BATF-JUN is critical for IRF4-mediated transcription in T cells. The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8 + T cells. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Foxp3 + regulatory T cells: differentiation, specification, subphenotypes. Natural regulatory T cells in infectious disease.
Adoptive immunotherapy for cancer: harnessing the T cell response. Regulatory circuits of T cell function in cancer. Regulation of immunity by self-reactive T cells. T-cell signalling and autoimmunity: molecular mechanisms of disease. Type 2 diabetes as an inflammatory disease. Inflammation-induced cancer: crosstalk between tumours, immune cells and microorganisms. Population variation and genetic control of modular chromatin architecture in humans. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Identification of genetic variants that affect histone modifications in human cells. Extensive variation in chromatin states across humans. DNase I sensitivity QTLs are a major determinant of human expression variation. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Integrative analysis of 111 reference human epigenomes. The accessible chromatin landscape of the human genome. An expansive human regulatory lexicon encoded in transcription factor footprints. Architecture of the human regulatory network derived from ENCODE data. An integrated encyclopedia of DNA elements in the human genome.
File juicer 4.34 drivers#
Genetic drivers of epigenetic and transcriptional variation in human immune cells. The allelic landscape of human blood cell trait variation and links to common complex disease. Intersection of population variation and autoimmunity genetics in human T cell activation. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Transcriptome and genome sequencing uncovers functional variation in humans. Population genomics of human gene expression. Systematic localization of common disease-associated variation in regulatory DNA. Genome-wide association studies for common diseases and complex traits. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression. Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4 + T cells in up to 105 healthy donors. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease.
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