3D clustering of co-regulated genes and its effect on gene expression

Du, Manyu; Bai, Lu

doi:10.1007/s00294-017-0712-9

Cited by 11 publications

(10 citation statements)

References 38 publications

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“…It will be interesting next to study how viral DNA contacts modulate cellular gene expression. Several studies identified clustering of co-regulated genes that cooperate with each other to enhance gene expression 48 , 49 . Moreover it has been shown that some genes in the cluster can influence the transcription of the other, highlighting the importance of this 3D organization in transcriptional regulation 49 , 50 .…”

Section: Discussionmentioning

confidence: 99%

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

et al. 2018

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Whether non-integrated viral DNAs distribute randomly or target specific positions within the higher-order architecture of mammalian genomes remains largely unknown. Here we use Hi-C and viral DNA capture (CHi-C) in primary human hepatocytes infected by either hepatitis B virus (HBV) or adenovirus type 5 (Ad5) virus to show that they adopt different strategies in their respective positioning at active chromatin. HBV contacts preferentially CpG islands (CGIs) enriched in Cfp1 a factor required for its transcription. These CGIs are often associated with highly expressed genes (HEG) and genes deregulated during infection. Ad5 DNA interacts preferentially with transcription start sites (TSSs) and enhancers of HEG, as well as genes upregulated during infection. These results show that DNA viruses use different strategies to infiltrate genomic 3D networks and target specific regions. This targeting may facilitate the recruitment of transcription factors necessary for their own replication and contribute to the deregulation of cellular gene expression.

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Section: Discussionmentioning

confidence: 99%

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

et al. 2018

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“…The 3C technique (chromosome conformation capture), via sequential formaldehyde cross linking, fragmentation and re-ligation of the cross-linked chromatin, allows identification of chromosomal elements interacted with each other in term of spatial proximity [ 21 ]. Considering the difficulty to establish HBV infection cell models for continues passage, even by using of HepG2-NTCP and PHH under our conditions, in this study we took the advantage of the recombinant covalently closed circular DNA (rcccDNA) cell model for producing a cccDNA surrogate [ 10–20 ]. By 3C technique, we did detect the spatial interaction between HBV minichromosome and 19p13.11 locus of host chromosome in Huh7 and HepG2 cells.…”

Section: Discussionmentioning

confidence: 99%

“…In the nucleus, both intrachromosomal and interchromosomal long-range associations have been demonstrated to bring widely separated functional DNA elements into close spatial proximity and create interactions between these elements [10][11]. For instance, the expression of human neuroglobin gene is controlled by a distal regulatory element located -70 kb upstream from the gene in neuroblastoma cells [12].…”

Section: Introductionmentioning

confidence: 99%

Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11

Shen

Feng

Mao

et al. 2020

Emerging Microbes & Infections

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HBV cccDNA stably exists in the nuclei of infected cells as an episomal munichromosome which is responsible for viral persistence and failure of current antiviral treatments. However, the regulatory mechanism of cccDNA transcription by viral and host cellular factors is not well understood. In this study, we investigated whether cccDNA could be recruited into a specific region of the nucleus via specific interaction with a cellular chromatin to regulate its transcription activity. To investigate this hypothesis, we used chromosome conformation capture (3C) technology to search for the potential interaction of cccDNA and cellular chromatin through rcccDNA transfection in hepatoma cells and found that cccDNA is specifically associated with human chromosome 19p13.11 region, which contains a highly active enhancer element. We also confirmed that cellular transcription factor Yin-Yang 1 (YY1) and viral protein HBx mediated the spatial regulation of HBV cccDNA transcription by 19p13.11 enhancer. Thus, These findings indicate that YY1 and HBx mediate the recruitment of HBV cccDNA minichromosomes to 19p13.11 region for transcription activation, and YY1 may present as a novel therapeutic target against HBV infection.

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“…It is possible that condensin-mediated clustering establishes structures much like 'transcription factories', in which co-regulated genes are clustered together to allow enrichment of regulators in one place (Branco and Pombo 2006;Du and Bai 2017). In S. pombe, reduction in tRNA gene clustering resulted in increased transcription (Iwasaki et al 2010).…”

Section: Condensin-mediated Clustering Of Specific Genomic Loci Inclumentioning

confidence: 99%

Condensin action and compaction

2018

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Condensin is a multi-subunit protein complex that belongs to the family of structural maintenance of chromosomes (SMC) complexes. Condensins regulate chromosome structure in a wide range of processes including chromosome segregation, gene regulation, DNA repair and recombination.Recent research defined the structural features and molecular activities of condensins, but it is unclear how these activities are connected to the multitude of phenotypes and functions attributed to condensins. In this review, we briefly discuss the different molecular mechanisms by which condensins may regulate global chromosome compaction, organization of topologically associated domains, clustering of specific loci such as tRNA genes, rDNA segregation, and gene regulation.

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3D clustering of co-regulated genes and its effect on gene expression

Cited by 11 publications

References 38 publications

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

Yin-Yang 1 and HBx protein activate HBV transcription by mediating the spatial interaction of cccDNA minichromosome with cellular chromosome 19p13.11

Condensin action and compaction

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