilize loop topology, and regulate transcription initiation and elongation.21 (B) Enhancer-promoter and promoter-promoter interactions in a single multigene complex. eRNA may possibly hold together the entire multigene complex.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215167&req=5

Figure 2: Figure 2. Topological domains and multigene complexes. (A) Chromosomes are organized into subchromosomal domains, referred to as TADs. CTCF, a sequence-specific DNA-binding protein, binds to consensus sites (CS) that frequently flank genes.24 At CS sites, the multiprotein cohesin ‘ring-like’ complex (including the Smc1-Smc3 heterodimer, Rad21 and Scc3/SA1/SA2) is loaded onto chromatin by Nipbl. The mediator complex may also be recruited to CTCF and/or cohesin occupied chromatin to stabilize loop topology, and regulate transcription initiation and elongation.21 (B) Enhancer-promoter and promoter-promoter interactions in a single multigene complex. eRNA may possibly hold together the entire multigene complex.
Mentions: High-throughput chromosome conformation capture in Drosophila, mouse and human cells have suggested that genomes are segregated into discrete megabase-sized local domains termed “topologically associating domains” or “topological domains” (TADs) (Fig. 2A).26-28 The highly stable and invariant nature of these domains suggests that they are a pervasive and intrinsic mechanism of chromatin organization within genomes. A characteristic feature of TADs is the enrichment of intra-domain chromatin contacts.26 FISH results confirm a spatial distinction between domains and contact arrangements within domains, as loci within a single domain are closer in nuclear space than those in different domains despite having similar genomic distances from one another.26,28 TADS therefore may provide a layer of structural regulation governing the principle of long-range chromatin contact.

Bottom Line: Recent functional studies have unveiled the significant role chromatin topology plays in gene regulation.Several lines of evidence suggest genes access necessary factors for transcription by forming chromatin loops.A clearer picture of the players involved in chromatin organization, including lncRNA, is emerging.

View Article: PubMed Central - PubMed

Affiliation: a Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research; Pretoria, Gauteng, South Africa.

ABSTRACT
Recent functional studies have unveiled the significant role chromatin topology plays in gene regulation. Several lines of evidence suggest genes access necessary factors for transcription by forming chromatin loops. A clearer picture of the players involved in chromatin organization, including lncRNA, is emerging.

Show MeSH