FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

Giresi, Paul G.; Kim, Jonghwan; McDaniell, Ryan M.; Iyer, Vishwanath R.; Lieb, Jason D.

doi:10.1101/gr.5533506

Cited by 834 publications

(777 citation statements)

References 47 publications

(71 reference statements)

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“…The peaks of nascent promoter RNAs flank a region that consistently exhibits low nucleosome density. 27,[32][33][34][35] Each RNAPII complex on DNA occupies approximately 50 nt and the space between the two RNAPII peaks seen at promoters is approximately 300 nts. This is essentially the same size as the NFR.…”

Section: Divergent Transcription In Yeastmentioning

confidence: 99%

Divergent transcription: A new feature of active promoters

Seila¹,

Core²,

Lis³

et al. 2009

Cell Cycle

166

161

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Section: Divergent Transcription In Yeastmentioning

confidence: 99%

Divergent transcription: A new feature of active promoters

Seila¹,

Core²,

Lis³

et al. 2009

Cell Cycle

166

161

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“…FAIRE experiments were performed as already described 38 , with some modifications. Briefly, after stimulation, 10 7 cells were fixed by 1% formaldehyde for 10 min, followed by 0.125 M Tris (pH 7.6) to stop the crosslinking reaction.…”

Section: Methodsmentioning

confidence: 99%

“…5e). Finally, to directly examine whether changes in chromatin accessibility occur at the IL-6 locus of neutrophils, we performed formaldehyde-assisted isolation of regulatory elements (FAIRE) 38 experiments. As shown in Fig.…”

mentioning

confidence: 99%

Chromatin remodelling and autocrine TNFα are required for optimal interleukin-6 expression in activated human neutrophils

et al. 2015

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Controversy currently exists about the ability of human neutrophils to produce IL-6. Here, we show that the chromatin organization of the IL-6 genomic locus in human neutrophils is constitutively kept in an inactive configuration. However, we also show that upon exposure to stimuli that trigger chromatin remodelling at the IL-6 locus, such as ligands for TLR8 or, less efficiently, TLR4, highly purified neutrophils express and secrete IL-6. In TLR8-activated neutrophils, but not monocytes, IL-6 expression is preceded by the induction of a latent enhancer located 14 kb upstream of the IL-6 transcriptional start site. In addition, IL-6 induction is potentiated by endogenous TNFa, which prolongs the synthesis of the IkBz co-activator and sustains C/EBPb recruitment and histone acetylation at IL-6 regulatory regions. Altogether, these data clarify controversial literature on the ability of human neutrophils to generate IL-6 and uncover chromatin-dependent layers of regulation of IL-6 in these cells.

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“…Furthermore, the tri-methylation signal, H3K4me3, was larger in NREs than non-NREs. Other indicators of functional regions such as UNC-FAIRE locations (Giresi et al 2007) and Regulome DNase I hypersensitive sites (Dorschner et al 2004) occurred as frequently or more frequently in the NREs than non-NREs (tabulated in Fig. 4A).…”

Section: Silencing Conferred By the Chicken Hs4 Insulatormentioning

confidence: 99%

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

Petrykowska¹,

Vockley²,

Elnitski³

2008

Genome Res.

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Silencers and enhancer-blockers (EBs) are cis-acting, negative regulatory elements (NREs) that control interactions between promoters and enhancers. Although relatively uncharacterized in terms of biological mechanisms, these elements are likely to be abundant in the genome. We developed an experimental strategy to identify silencers and EBs using transient transfection assays. A known insulator and EB from the chicken beta-globin locus, cHS4, served as a control element for these assays. We examined 47 sequences from a 1.8-Mb region of human chromosome 7 for silencer and EB activities. The majority of functional elements displayed directional and promoter-specific activities. A limited number of sequences acted in a dual manner, as both silencers and EBs. We examined genomic data, epigenetic modifications, and sequence motifs within these regions. Strong silencer elements contained a novel CT-rich motif, often in multiple copies. Deletion of the motif from three regions caused a measurable loss of silencing ability in these sequences. Moreover, five duplicate occurrences of this motif were identified in the cHS4 insulator. These motifs provided an explanation for an uncharacterized silencing activity we measured in the insulator element. Overall, we identified 15 novel NREs, which contribute new insights into the prevalence and composition of sequences that negatively regulate gene expression.

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FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

Cited by 834 publications

References 47 publications

Divergent transcription: A new feature of active promoters

Divergent transcription: A new feature of active promoters

Chromatin remodelling and autocrine TNFα are required for optimal interleukin-6 expression in activated human neutrophils

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

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