Long-range enhancer–promoter contacts in gene expression control

An integrated encyclopedia of DNA elements in the human genome

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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Capturing Chromosome Conformation

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Spatial partitioning of the regulatory landscape of the X-inactivation centre

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Coactivator condensation at super-enhancers links phase separation and gene control

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A unique chromatin signature uncovers early developmental enhancers in humans

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Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

Perlman, B. S., Burget, N. G., Zhou, Y., Schwartz, G. W., Petrovic, J., Modrusan, Z. D., & Faryabi, R. B. (2024) · Nature Communications · doi:10.1038/s41467-024-52375-6 · Cited by 23

Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale)

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OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity

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DNA Methylation of a Novel Regulatory Element Within the Tyrosine Hydroxylase Gene (TH) is Dysregulated by Chronic Cocaine Dependence in the Human Striatum

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Distinct transcription kinetics of pluripotent cell states

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Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve

Chignon, A., Argaud, D., Boulanger, M.-C., Mkannez, G., Bon-Baret, V., Li, Z.-L., Thériault, S., Bossé, Y., & Mathieu, P. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010010 · Cited by 17

Chromatin Rewiring by Mismatch Repair Protein MSH2 Alters Cell Adhesion Pathways and Sensitivity to BET Inhibition in Gastric Cancer

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How to tame your genes: mechanisms of inflammatory gene repression by glucocorticoids

Strickland, B. A., Ansari, S. A., Dantoft, W., & Uhlenhaut, N. H. (2022) · FEBS Letters · doi:10.1002/1873-3468.14409 · Cited by 22

Global hypomethylation in childhood asthma identified by genome‐wide DNA‐methylation sequencing preferentially affects enhancer regions

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MSL2 ensures biallelic gene expression in mammals

Sun, Y., Wiese, M., Hmadi, R., Karayol, R., Seyfferth, J., Greene, J. A. M., Erdogdu, N. U., Deboutte, W., Arrigoni, L., Holz, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06781-3 · Cited by 22

The Impact of Space and Time on the Functional Output of the GenomePreprint

Nollmann, M., Bennabi, I., Götz, M., & Gregor, T. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040378 · Cited by 23

Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome

Powell, S. K., O’Shea, C. P., Brennand, K., & Akbarian, S. (2020) · Biological Psychiatry · doi:10.1016/j.biopsych.2020.06.033 · Cited by 21

Transcription bursting and epigenetic plasticity: an updated view

Beckman, W. F., Jiménez, M. Á. L., & Verschure, P. J. (2021) · Epigenetics Communications · doi:10.1186/s43682-021-00007-1 · Cited by 22

Emerging roles of RNA – RNA interactions in transcriptional regulation

Wang, D., Ye, R., Cai, Z., & Xue, Y. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1712 · Cited by 20

Single nucleosome tracking to study chromatin plasticity

Lakadamyali, M. (2022) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2021.12.005 · Cited by 19

Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype

Fritz, A. J., Dika, M. E., Toor, R. H., Rodriguez, P. D., Foley, S. J., Ullah, R., Nie, D., Banerjee, B., Lohese, D., Tracy, K. M., et al. (2022) · Results and problems in cell differentiation · doi:10.1007/978-3-031-06573-6_12 · Cited by 23

Remembering through the genome: the role of chromatin states in brain functions and diseases

Arzate‐Mejía, R. G., & Mansuy, I. M. (2023) · Translational Psychiatry · doi:10.1038/s41398-023-02415-4 · Cited by 22

Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss

Jin, L. G., Wang, D., Zhang, J., Liu, P., Wang, Y., Yu, L., Liu, C., Han, Z., Long, K., Li, D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39191-0 · Cited by 21

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

Xie, F., Armand, E. J., Yao, Z., Liu, H., Bartlett, A., Behrens, M. M., Li, Y. E., Lucero, J. D., Luo, C., Nery, J. R., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100342 · Cited by 21

MICA: a multi-omics method to predict gene regulatory networks in early human embryos

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ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

Zhang, M., Huang, H., Li, J., & Wu, Q. (2024) · Cell Reports · doi:10.1016/j.celrep.2023.113663 · Cited by 20

The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation

Monteagudo, A., Albert, J. R., Scarpa, M., Noordermeer, D., & Greenberg, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae724 · Cited by 22

A gene signal amplifier platform for monitoring the unfolded protein response

Marmolejo, C. A. O., Bachhav, B., Patibandla, S. D., Yang, A. L., & Segatori, L. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0497-x · Cited by 18

Epigenetic gene regulation in plasma cells

Patterson, D. G., Kania, A. K., Zuo, Z., Scharer, C. D., & Boss, J. M. (2021) · Immunological Reviews · doi:10.1111/imr.12975 · Cited by 19

Alterations in Chromatin Structure and Function in the Microglia

Fujita, Y., & Yamashita, T. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.626541 · Cited by 22

Models behind the mystery of establishing enhancer-promoter interactions

Monfils, K., & Barakat, T. S. (2021) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2021.151170 · Cited by 19

Embryonic heat conditioning in chicks induces transgenerational heat/immunological resilience via methylation on regulatory elements

Rosenberg, T., Marco, A., Kisliouk, T., Haron, A., Shinder, D., Druyan, S., & Meiri, N. (2022) · The FASEB Journal · doi:10.1096/fj.202101948r · Cited by 17

Selective effects of a short transient environmental fluctuation on a natural population

Pfenninger, M., Foucault, Q., Waldvogel, A., & Feldmeyer, B. (2022) · Molecular Ecology · doi:10.1111/mec.16748 · Cited by 18

Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization

Thuma, J. L., Chung, Y.-C., & Tu, L. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1173545 · Cited by 21

CRISPR/Cas9-Mediated Editing of BmEcKL1 Gene Sequence Affected Silk Gland Development of Silkworms (Bombyx mori)

Li, S., Lao, J., Sun, Y., Hua, X., Lin, P., Wang, F., Shen, G., Zhao, P., & Xia, Q. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031907 · Cited by 18

METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence

Wang, C., Tanizawa, H., Hill, C., Havas, A. P., Zhang, Q., Liao, L., Xue, H., Lei, X., Wang, L., Nie, H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49745-5 · Cited by 23

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia

Gambi, G., Boccalatte, F. E., Rodriguez-Hernaez, J., Lin, Z., Nadorp, B., Polyzos, A., Tan, J., Avrampou, K., Inghirami, G., Kentsis, A., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.040 · Cited by 18

Genetic risk for neurodegenerative conditions is linked to disease-specific microglial pathways

Askarova, A., Yaa, R. M., Marzi, S. J., & Nott, A. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011407 · Cited by 21

Investigating the role of super-enhancer RNAs underlying embryonic stem cell differentiation

Chang, H.-C., Huang, H., Juan, H., & Hsu, C. (2019) · BMC Genomics · doi:10.1186/s12864-019-6293-x · Cited by 18

Multi‐omics analysis reveals the functional transcription and potential translation of enhancers

Wu, Y., Yang, Y., Gu, H., Tao, B., Zhang, E., Wei, J., Wang, Z., Liu, A., Sun, R., Chen, M., et al. (2020) · International Journal of Cancer · doi:10.1002/ijc.33132 · Cited by 18

Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci

Kyryachenko, S., Georges, A. B., Yu, M., Berrandou, T.-E., Guo, L., Bruneval, P., Rubio, T., Gronwald, J., Baraki, H., Kutschka, I., et al. (2021) · Circulation Research · doi:10.1161/circresaha.120.317581 · Cited by 18

The logic of native enhancer-promoter compatibility and cell-type-specific gene expression variationPreprint

Narita, T., Higashijima, Y., Kilic, S., Maskey, E., Neumann, K., & Choudhary, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.18.500456 · Cited by 17

The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression

Agelopoulos, M., Foutadakis, S., & Thanos, D. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.682397 · Cited by 19

Histone Methyltransferase SETDB1 Regulates the Development of Cortical Htr3a-Positive Interneurons and Mood Behaviors

Li, J., Zheng, S., Dong, Y., Xu, H., Zhu, Y., Weng, J., Sun, D., Wang, S., Xiao, L., & Jiang, Y. (2022) · Biological Psychiatry · doi:10.1016/j.biopsych.2022.08.021 · Cited by 17

Regulation of chromatin organization during animal regeneration

Jia, X., Lin, W., & Wang, W. (2023) · Cell Regeneration · doi:10.1186/s13619-023-00162-x · Cited by 18

Three‐dimensional genome structure and function

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Unexpected nuclear hormone receptor and chromatin dynamics regulate estrous cycle dependent gene expression

Jefferson, W. N., Wang, T., Padilla‐Banks, E., & Williams, C. J. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae714 · Cited by 17

Genetic coupling of enhancer activity and connectivity in gene expression control

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On the role of transcription in positioning nucleosomes

Jiang, Z., & Zhang, B. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008556 · Cited by 17

EPIsHilbert: Prediction of Enhancer-Promoter Interactions via Hilbert Curve Encoding and Transfer Learning

Zhang, M., Hu, Y., & Zhu, M. (2021) · Genes · doi:10.3390/genes12091385 · Cited by 17

KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid

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First-passage statistics of colloids on fractals: Theory and experimental realization

Zunke, C., Bewerunge, J., Platten, F., Egelhaaf, S. U., & Godec, A. (2022) · Science Advances · doi:10.1126/sciadv.abk0627 · Cited by 16

Sister chromatid–sensitive Hi-C to map the conformation of replicated genomes

Mitter, M., Takács, Z., Köcher, T., Micura, R., Langer, C. C. H., & Gerlich, D. W. (2022) · Nature Protocols · doi:10.1038/s41596-022-00687-6 · Cited by 16

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

Qin, T., Lee, C., Li, S., Cavalcante, R. G., Orchard, P., Yao, H., Zhang, H., Wang, S., Patil, S. B., Boyle, A. P., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02668-0 · Cited by 19

Long-Distance Repression by Human Silencers: Chromatin Interactions and Phase Separation in Silencers

Zhang, Y., See, Y. X., Tergaonkar, V., & Fullwood, M. J. (2022) · Cells · doi:10.3390/cells11091560 · Cited by 17

CDC20-Mediated hnRNPU Ubiquitination Regulates Chromatin Condensation and Anti-Cancer Drug Response

Wavelet-Vermuse, C., Odnokoz, O., Xue, Y., Lu, X., Cristofanilli, M., & Wan, Y. (2022) · Cancers · doi:10.3390/cancers14153732 · Cited by 16

XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation

Haque, F., Honjo, T., & Begum, N. A. (2022) · Science Advances · doi:10.1126/sciadv.add1466 · Cited by 18

Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

Xie, Y., Ruan, F., Li, Y., Luo, M., Zhang, C., Chen, Z., Xie, Z., Weng, Z., Chen, W., Chen, W., et al. (2023) · eLife · doi:10.7554/elife.87868 · Cited by 19

Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer

Kim, K., Kim, M., Lee, A., Song, S., Kang, J., Eom, J., Kang, G. H., Bae, J. M., Min, S., Kim, Y. S., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112778 · Cited by 17

High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription

Bressin, A., Jasnovidova, O., Arnold, M., Altendorfer, E., Trajkovski, F., Kratz, T. A., Handzlik, J. E., Hnisz, D., & Mayer, A. (2023) · Nature Communications · doi:10.1038/s41467-023-40633-y · Cited by 22

DNA looping mediates cooperative transcription activation

Han, S., Jiang, Y., You, L., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01149-7 · Cited by 16

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network

Yao, L., Xie, P., Guan, J., Chung, C., Huang, Y., Pang, Y., Wu, H., Chiang, Y., & Lee, T.-Y. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00546 · Cited by 16

Biological roles of enhancer RNA m6A modification and its implications in cancer

Han, Y., Sun, J., Yao, M., Miao, L., & Li, M. (2025) · Cell Communication and Signaling · doi:10.1186/s12964-025-02254-4 · Cited by 19

Towards a Better Classification and Novel Therapies Based on the Genetics of Systemic Sclerosis

Acosta‐Herrera, M., López‐Isac, E., & Martin, J. J. (2019) · Current Rheumatology Reports · doi:10.1007/s11926-019-0845-6 · Cited by 14

Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin

Melters, D. P., & Dalal, Y. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.11.019 · Cited by 16

Understanding transcription across scales: From base pairs to chromosomes

Vos, S. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.002 · Cited by 18

Engineering three-dimensional genome folding

Zhang, D., Lam, J. C., & Blobel, G. A. (2021) · Nature Genetics · doi:10.1038/s41588-021-00860-9 · Cited by 17

Enhancers navigate the three-dimensional genome to direct cell fate decisions

Kim, J., & Dean, A. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.06.005 · Cited by 15

Interplay between regulatory elements and chromatin topology in cellular lineage determination

Shukla, V., Cetnarowska, A., Hyldahl, M., & Mandrup, S. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.05.011 · Cited by 15

Integrative analysis identifies the association between CASZ1 methylation and ischemic stroke

Mo, X.-B., Zhang, H., Wang, A., Xu, T., & Zhang, Y.-H. (2020) · Neurology: Genetics · doi:10.1212/nxg.0000000000000509 · Cited by 10

A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors

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Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants

Xiao, Y., Jiao, S., He, M., Lin, D., Zuo, H., Han, J., Sun, Y., Cao, G., Chen, Z., & Liu, H. (2022) · International Journal of Oral Science · doi:10.1038/s41368-022-00194-0 · Cited by 15

Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis

Hong, D., Lin, H., Liu, L., Shu, M., Dai, J., Lu, F., Tong, M., & Huang, J. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac508 · Cited by 15

Elevated nuclear PIGL disrupts the cMyc/BRD4 axis and improves PD-1 blockade therapy by dampening tumor immune evasion

Yu, H. T., Shi, T., Yao, L., Xu, D., Ding, Y., Xia, Q., Liu, W., & Wang, X. (2023) · Cellular and Molecular Immunology · doi:10.1038/s41423-023-01048-3 · Cited by 15

Enhancer Function in the 3D Genome

Razin, S. V., Ulianov, S. V., & Iarovaia, O. V. (2023) · Genes · doi:10.3390/genes14061277 · Cited by 15

Molecular basis for SOX2-dependent regulation of super-enhancer activity

Yoo, W., Song, Y. W., Kim, J., Ahn, J., Kim, J., Shin, Y., Ryu, J., & Kim, K. K. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad908 · Cited by 17

Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells

Li, J., Zhu, J., Gray, O., Sobreira, D. R., Wu, D., Huang, R., Miao, B. A., Sakabe, N. J., Krause, M. D., Kaikkonen, M. U., et al. (2023) · The Journal of Cell Biology · doi:10.1083/jcb.202211125 · Cited by 16

The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation

Tang, X., Zeng, P., Liu, K., Li, Q., Sun, Y., Liu, X., Lu, L., Wei, C., Wang, J., Jiang, S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47048-3 · Cited by 17

Integration of functional genomics and statistical fine-mapping systematically characterizes adult-onset and childhood-onset asthma genetic associations

Zhong, X., Mitchell, R., Billstrand, C., Thompson, E. E., Sakabe, N. J., Aneas, I., Salamone, I. M., Gu, J., Sperling, A. I., Schoettler, N., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01459-z · Cited by 18

CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions

Feldmann, A., Dimitrova, E., Kenney, A., Lastuvkova, A., & Klose, R. J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa064 · Cited by 15

Diet-dependent natriuretic peptide receptor C expression in adipose tissue is mediated by PPARγ via long-range distal enhancers

Shi, F., Simándi, Z., Nagy, L., & Collins, S. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100941 · Cited by 15

The histone variant macroH2A1.1 regulates RNA polymerase II-paused genes within defined chromatin interaction landscapes

Recoules, L., Heurteau, A., Raynal, F., Karasu, N., Moutahir, F., Bejjani, F., Jariel‐Encontre, I., Cuvier, O., Sexton, T., Lavigne, A.-C., et al. (2022) · Journal of Cell Science · doi:10.1242/jcs.259456 · Cited by 17

The role of noncoding mutations in blood cancers

Rahman, S., & Mansour, M. R. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.041988 · Cited by 16

Controlling gene activation by enhancers through a drug-inducible topological insulator

Tsujimura, T., Takase, O., Yoshikawa, M., Sano, E., Hayashi, M., Hoshi, K., Takato, T., Toyoda, A., Okano, H., & Hishikawa, K. (2020) · eLife · doi:10.7554/elife.47980 · Cited by 17

A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions

Vanhaeren, T., Divina, F., García-Torres, M., Gómez-Vela, F., Vanhoof, W., & Martínez‐García, P. M. (2020) · Genes · doi:10.3390/genes11090985 · Cited by 15

PHACTR-1 (Phosphatase and Actin Regulator 1) Deficiency in Either Endothelial or Smooth Muscle Cells Does Not Predispose Mice to Nonatherosclerotic Arteriopathies in 3 Transgenic Mice

Rubin, S., Bougaran, P., Martin, S., Abélanet, A., Delobel, V., Pernot, M., Jeanningros, S., Bats, M., Combe, C., Dufourcq, P., et al. (2022) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.122.317431 · Cited by 15

Three-dimensional chromatin organization in brain function and dysfunction

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A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes

Sakata, T., Tei, S., Izumi, K., Krantz, I. D., Bando, M., & Shirahige, K. (2025) · Current Biology · doi:10.1016/j.cub.2025.01.044 · Cited by 12

Disentangling the architectural and non-architectural functions of CTCF and cohesin in gene regulation

Narita, T., Kilic, S., Higashijima, Y., Scherer, N. M., Pappas, G., Maskey, E., & Choudhary, C. (2025) · Nature Genetics · doi:10.1038/s41588-025-02404-x · Cited by 20

Structural Variation at a Disease Mutation Hotspot: Strategies to Investigate Gene Regulation and the 3D Genome

Boyling, A., Pérez‐Siles, G., & Kennerson, M. L. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.842860 · Cited by 15

A comprehensive review of bioinformatics tools for chromatin loop calling

Liu, L., Han, K., Sun, H., Han, L., Gao, D., Xi, Q., Zhang, L., & Lin, H. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad072 · Cited by 14

Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

Wang, R., Xu, Q., Wang, C., Tian, K., Wang, H., & Ji, X. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad401 · Cited by 13

3′UTR of ALV-J can affect viral replication through promoting transcription and mRNA nuclear export

Xu, M., Qian, K., Shao, H., Yao, Y., Nair, V., Ye, J., & Qin, A. (2023) · Journal of Virology · doi:10.1128/jvi.01152-23 · Cited by 15

MYCN drives oncogenesis by cooperating with the histone methyltransferase G9a and the WDR5 adaptor to orchestrate global gene transcription

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Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering

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UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C

Ramos-Rodríguez, M., Subirana-Granés, M., & Pasquali, L. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab392 · Cited by 14

Differences in nanoscale organization of regulatory active and inactive human chromatin

Brandstetter, K., Zülske, T., Ragoczy, T., Hörl, D., Guirao‐Ortiz, M., Steinek, C., Barnes, T., Stumberger, G., Schwach, J., Haugen, E., et al. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.02.009 · Cited by 15

A unique H2B acetylation signature marks active enhancers and predicts their target genesPreprint

Narita, T., Higashijima, Y., Kilic, S., Liebner, T., Walter, J., & Choudhary, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.18.500459 · Cited by 14

Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercisePreprint

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Cis-Regulatory Control of Mammalian Sex Determination

Ridnik, M., Schoenfelder, S., & Gonen, N. (2021) · Sexual Development · doi:10.1159/000519244 · Cited by 14

The retinoic acid receptor co-factor NRIP1 is uniquely upregulated and represents a therapeutic target in acute myeloid leukemia with chromosome 3q rearrangements

Grasedieck, S., Cabantog, A., MacPhee, L., Im, J., Rueß, C., Demir, B., Sperb, N., Rücker, F. G., Döhner, K., Herold, T., et al. (2021) · Haematologica · doi:10.3324/haematol.2021.276048 · Cited by 13

LncRNAEPRregulates intestinal mucus production and protects against inflammation and tumorigenesis

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Transcription factor expression is the main determinant of variability in gene co‐activity

van Duin, L., Krautz, R., Rennie, S., & Andersson, R. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211392 · Cited by 11

EpiMix is an integrative tool for epigenomic subtyping using DNA methylation

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Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak

Li, J., Chen, Z., Bai, Y., Wei, Y., Guo, D., Liu, Z., Niu, Y., Shi, B., Zhang, X., Cai, Y., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms25010158 · Cited by 15

A model of active transcription hubs that unifies the roles of active promoters and enhancers

Zhu, I., Song, W., Ovcharenko, I., & Landsman, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab235 · Cited by 55

Regeneration and Developmental Enhancers are Differentially Compatible with Minimal Promoters

Begeman, I. J., Emery, B. F., Kurth, A., & Kang, J. (2022) · Developmental Biology · doi:10.1016/j.ydbio.2022.09.007 · Cited by 7

Compatibility logic of human enhancer and promoter sequencesPreprint

Bergman, D. T., Jones, T., Liu, V., Siraj, L., Kang, H., Nasser, J., Kane, M., Nguyen, T. H., Grossman, S. R., Fulco, C. P., et al. (2021) · bioRxiv · doi:10.1101/2021.10.23.462170 · Cited by 5

Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers

Bardales, J. A., Wieser, E., Kawaji, H., Murakawa, Y., & Darzacq, X. (2018) · Genes · doi:10.3390/genes9060270 · Cited by 5

Compatibility rules of human enhancer and promoter sequences

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