High Throughput Next Generation Sequencing: supports genomics and epigenomics research in muscle, skin, bone and autoimmune diseases

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The Genome Technology Section has been actively involved in a large number of NIAMS research projects, including the following: -Analysis of genomic organization of T lymphocytes to understand gene regulatory mechanisms for T helper cell fate specification and function. ATAC-seq, RNA-Seq and ChIP-Seq have been used to draw maps of chromatin states, chromatin accessibility and transcriptome revealing molecular mechanism for cell fate specification and function. - Study of specific regions of the bone sialoprotein (BSP) to determine specific regions of the BSP molecule responsible for promoting tooth root formation, through interacting with integrins, and regulating mineral formation during cementogenesis. - Study of somatic mutations in UBA1 and severe adult-onset Autoinflammarory Disease. - Dynamics of change in the epigenetic features observed during cellular activation of B-cells and its impacts on cellular activation by comparison of histone marks, nucleosome binding, transcription factor binding, DNA (de)methylation and 3-D nuclear structure using different sequencing technologies (ChIP-Seq, mRNA-seq, whole genome methyl-seq, 4C, Hi-C). - Impact of RNA binding proteins (RBPs) on posttranscriptional gene regulation (PTGR). - Impact of select RBPs on translation initiation and elongation. - Mutual crosstalk that occurs between the skin, the microbiota and resident leukocytes during steady-state and inflammation. - Specification and maintenance of cell lineages in the skin, and study of the regulation of stem cells in the skin. - Understanding the activity of chromatin regulators such as Polycomb proteins, the transcription factor Pst1, Ago2 and eRNAs in regulating gene expression during muscle differentiation. - Discovering the molecular mechanisms regulating metabolism and epigenetics during specification, differentiation, and regeneration of skeletal muscle cells. - Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus. - Homeostatic Control of Sebaceous Glands by Innate Lymphoid Cells Regulates Commensal Bacteria Equilibrium. -Analysis of chromatin accessibility and genomic organization of quiescent and differentiating muscle stem cells (satellite cells) by ATAC-seq. - Analysis of single cell transcriptome in several human and mouse models of disease and differentiation/cell fate specification. -Understanding the roll of cutaneous microbiome in eczematous skin diseases, including atopic dermatitis. -Sex differences in neutrophil biology modulate response to type I interferons and immunometabolism. -MicroRNA-221 and -222 modulate intestinal inflammatory Th17 cell response as negative feedback regulators downstream of interleukin-23. -Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of Natural Killer Cells. -Protocol for RNA-seq library preparation starting from a rare muscle stem cell population or a limited number of mouse embryonic stem cells. -FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age. -CTCF orchestrates long-range cohesin-driven V(D)J recombinational scanning. -Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. -A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol. -Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. -Loss of DLX3 tumor suppressive function promotes progression of squamous cell carcinoma through EGFRERBB2 pathway.