The selection and function of cell type-specific enhancers

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6. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
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7. Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms
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8. IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer’s Disease
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12. Super-enhancers and the super-enhancer reader BRD4: tumorigenic factors and therapeutic targets
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14. Super-Enhancers Promote Transcriptional Dysregulation in Nasopharyngeal Carcinoma
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17. Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers
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19. Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo
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20. The Mediator kinase module: an interface between cell signaling and transcription
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21. Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling
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22. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation
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23. Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription
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24. Intragenic Enhancers Attenuate Host Gene Expression
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26. A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface
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27. Targeting Super-Enhancers for Disease Treatment and Diagnosis.
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28. Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression
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30. An immunoregulatory and tissue-residency program modulated by c-MAF in human TH17 cells
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31. Transcriptional Regulation of Inflammasomes
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33. Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells
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34. Progress and challenges in bioinformatics approaches for enhancer identification
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35. Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers
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36. Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
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37. LINE-1 transcription activates long-range gene expression
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39. An expanded registry of candidate cis-regulatory elements
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40. The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells
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41. INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma
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42. Perivascular mesenchymal cells control adipose-tissue macrophage accrual in obesity
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43. Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A
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44. McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
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45. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex
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46. Molecular principles underlying aggressive cancers
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47. Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-β/SMAD3 pathway
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48. From thymus to tissues and tumors: A review of T-cell biology
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49. Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation
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50. Super-enhancer RNA m6A promotes local chromatin accessibility and oncogene transcription in pancreatic ductal adenocarcinoma
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51. Metformin inhibits pancreatic cancer metastasis caused by SMAD4 deficiency and consequent HNF4G upregulation
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52. OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation
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53. An autonomous CEBPA enhancer specific for myeloid-lineage priming and neutrophilic differentiation
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54. Enhancers with tissue-specific activity are enriched in intronic regions
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55. Invited Review: Epigenetics in neurodevelopment
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56. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
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57. Is a super-enhancer greater than the sum of its parts?
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58. Nuclei isolation of multiple brain cell types for omics interrogation
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59. Transcriptional control by enhancers and enhancer RNAs
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60. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages
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61. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
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64. Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function
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65. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
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66. Pregnancy, preeclampsia and maternal aging: From epidemiology to functional genomics
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67. LDB1-mediated enhancer looping can be established independent of mediator and cohesin
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68. STARR‐seq and UMI‐STARR‐seq: Assessing Enhancer Activities for Genome‐Wide‐, High‐, and Low‐Complexity Candidate Libraries
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69. Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
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70. Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics
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71. Physiological inputs regulate species-specific anatomy during embryogenesis and regeneration
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72. Topoisomerases and the regulation of neural function
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73. Epigenomes in Cardiovascular Disease
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74. Targeted Enhancer Activation by a Subunit of the Integrator Complex
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75. Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision
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76. The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling
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77. ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
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78. Epigenetic and metabolic programming of innate immunity in sepsis
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79. Integrative machine learning framework for the identification of cell-specific enhancers from the human genome
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80. RETRACTED: Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers
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81. Epigenetic Regulation of Kupffer Cell Function in Health and Disease
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82. Glucocorticoid receptor action in metabolic and neuronal function
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83. A shared Runx1-bound Zbtb16 enhancer directs innate and innate-like lymphoid lineage development
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84. Interplay of BAF and MLL4 promotes cell type-specific enhancer activation
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85. Irx3 is required for postnatal maturation of the mouse ventricular conduction system
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86. Monocyte and haematopoietic progenitor reprogramming as common mechanism underlying chronic inflammatory and cardiovascular diseases
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87. The interdependence of gene-regulatory elements and the 3D genome
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88. Spirits in the Material World: Enhancer RNAs in Transcriptional Regulation
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89. Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers
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90. Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching
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91. Pancreatic Cancer Heterogeneity Can Be Explained Beyond the Genome
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92. Signal Integration of IFN-I and IFN-II With TLR4 Involves Sequential Recruitment of STAT1-Complexes and NFκB to Enhance Pro-inflammatory Transcription
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93. Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis
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94. Pontin arginine methylation by CARM1 is crucial for epigenetic regulation of autophagy
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95. A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency
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96. MAnorm2 for quantitatively comparing groups of ChIP-seq samples
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97. ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells
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98. A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas
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99. Colocalization analyses of genomic elements: approaches, recommendations and challenges
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100. Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases
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