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Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor
Open accessAbstract
Chromatin loops juxtapose distal enhancers with active promoters, but their molecular architecture and relationship with transcription remain unclear. In erythroid cells, the locus control region (LCR) and β-globin promoter form a chromatin loop that requires transcription factor GATA1 and the associated molecule Ldb1. We employed artificial zinc fingers (ZF) to tether Ldb1 to the β-globin promoter in GATA1 null erythroblasts, in which the β-globin locus is relaxed and inactive. Remarkably, targeting Ldb1 or only its self-association domain to the β-globin promoter substantially activated β-globin transcription in the absence of GATA1. Promoter-tethered Ldb1 interacted with endogenous Ldb1 complexes at the LCR to form a chromatin loop, causing recruitment and phosphorylation of RNA polymerase II. ZF-Ldb1 proteins were inactive at alleles lacking the LCR, demonstrating that their activities depend on long-range interactions. Our findings establish Ldb1 as a critical effector of GATA1-mediated loop formation and indicate that chromatin looping causally underlies gene regulation.
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“In contrast to YY1 and ZNF143, LDB1 has been shown to form loops independently of both cohesin and CTCF [371, 375].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [371]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“LDB1 was first identified as a looping factor in the mouse β-globin locus [317, 371].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [371]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“The functional significance of the physical approximation of the promoter to the enhancer was demonstrated in experiments on the activation of transcription through the forced formation of enhancer-promoter loops [87,88].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [88]
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“Stimulation of promoter activity by forced looping with an enhancer is a strong argument in favor of this model [87,88,110,111].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [88]
In the citing paper
“and physical contact between enhancer-promoter pairs appears to be sufficient for gene activation.26”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [26]
In the citing paper
“Tethering the SA domain to the LCR (L-SA in Figure 1) or β-major promoter (Deng et al., 2012, and data not shown) did not activate βh1-globin expression”
From Reactivation of developmentally silenced globin genes by forced chromatin looping (2014) · cites this paper as Deng et al., 2012
In the citing paper
“In adult type murine erythroid cells, Ldb1 is required for the juxtaposition between the LCR and the adult β-major globin gene (Deng et al., 2012; Song et al., 2007).”
From Reactivation of developmentally silenced globin genes by forced chromatin looping (2014) · cites this paper as Deng et al., 2012
In the citing paper
“These results demonstrated that forced juxtaposition of an enhancer and promoter via chromatin looping can trigger gene activation”
From Reactivation of developmentally silenced globin genes by forced chromatin looping (2014) · cites this paper as Deng et al., 2012
In the citing paper
“Finally, previous 3C experiments demonstrated the sufficiency of tethered Ldb1 for full reconstitution of an LCR-β-globin promoter loop in immature adult erythroid cells in which the globin locus is otherwise unlooped (Deng et al., 2012).”
From Reactivation of developmentally silenced globin genes by forced chromatin looping (2014) · cites this paper as Deng et al., 2012
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Citations
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Regulatory elements can be essential for maintaining broad chromatin organization and cell viability
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“LDB1 acts as a bridging factor to bring protein complexes bound at distant DNA binding sites in close proximity for interaction with one another via DNA looping.(35) LDB1 has a C-terminal LIM domain allowing the protein to interact other members of the complex by binding LMO2.”
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“Also shown are locations of known interacting components at EHS1 that includes the Gata/Tal1/Lmo2/Ldb1 multi-protein complex, Smad5, Riok2, P300/CBP, and DEK proteins (3, 31, 32, 52, 55, 71 – 73), along with the new interactions between DDX5 with DEK and CTCF identi fi ed in the present study.”
BackgroundNucleotide Substitution Models and Evolutionary Distances
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“Meanwhile, our findings suggest that the spatial arrangement of genes has important effects on their regulation relationships and thus their biological functions, and the spatial effect may be exploited in practice to modulate gene expression based on 3D distance through gene editing approaches such as TALEN or CRISPR…”
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“Activation of enhancers is not only characterized by various histone modifications, but also accompanied by formation of long-range chromatin interactions between the distal cis-regulatory elements and the target gene promoters (Deng et al., 2012; Gorkin et al., 2014).”
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Role of Chromatin Looping Factors in Leukemia
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“These two regions interact with the b1 TSS in a manner that correlates with b1 expression levels, suggesting that they may function as novel distal regulatory elements.”
BackgroundInsights from Space: Potential Role of Diet in the Spatial Organization of Chromosomes
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“Forced looping at the globin locus has been shown to be able to over-ride the stringent developmental gene expression program, confirming that looping is a causal event in transcription [65,66].”
BackgroundCRISPR /Cas9 genome editing throws descriptive 3‐D genome folding studies for a loop
Beagan, J. A., & Phillips‐Cremins, J. E. (2016) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1338 · Cited by 3
“69 In a follow-up study, Deng et al. showed that directing ZF-Ldb1 proteins to developmentally silenced fetal γ -globin genes and nearby enhancers in erythroblasts was able to re-activate these genes.”
BackgroundZouari, Y. B., Molitor, A. M., & Sexton, T. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803480-4.00019-3 · Cited by 3
Genomic Features: Content Sensors, Nucleotide Skew Plot, Strand Asymmetry, and DNA Methylation
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-319-90684-3_11 · Cited by 3
Bioinformatics and Translation Initiation
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_10 · Cited by 3
Camino, E. M., Weinstein, M. L., List, M. P., Vellky, J. E., Rebeiz, M., & Williams, T. M. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.401033 · Cited by 3
Repurposing of the enhancer-promoter communication underlies the compensation of Mesp2 by Mesp1
Okada, H., & Saga, Y. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010000 · Cited by 5
Pandupuspitasari, N. S., Khan, F. A., Huang, C., Ali, A., Yousaf, M. R., Shakeel, F., Putri, E. M., Negara, W., Muktiani, A., Prasetiyono, B. W. H. E., et al. (2023) · Functional & Integrative Genomics · doi:10.1007/s10142-023-01146-5 · Cited by 3
“…between the mouse-globin (Hbb) promoter and its gene control domain enhancer results in the strong transcriptional activation of the Hbb gene, even in the absence of the key transcriptional activator GATA1, implying that enhancer–promoter contacts may improve transcription (Deng et al. 2012).”
BackgroundResultTav, C., Fournier, É., Fournier, M., Khadangi, F., Baguette, A., Côté, M. C., Silveira, M. A. D., Bérubé‐Simard, F., Bourque, G., Droit, A., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1237092 · Cited by 4
“Furthermore, it is generally accepted that physical proximity between enhancer and promoter regions is responsible for transmitting the effect of distally bound transcription factors to promoter regions (Deng et al., 2012; 2014; Lee et al., 2015; Chen et al., 2018).”
BackgroundFagnan, A., Aid, Z., Baille, M., Drakul, A., Robert, E., Lopez, C. K., Thirant, C., Lécluse, Y., Rivière, J., Ignacimouttou, C., et al. (2024) · HemaSphere · doi:10.1002/hem3.90 · Cited by 4
“52,56 Therefore, it is possible that the tetramerization properties of ETO2 similarly controls chromatin organization to enforce expression of this activated gene program that antagonizes differentiation but maintains immature progenitor states.”
DNA regulatory element cooperation and competition in transcription
Lee, H., Friedman, M. J., Kim, S. B., & Oh, S. (2024) · BMB Reports · doi:10.5483/bmbrep.2024-0069 · Cited by 4
“At the -globin gene locus, te-thering the lim domain binding 1 (LDB1) dimerization domain to either the HBB promoter (11) or the promoters of the HBG1/2 genes (12) via a customized ZF is sufficient to drive expression in a selective fashion (Fig.”
Multilayered Mechanisms for Long-range Regulatory Interactions in Eukaryotic Transcription
Fukaya, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169311 · Cited by 3
Protein Isoelectric Point and Helicobacter pylori
Xia, X. (2018) · Springer eBooks · doi:10.1007/978-3-032-18842-7_14 · Cited by 3
Faster, higher, stronger: timely and robust cell fate/identity commitment in stem cell lineages
Liu, K., Xu, K., & Song, Y. (2019) · Open Biology · doi:10.1098/rsob.180243 · Cited by 3
Fong, H. T., Hagen, T., & Inoue, T. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194577 · Cited by 3
Fok, E. T., Fanucchi, S., Bystricky, K., & Mhlanga, M. M. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0664-3_11 · Cited by 4
How chromosome topologies get their shape: views from proximity ligation and microscopy methods
Huang, Y., Neijts, R., & de Laat, W. L. (2020) · FEBS Letters · doi:10.1002/1873-3468.13961 · Cited by 3
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Laugsch, M., Bartusel, M., Alirzayeva, H., Karaolidou, A., Rehimi, R., Crispatzu, G., Nikolić, M., Bleckwehl, T., Kolovos, P., van IJcken, W. F. J., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3155617 · Cited by 3
Stefano, M. D., Stadhouders, R., Farabella, I., Castillo, D., Serra, F., Graf, T., & Martı́-Renom, M. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/642009 · Cited by 3
Jiang, Q., Zagozewski, J., Godbout, R., & Eisenstat, D. (2020) · bioRxiv · doi:10.1101/2020.04.09.012385 · Cited by 5
“It has been reported that the LIM domain-binding protein 1 (LDB1) is capable of mediating promoter:enhancer looping through LDB1 homodimerization (Deng et al., 2012; Krivega, Dale, & Dean, 2014).”
BackgroundKubo, N., Hu, R., Ye, Z., & Ren, B. (2021) · bioRxiv · doi:10.1101/2021.03.17.435905 · Cited by 2
A novel enhancer that regulates Bdnf expression in developing neuronsPreprint
Brookes, E., Au, H. Y. A., Varsally, W., Barrington, C., Hadjur, S., & Riccio, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.18.469096 · Cited by 3
“Enhancer-promoter proximity can be critical for appropriate gene expression (Bartman et al., 2016; Deng et al., 2012; Greenwald et al., 2019; Kim et al., 2019; Morgan et al., 2017).”
BackgroundSuper-silencers regulated by chromatin interactions control apoptotic genesPreprint
Zhang, Y., Chen, K., Cai, Y., Niibori-Nambu, A., See, Y. X., Fu, C., Raju, A., Lakshmanan, M., Osato, M., Tergaonkar, V., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.17.476559 · Cited by 3
“…this, we first performed 4C-seq using FGF18 promoter as the viewpoint in different clones (EV, S1KO and DKO) since chromatin interactions are the key determinants for modulating gene expression (Babu & Fullwood, 2015; Deng et al., 2012; Q. Li, Barkess, & Qian, 2006; Perino & Veenstra, 2016).”
MethodTheoretical Principles of Enhancer-Promoter Communication in Transcriptional BurstingPreprint
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Competition between transcription and loop extrusion modulates promoter and enhancer dynamicsPreprint
Sexton, T., Platania, A., Erb, C., Barbieri, M., Molcrette, B., Grandgirard, E., de Kort, M. A. C., Meaburn, K. J., Taylor, T., Shchuka, V. M., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3164817/v1 · Cited by 3
Large-scale analysis of the integration of enhancer-enhancer signals by promotersPreprint
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Learning induces persistent chromatin loops underlying robust gene expression during memory recallPreprint
Xu, P., Chandradoss, K. R., Lukasak, B. J., Paranjapye, A., Waldman, A. J., Pham, K., Ryu, H.-S., Liu, C., Titus, K. R., Sureka, R., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.30.678146 · Cited by 3
MYB represses ζ-globin expression through upregulating ETO2
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Distal enhancers loop to proximal enhancers, not to promoters
Struhl, K. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00889-2 · Cited by 2
“6).”
InfluentialThree-dimensional genome reorganization in hematopoietic stem cells
Nakajima, A., Kirito, K., Nakanishi, M., & Takayama, N. (2025) · Experimental Hematology · doi:10.1016/j.exphem.2025.105249 · Cited by 2
Transcription factors as drivers of 3D enhancer-promoter interactions
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The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing
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Chromatin architecture and topology in pluripotent stem cells
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How Transcription Factor Clusters Shape the Transcriptional Landscape
Munshi, R. (2024) · Biomolecules · doi:10.3390/biom14070875 · Cited by 3
“Chromatin folding facilitates the formation of loops [31,32], bringing distant enhancers into close proximity, enabling interactions among enhancer-associated protein clusters [33,34].”
BackgroundEnhancer‐dependent gene regulation in space, time, and malignancies
Blum, B., Dachtler, V., & Feldmann, A. (2025) · International Journal of Cancer · doi:10.1002/ijc.35350 · Cited by 2
“P proximity can cause gene activation 54,73,74 and global prevention of new interactions in cohesin depletion experiments is associated with reduced gene activation.”
Machine learning tools for deciphering the regulatory logic of enhancers in health and disease
Foutadakis, S., Bourika, V., Styliara, I., Koufargyris, P., Safarika, A., & Karakike, E. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1603687 · Cited by 2
“In support of the looping model and more speci fi cally its instructive nature, targeted tethering of a looping factor allowed the de novo formation of a chromatin loop and activation of transcription (Deng et al., 2012).”
Decoding the molecular logic of rapidly evolving ZAD zinc finger proteins in Drosophila
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“In mammals, ubiquitously expressed DNA binding proteins YY1 and Ldb1 are suggested to mediate long-range interactions through homotypic protein-protein interactions mediated by their dimerization domains ( 63 , 64 ).”
Plautz, C. Z., Zirkle, B., Deshotel, M. J., & Grainger, R. M. (2014) · Developmental Dynamics · doi:10.1002/dvdy.24193 · Cited by 2
“…order oligomers (Cross et al., 2010) and may be sufficient for chromatin looping and transcriptional activation of bglobin in erythroid cells (Deng et al., 2012; Krivega et al., 2014), the C-terminal LIM interaction domain (LID) mediates interactions with transcription factors including lhx1…”
Background
Metadata
- Authors
- Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A., & Blobel, G. A.
- Affiliations
- Children's Hospital of Philadelphia (US)
- National Institutes of Health (US)
- Sangamo BioSciences (United States) (US)
- Corresponding author
- Blobel, Gerd A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-06
- Volume
- 149
- Issue
- 6
- Pages
- 1233-1244
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3372860
- OpenAlex
- W1970831058
- Cited by
- 734
- References
- 49
- Citations by year
- 2026: 22 · 2025: 42 · 2024: 48 · 2023: 54 · 2022: 48 · 2021: 58 · 2020: 60 · 2019: 70 · 2018: 57 · 2017: 50 · 2016: 51 · 2015: 60 · 2014: 62 · 2013: 45 · 2012: 7
- FWCI
- 22.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R01HL119479)
- National Institute of Diabetes and Digestive and Kidney Diseases (R37DK058044, R01DK054937)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Health Sciences › Medicine › Genetics (clinical) › Hemoglobinopathies and Related Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromatin looping, locus control region, beta-globin promoter, LDB1, GATA-1, erythroid cells, enhancer-promoter interactions, RNA polymerase II phosphorylation, transcriptional activation
- MeSH terms
- Animals, Cell Line, Cell Separation, Chromatin, DNA-Binding Proteins, Embryo, Mammalian, Erythroblasts, Female, Gene Expression Regulation, Male, Promoter Regions, Genetic, Transcription, Genetic, Zinc Fingers, Protein Structure, Tertiary, GATA1 Transcription Factor, Mice, beta-Globins, LIM Domain Proteins
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