The selection and function of cell type-specific enhancers

An integrated encyclopedia of DNA elements in the human genome

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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

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

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Development and Applications of CRISPR-Cas9 for Genome Engineering

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The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expressionPreprint

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

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Super-enhancers in the control of cell identity and disease

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

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Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition

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Locus-specific induction of gene expression from heterochromatin loci during cellular senescence

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MLL3 enhances the transcription of PD-L1 and regulates anti-tumor immunity

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SOX-5 activates a novel RORγt enhancer to facilitate experimental autoimmune encephalomyelitis by promoting Th17 cell differentiation

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CBP/p300 HAT maintains the gene network critical for β cell identity and functional maturity

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Induction of OCT2 contributes to regulate the gene expression program in human neutrophils activated via TLR8

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A comprehensive integrated post-GWAS analysis of Type 1 diabetes reveals enhancer-based immune dysregulation

Kim, S., Hudgins, A. D., Yang, J., Zhu, Y., Tu, Z., Rosenfeld, M. G., DiLorenzo, T. P., & Suh, Y. (2021) · PLoS ONE · doi:10.1371/journal.pone.0257265 · Cited by 25

Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs

Shen, Z., Li, R. Z., Prohaska, T. A., Hoeksema, M. A., Spann, N. J., Tao, J., Fonseca, G. J., Le, T., Stolze, L. K., Sakai, M., et al. (2022) · eLife · doi:10.7554/elife.70878 · Cited by 25

Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens

Barajas-Mora, E. M., Lee, L., Lu, H., Valderrama, J. A., Bjånes, E., Nizet, V., Feeney, A. J., Hu, M., & Murre, C. (2023) · Nature Immunology · doi:10.1038/s41590-022-01402-z · Cited by 26

Dynamic enhancer function in the chromatin context

Goldstein, I., & Hager, G. L. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1390 · Cited by 25

Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells

Rhee, C., Lee, B.-K., Beck, S., LeBlanc, L., Tucker, H., & Kim, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx692 · Cited by 24

Regeneration enhancers: Starting a journey to unravel regulatory events in tissue regeneration

Rodriguez, A., & Kang, J. (2019) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2019.04.003 · Cited by 25

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer

Weigel, C., Chaisaingmongkol, J., Assenov, Y., Kuhmann, C., Winkler, V. F., Santi, I., Bogatyrova, O., Kaucher, S., Bermejo, J. L., Leung, S. Y., et al. (2019) · Clinical Epigenetics · doi:10.1186/s13148-019-0666-5 · Cited by 25

Mechanisms Underlying the Selection and Function of Macrophage-Specific EnhancersPreprint

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Chromatin Landscape During Skeletal Muscle Differentiation

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Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals

Alizada, A., Khyzha, N., Wang, L., Antounians, L., Chen, X., Khor, M., Liang, M., Rathnakumar, K., Weirauch, M. T., Medina-Rivera, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20765-1 · Cited by 24

A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation

Donohue, L. K. H., Guo, M. G., Zhao, Y., Jung, N., Bussat, R. T., Kim, D. S., Neela, P. H., Kellman, L. N., Garcia, O. S., Meyers, R. M., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100191 · Cited by 25

MyoD-Induced Trans-Differentiation: A Paradigm for Dissecting the Molecular Mechanisms of Cell Commitment, Differentiation and Reprogramming

Battistelli, C., Garbo, S., & Maione, R. (2022) · Cells · doi:10.3390/cells11213435 · Cited by 24

Transcription factor antagonism regulates heterogeneity in embryonic stem cell states

Hu, S., Metcalf, E., Mahat, D. B., Chan, L., Sohal, N., Chakraborty, M., Hamilton, M., Singh, A., Singh, A., Lees, J. A., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.10.022 · Cited by 24

Anchoring super-enhancer-driven oncogenic lncRNAs for anti-tumor therapy in hepatocellular carcinoma

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Efficient knock-in method enabling lineage tracing in zebrafish

Mi, J., & Andersson, O. (2023) · Life Science Alliance · doi:10.26508/lsa.202301944 · Cited by 25

Enhancer-MDLF: a novel deep learning framework for identifying cell-specific enhancers

Zhang, Y., Zhang, P., & Wu, H. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae083 · Cited by 25

Genome-wide epigenetic analysis of MEF2A and MEF2C transcription factors in mouse cortical neurons

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Late-phase synthesis of IκBα insulates the TLR4-activated canonical NF-κB pathway from noncanonical NF-κB signaling in macrophages

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Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity

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Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types

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Histone chip-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity

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TBX2 acts as a potent transcriptional silencer of tumour suppressor genes through interaction with the CoREST complex to sustain the proliferation of breast cancers

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Transcriptional Activation of Ecdysone-Responsive Genes Requires H3K27 Acetylation at Enhancers

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Integrative Functional Genomics Identifies Systemic Lupus Erythematosus Causal Genetic Variant in the IRF5 Risk Locus

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miRNA-Mediated RNAa by Targeting Enhancers

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Chromatin reprogramming in breast cancer

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Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia

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Enhancer and super-enhancer landscape in polycystic kidney disease

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Function of BRD4 in the pathogenesis of high glucose‑induced cardiac hypertrophy

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Kupffer cells in liver homeostasis and disease: from immune sentinels to metabolic gatekeepers

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Mechanism and regulation of class switch recombination by IgH transcriptional control elements

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Epigenetic mechanisms underlying enhancer modulation of neuronal identity, neuronal activity and neurodegeneration

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Spatiotemporal dynamics of SETD5-containing NCoR–HDAC3 complex determines enhancer activation for adipogenesis

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Interplay between nuclear factor-κB, p38 MAPK, and glucocorticoid receptor signaling synergistically induces functional TLR2 in lung epithelial cells

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PHF20 is crucial for epigenetic control of starvation-induced autophagy through enhancer activation

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Epigenetics of neural differentiation: Spotlight on enhancers

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Cancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens

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Acetyltransferases CBP/p300 Control Transcriptional Switch of β-Catenin and Stat1 Promoting Osteoblast Differentiation

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The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm

Cheng, D., Cheng, T., Yang, X., Zhang, Q., Fu, J., Feng, T., Gong, J., & Xia, Q. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0216-y · Cited by 22

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection

Denisenko, E., Guler, R., Mhlanga, M. M., Suzuki, H., Brombacher, F., & Schmeier, S. (2019) · BMC Genomics · doi:10.1186/s12864-019-5450-6 · Cited by 22

An ensemble of regulatory elements controls Runx3 spatiotemporal expression in subsets of dorsal root ganglia proprioceptive neuronsPreprint

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Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolutionPreprint

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MeCP2 and non-CG DNA methylation stabilize the expression of long genes that distinguish closely related neuron types

Moore, J. R., Nemera, M. T., D’Souza, R. D., Hamagami, N., Clemens, A. W., Beard, D. C., Urman, A., Razia, Y., Mendoza, V. R., Law, T. E., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-01947-w · Cited by 21

Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

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Computational prediction and characterization of cell-type-specific and shared binding sites

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Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells

Zhao, M., Shao, N., Hu, S., Ma, N., Srinivasan, R., Jahanbani, F., Lee, J., Zhang, S., Snyder, M. P., & Wu, J. C. (2017) · Circulation Research · doi:10.1161/circresaha.117.311367 · Cited by 21

From association to mechanism in complex disease genetics: the role of the 3D genome

Fu, Y., Tessneer, K. L., Li, C., & Gaffney, P. M. (2018) · Arthritis Research & Therapy · doi:10.1186/s13075-018-1721-x · Cited by 21

Biology and targeting of the Jumonji-domain histone demethylase family in childhood neoplasia: a preclinical overview

McCann, T. S., Sobral, L. M., Self, C., Hsieh, J. C. Y., Sechler, M., & Jedlicka, P. (2019) · Expert Opinion on Therapeutic Targets · doi:10.1080/14728222.2019.1580692 · Cited by 21

Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility

Molineros, J. E., Singh, B., Terao, C., Okada, Y., Kaplan, J., McDaniel, B., Akizuki, S., Sun, C., Webb, C. F., Looger, L. L., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01066 · Cited by 21

B-cell leukemia transdifferentiation to macrophage involves reconfiguration of DNA methylation for long-range regulation

Bueno-Costa, A., Piñeyro, D., Soler, M., Javierre, B. M., Raurell‐Vila, H., Subirana-Granés, M., Pasquali, L., Martinez-Climent, J. A., & Esteller, M. (2019) · Leukemia · doi:10.1038/s41375-019-0643-1 · Cited by 21

3D genome organization during lymphocyte development and activation

Schoonhoven, A. O.-V., Huylebroeck, D., Hendriks, R. W., & Stadhouders, R. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz030 · Cited by 24

Context‐dependent transcriptional regulation of microglial proliferation

Belhocine, S., Xavier, A. M., Distéfano‐Gagné, F., Fiola, S., Rivest, S., & Gosselin, D. (2021) · Glia · doi:10.1002/glia.24124 · Cited by 21

Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation

Viiri, L. E., Rantapero, T., Kiamehr, M., Alexanova, A., Oittinen, M., Viiri, K. M., Niskanen, H., Nykter, M., Kaikkonen, M. U., & Aalto‐Setälä, K. (2019) · Scientific Reports · doi:10.1038/s41598-019-39215-0 · Cited by 21

Transcription activation depends on the length of the RNA polymerase II C‐terminal domain

Sawicka, A., Villamil, G., Lidschreiber, M., Darzacq, X., Dugast‐Darzacq, C., Schwalb, B., & Cramer, P. (2021) · The EMBO Journal · doi:10.15252/embj.2020107015 · Cited by 22

A Super-Enhancer Driven by FOSL1 Controls miR-21-5p Expression in Head and Neck Squamous Cell Carcinoma

Wan, Y., Hoyle, R. G., Xie, N., Wang, W., Cai, H., Zhang, M., Ma, Z., Xiong, G., Xu, X., Huang, Z., et al. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.656628 · Cited by 20

An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo

Chan, Y.-C., Kienle, E., Oti, M., Liddo, A. D., Méndez-Lago, M., Aschauer, D. F., Peter, M., Pagani, M., Arnold, C. D., Vonderheit, A., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-33448-w · Cited by 21

JUN-induced super-enhancer RNA forms R-loop to promote nasopharyngeal carcinoma metastasis

Jia, Q., Tan, Y., Li, Y., Yao, W., Wang, J., & Tang, F. (2023) · Cell Death and Disease · doi:10.1038/s41419-023-05985-9 · Cited by 21

TEAD1 is crucial for developmental myelination, Remak bundles, and functional regeneration of peripheral nerves

Grove, M., Kim, H., Pang, S., Amaya, J. P., Hu, G., Zhou, J., Lemay, M. A., & Son, Y. (2024) · eLife · doi:10.7554/elife.87394 · Cited by 20

EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases

Mao, F., Liu, Q., Zhao, X., Yang, H., Guo, S., Xiao, L., Li, X., Teng, H., Sun, Z. S., & Dou, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx918 · Cited by 20

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 25

State-specific enhancer landscapes govern microglial plasticity

Hamagami, N., Kapadia, D., Barclay, K. M., Yanlong, H., Abduljawad, N., Cheng, Z., McLaughlin, L., Singhania, D., Ding, X., Yang, J., et al. (2026) · Immunity · doi:10.1016/j.immuni.2025.11.023 · Cited by 20

LSD1 is required for euchromatic origin firing and replication timing

Wang, Y., Huang, Y., Cheng, E., Liu, X., Zhang, Y., Yang, J., Young, J. T. F., Brown, G. W., Yang, X., & Shang, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00927-x · Cited by 19

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Mu, W.-C., Sarkar, H., Srivastava, A., Choi, K., Patro, R., & Love, M. (2021) · bioRxiv · doi:10.1093/bioinformatics/btac212 · Cited by 19

The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation

Mantica, F., & Irimia, M. (2022) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020653 · Cited by 20

TGFβ1-Induced EMT in the MCF10A Mammary Epithelial Cell Line Model Is Executed Independently of SNAIL1 and ZEB1 but Relies on JUNB-Coordinated Transcriptional Regulation

Antón-García, P., Haghighi, E. B., Rose, K., Vladimirov, G., Boerries, M., & Hecht, A. (2023) · Cancers · doi:10.3390/cancers15020558 · Cited by 19

A genomic enhancer signature associates with hepatocellular carcinoma prognosis

Jeon, A., Anene-Nzelu, C. G., Teo, Y.-Y., Chong, S. L., Sekar, K., Wu, L., Chew, S.-C., Chen, J., Kendarsari, R. I., Lai, H. L. H., et al. (2023) · JHEP Reports · doi:10.1016/j.jhepr.2023.100715 · Cited by 19

Miswired Proprioception in Amyotrophic Lateral Sclerosis in Relation to Pain Sensation (and in Delayed Onset Muscle Soreness)—Is Piezo2 Channelopathy a Principal Transcription Activator in Proprioceptive Terminals Besides Being the Potential Primary Damage?

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Likely Pathogenic Variants of Cav1.3 and Nav1.1 Encoding Genes in Amyotrophic Lateral Sclerosis Could Elucidate the Dysregulated Pain Pathways

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Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease

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

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Macrophage SREBP1 regulates skeletal muscle regeneration

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Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genesPreprint

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