Erythroid specific activator GATA-1-dependent interactions between CTCF sites around the β-globin locus

Kang, Young-Seok; Kim, Yea Woon; Kang, Jin Gu; Yun, Won Ju; Kim, AeRi

doi:10.1016/j.bbagrm.2017.01.013

Cited by 15 publications

(31 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These interactions were readily detected in purified nuclei, as they were in intact cells ( Figure S1). Third, 5C analysis of a 1 Mb region surrounding the beta-globin locus showed that known CTCF-mediated interactions were also preserved ( Figure S1; Kang et al, 2017;Splinter et al, 2006;Tolhuis et al, 2002). Fourth, genome-wide Hi-C analysis ) confirmed that chromosome territories, compartments (determined by principle component analysis, with compartments captured by the first principle component (PC1 ), TADs, and CTCF-CTCF loops were intact in isolated nuclei and quantitatively similar to those in intact cells ( Figure S1).…”

Section: Chromosome Conformation In Isolated Nucleimentioning

confidence: 99%

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

Belaghzal

Borrman

Stephens³

et al. 2019

Preprint

View full text Add to dashboard Cite

Highlights• Liquid chromatin Hi-C detects chromatin interaction dissociation rates genome-wide • Chromatin conformations in distinct nuclear compartments differ in stability • Stable heterochromatic associations are major drivers of chromatin phase separation • CTCF-CTCF loops are stabilized by encirclement of loop bases by cohesin ringsFigures 1-7 Methods Supplemental Figures S1-S6 Supplemental Tables S1-S3 Supplemental Movies S1-S2. 2 SUMMARYChromosomes are folded so that active and inactive chromatin domains are spatially segregated. Compartmentalization is thought to occur through polymer phase/microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci. Before fixation and Hi-C, chromosomes are fragmented removing the strong polymeric constraint to enable detection of intrinsic locus-locus interaction stabilities.Compartmentalization is stable when fragments are over 10-25 kb. Fragmenting chromatin into pieces smaller than 6 kb leads to gradual loss of genome organization. Dissolution kinetics of chromatin interactions vary for different chromatin domains. Lamin-associated domains are most stable, while interactions among speckle and polycomb-associated loci are more dynamic.Cohesin-mediated loops dissolve after fragmentation, possibly because cohesin rings slide off nearby DNA ends. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics.3

show abstract

Section: Chromosome Conformation In Isolated Nucleimentioning

confidence: 99%

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

Belaghzal

Borrman

Stephens³

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Instead, cohesin complex consisting of Smc1, Smc3 and Rad21 subunits occupies both enhancers and CTCF sites (Kagey et al, 2010) and is found at the β-globin LCR HSs and CTCF sites in erythroid cells (Chien et al, 2011). The binding of Rad21 to the β-globin LCR HSs is dependent on GATA-1 in K562 cells (Kang et al, 2017). Thus, GATA-1 could contribute to H3K27ac at CTCF sites by recruiting histone acetyltransferases and transferring them to CTCF sites using cohesin.…”

Section: Discussionmentioning

confidence: 99%

“…In another possibility, enhancer-promoter interaction mediated by GATA-1 can affect CTCF sites around the β-globin locus. However interactions between the CTCF sites are maintained in another erythroid activator TAL1 KD cells where the enhancer-promoter interaction is disrupted (Kang et al, 2017;Yun et al, 2014). Thus, GATA-1 might have a direct role in H3K27ac at neighboring CTCF sites, contributing to chromatin interaction between the CTCF sites.…”

Section: Discussionmentioning

confidence: 99%

“…Five CTCF sites exist around the βglobin locus ( Fig 1A). The C3 and C7 sites on both ends interact with each other, establishing a stable β-globin TAD, and other CTCF sites form erythroid specific sub-TADs (Huang et al, 2017;Kang et al, 2017). Our previous study showed that interactions between CTCF sites corresponding to sub-TADs are dependent on erythroid specific activator GATA-1 that binds to the LCR hypersensitive sites (HSs) (Kang et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…The C3 and C7 sites on both ends interact with each other, establishing a stable β-globin TAD, and other CTCF sites form erythroid specific sub-TADs (Huang et al, 2017;Kang et al, 2017). Our previous study showed that interactions between CTCF sites corresponding to sub-TADs are dependent on erythroid specific activator GATA-1 that binds to the LCR hypersensitive sites (HSs) (Kang et al, 2017). GATA-1 mediates chromatin interaction between enhancers and promoters in the β-globin locus (Kim et al, 2011) and recruits co-activators such as histone acetyltransferase CBP and p300 to enhancers (Kiekhaefer et al, 2002;Letting et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

GATA-1-dependent histone H3K27ac mediates erythroid cell-specific interaction between CTCF sites

Kim

Kang

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

CTCF sites interact with each other in the chromatin environment, establishing domains. Our previous study showed that interaction between CTCF sites is cell type-specific around the βglobin locus and is dependent on erythroid specific activator GATA-1. To find out molecular mechanisms of the cell type-specific interaction, we directly inhibited GATA-1 binding to the β-globin enhancers by deleting its binding motifs and found that histone H3K27 acetylation (H3K27ac) was decreased at CTCF sites surrounding the β-globin locus, even though CTCF binding itself was maintained at the sites. Forced H3K27ac by TSA treatment or CBP/p300 KD affected the interactions between CTCF sites around the β-globin locus. Analysis of public ChIA-PET data revealed that H3K27ac is higher at CTCF sites forming short chromatin interactions than long interactions. The short interactions contain erythropoiesisassociated genes and GATA-1 binding sites in erythroid K562 cells. Depletion of GATA-1 reduced H3K27ac at CTCF sites near erythroid enhancers. These results indicate that GATA-1-dependent histone H3K27ac at neighboring CTCF sites mediates erythroid specific chromatin interaction between them.

show abstract

Histone variants H3.3 and H2A.Z are incorporated into the β-globin locus during transcription activation via different mechanisms

Kang

Kim

2018

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

View full text Add to dashboard Cite

Erythroid specific activator GATA-1-dependent interactions between CTCF sites around the β-globin locus

Cited by 15 publications

References 53 publications

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

GATA-1-dependent histone H3K27ac mediates erythroid cell-specific interaction between CTCF sites

Histone variants H3.3 and H2A.Z are incorporated into the β-globin locus during transcription activation via different mechanisms

Contact Info

Product

Resources

About