Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

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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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

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Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing

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

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The accessible chromatin landscape of the human genome

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

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Widespread transcription at neuronal activity-regulated enhancers

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A unique chromatin signature uncovers early developmental enhancers in humans

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Exploiting genomics and natural genetic variation to decode macrophage enhancers

Romanoski, C. E., Link, V. M., Heinz, S., & Glass, C. K. (2015) · Trends in Immunology · doi:10.1016/j.it.2015.07.006 · Cited by 35

Epigenetic histone modifications and master regulators as determinants of context dependent nuclear receptor activity in bone cells

Pike, J. W., Meyer, M. B., John, H. C. S., & Benkusky, N. A. (2015) · Bone · doi:10.1016/j.bone.2015.03.012 · Cited by 35

Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS

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Chromatin remodeling effects on enhancer activity

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The transcription factor PU.1 mediates enhancer-promoter looping that is required for IL-1β eRNA and mRNA transcription in mouse melanoma and macrophage cell lines

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Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages

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Histone H3K4 Methyltransferases as Targets for Drug-Resistant Cancers

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Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cellsPreprint

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IL-1β+ macrophages and the control of pathogenic inflammation in cancer

Caronni, N., Terza, F. L., Frosio, L., & Ostuni, R. (2025) · Trends in Immunology · doi:10.1016/j.it.2025.03.001 · Cited by 36

There goes the neighborhood: Assembly of transcriptional complexes during the regulation of metabolism and inflammation by the glucocorticoid receptor

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Neurobiological basis for pain vulnerability: why me?

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Transcriptional repression in macrophages—basic mechanisms and alterations in metabolic inflammatory diseases

Treuter, E., Fan, R., Huang, Z., Jakobsson, T., & Venteclef, N. (2017) · FEBS Letters · doi:10.1002/1873-3468.12850 · Cited by 37

Diverse mechanisms of IRF5 action in inflammatory responses

Khoyratty, T. E., & Udalova, I. A. (2018) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2018.03.012 · Cited by 34

PHLPP1 counter-regulates STAT1-mediated inflammatory signaling

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Histone–lysine N-methyltransferase 2 (KMT2) complexes – a new perspective

Poręba, E., Leśniewicz, K., & Durzyńska, J. (2022) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2022.108443 · Cited by 34

Super-enhancer lncs to cardiovascular development and disease

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Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemiaPreprint

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Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation

Boileau, R. M., Chen, K. X., & Blelloch, R. H. (2023) · Genome biology · doi:10.1186/s13059-023-02883-3 · Cited by 35

Preparing the First Responders: Building the Inflammatory Transcriptome from the Ground Up

Rogatsky, I., & Adelman, K. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.03.038 · Cited by 33

Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers

Soldi, M., Mari, T., Nicosia, L., Musiani, D., Sigismondo, G., Cuomo, A., Pavesi, G., & Bonaldi, T. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx821 · Cited by 38

Integration of transcriptional and metabolic control in macrophage activation

Natoli, G., Pileri, F., Gualdrini, F., & Ghisletti, S. (2021) · EMBO Reports · doi:10.15252/embr.202153251 · Cited by 33

Molecular and Genomic Landscape of Peripheral T-Cell Lymphoma

Iqbal, J., Amador, C., McKeithan, T. W., & Chan, W. C. (2018) · Cancer treatment and research · doi:10.1007/978-3-319-99716-2_2 · Cited by 35

Genome-wide interaction target profiling reveals a novel Peblr20-eRNA activation pathway to control stem cell pluripotency

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Aberrant Activity of Histone–Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis

Poręba, E., Leśniewicz, K., & Durzyńska, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21249340 · Cited by 31

Regulation of Macrophage Activation and Differentiation in Atherosclerosis

Park, S. H. (2021) · Journal of Lipid and Atherosclerosis · doi:10.12997/jla.2021.10.3.251 · Cited by 33

Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells

Moreau, P. R., Örd, T., Downes, N. L., Niskanen, H., Bouvy‐Liivrand, M., Aavik, E., Ylä‐Herttuala, S., & Kaikkonen, M. U. (2018) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2018.00159 · Cited by 32

Epigenetic Mechanisms Regulating Adaptive Responses to Targeted Kinase Inhibitors in Cancer

Angus, S. P., Zawistowski, J. S., & Johnson, G. L. (2017) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010617-052954 · Cited by 32

Monocyte Enhancers are Highly Altered in Systemic Lupus Erythematosus

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Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis

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Efficient mutation screening for cervical cancers from circulating tumor DNA in blood

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Inhibition of Interleukin 1β (IL-1β) Expression by Anthrax Lethal Toxin (LeTx) Is Reversed by Histone Deacetylase 8 (HDAC8) Inhibition in Murine Macrophages

Ha, S.-D., Reid, C., Meshkibaf, S., & Kim, S. O. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.695809 · Cited by 30

Divergent transcription and epigenetic directionality of human promoters

Lacadie, S. A., Ibrahim, M. M., Gokhale, S., & Ohler, U. (2016) · FEBS Journal · doi:10.1111/febs.13747 · Cited by 28

eRNA binding produces tailored CBP activity profiles to regulate gene expression

Bose, D. A., & Berger, S. L. (2017) · RNA Biology · doi:10.1080/15476286.2017.1353862 · Cited by 29

Long non-coding RNAs regulating macrophage functions in homeostasis and disease

Scacalossi, K. R., Solingen, C. V., & Moore, K. J. (2018) · Vascular Pharmacology · doi:10.1016/j.vph.2018.02.011 · Cited by 29

Beyond association: successes and challenges in linking non-coding genetic variation to functional consequences that modulate Alzheimer’s disease risk

Novikova, G., Andrews, S. J., Renton, A. E., & Marcora, E. M. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00449-0 · Cited by 31

It’s a DoG-eat-DoG world—altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production

Morgan, M. A., Shiekhattar, R., Shilatifard, A., & Lauberth, S. M. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.04.008 · Cited by 32

Genome-wide profiling of transcribed enhancers during macrophage activation

Denisenko, E., Guler, R., Mhlanga, M. M., Suzuki, H., Brombacher, F., & Schmeier, S. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0158-9 · Cited by 29

PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution

Vihervaara, A., Versluis, P. P., Himanen, S. V., & Lis, J. T. (2023) · Nature Communications · doi:10.1038/s41467-023-42715-3 · Cited by 29

Particle uptake by macrophages triggers bifurcated transcriptional pathways that differentially regulate inflammation and lysosomal gene expression

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Epigenetic Regulation of Myeloid Cells

Ivashkiv, L. B., & Park, S. H. (2016) · Microbiology Spectrum · doi:10.1128/microbiolspec.mchd-0010-2015 · Cited by 27

Tunable, division-independent control of gene activation timing by a polycomb switch

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Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

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Functional noncoding SNPs in human endothelial cells fine-map vascular trait associationsPreprint

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Glucocorticoid receptor-regulated enhancers play a central role in the gene regulatory networks underlying drug addiction

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Accelerating promoter identification and design by deep learning

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Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation

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Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses

Devenish, L. P., Mhlanga, M. M., & Negishi, Y. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.662565 · Cited by 27

Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients

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Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality

Pundhir, S., Bagger, F. O., Lauridsen, F. B., Rapin, N., & Porse, B. T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw250 · Cited by 26

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

Moreau, P. R., Bosch, V. T., Bouvy‐Liivrand, M., Õunap, K., Örd, T., Pulkkinen, H. H., Pölönen, P., Heinäniemi, M., Ylä‐Herttuala, S., Laakkonen, J. P., et al. (2021) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.121.315579 · Cited by 26

Resetting the epigenome for heart regeneration.

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Transcriptional regulation by the KMT2 histone H3K4 methyltransferases

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

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Role of Enhancers in Development and Diseases

Maurya, S. S. (2021) · Epigenomes · doi:10.3390/epigenomes5040021 · Cited by 26

Dynamic interplay between non-coding enhancer transcription and gene activity in development

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Mechanisms Underlying the Selection and Function of Macrophage-Specific EnhancersPreprint

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Inflammatory tissue priming: novel insights and therapeutic opportunities for inflammatory rheumatic diseases

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Establishment and function of chromatin modification at enhancers

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Trained Immunity as a Preventive Measure for Surgical Site Infections

ter Steeg, L., Domínguez‐Andrés, J., Netea, M. G., Joosten, L. A. B., & van Crevel, R. (2021) · Clinical Microbiology Reviews · doi:10.1128/cmr.00049-21 · Cited by 24

3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells

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Loss of Kmt2c in vivo leads to EMT, mitochondrial dysfunction and improved response to lapatinib in breast cancer

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Genetic and Genomic Approaches to Understanding Macrophage Identity and Function

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CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands

van de Lagemaat, L. N., Flenley, M., Lynch, M., Garrick, D., Tomlinson, S. R., Kranc, K. R., & Vernimmen, D. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0230-0 · Cited by 24

H. pylori infection confers resistance to apoptosis via Brd4-dependent BIRC3 eRNA synthesis

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Phase separation drives the formation of biomolecular condensates in the immune system

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Chromatin reprogramming in breast cancer

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

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Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation

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The MLL/SET family and haematopoiesis

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Vespucci: a system for building annotated databases of nascent transcripts

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Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development

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

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Characterization of sequence determinants of enhancer function using natural genetic variation

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Isolation of the protein and RNA content of active sites of transcription from mammalian cells

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Functional genomics of autoimmune diseases

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Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies

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KMT2C-deficient tumors have elevated APOBEC mutagenesis and genomic instability in multiple cancers

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Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status

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Dysregulation of macrophage development and phenotype in diabetic human macrophages can be rescued by Hoxa3 protein transduction

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The therapeutic and diagnostic potential of regulatory noncoding RNAs in medulloblastoma

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Chromatin structure and gene regulation: a dynamic view of enhancer function

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DNA methylation and histone modifications drive the trained immunity duration

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The genome-wide molecular signature of transcription factors in leukemia

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Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

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MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping

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