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chromhmm model  (Epigenomics ag)

 
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    Structured Review

    Epigenomics ag chromhmm model
    rs138300818 G insertion allele—protecting from early-onset T1D—creates a thymocyte motif ( a ). At the same time, this motif disrupts the RFX5/7 binding motif which is present with the rs138300818 reference (null) allele ( b ). rs138300818 is located intronic in PTPRK . Non-coding RNA transcription was detected overlapping rs138300818 (grey vertical line) in all four studied thymocyte cell types (dark blue peaks). <t>Roadmap</t> Epigenomics chromatin state data for fetal thymus (PrimaryHMM) indicated strong transcription (state 4, green bar) overlapping the SNP flanking region ( c ). PCHiC data in fetal thymocytes and in naïve CD8 cells suggests that rs138300818 interacts with both PTPRK and THEMIS transcription start sites. The genetic association signal for early-onset T1D is colocalized with eQTL signal for THEMIS in human whole blood; rs138300818 reference allele—which forms the RFX7/5 binding motif—is associated with higher THEMIS expression ( d ).
    Chromhmm Model, supplied by Epigenomics ag, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants"

    Article Title: Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants

    Journal: Scientific Reports

    doi: 10.1038/s41598-022-18296-4

    rs138300818 G insertion allele—protecting from early-onset T1D—creates a thymocyte motif ( a ). At the same time, this motif disrupts the RFX5/7 binding motif which is present with the rs138300818 reference (null) allele ( b ). rs138300818 is located intronic in PTPRK . Non-coding RNA transcription was detected overlapping rs138300818 (grey vertical line) in all four studied thymocyte cell types (dark blue peaks). Roadmap Epigenomics chromatin state data for fetal thymus (PrimaryHMM) indicated strong transcription (state 4, green bar) overlapping the SNP flanking region ( c ). PCHiC data in fetal thymocytes and in naïve CD8 cells suggests that rs138300818 interacts with both PTPRK and THEMIS transcription start sites. The genetic association signal for early-onset T1D is colocalized with eQTL signal for THEMIS in human whole blood; rs138300818 reference allele—which forms the RFX7/5 binding motif—is associated with higher THEMIS expression ( d ).
    Figure Legend Snippet: rs138300818 G insertion allele—protecting from early-onset T1D—creates a thymocyte motif ( a ). At the same time, this motif disrupts the RFX5/7 binding motif which is present with the rs138300818 reference (null) allele ( b ). rs138300818 is located intronic in PTPRK . Non-coding RNA transcription was detected overlapping rs138300818 (grey vertical line) in all four studied thymocyte cell types (dark blue peaks). Roadmap Epigenomics chromatin state data for fetal thymus (PrimaryHMM) indicated strong transcription (state 4, green bar) overlapping the SNP flanking region ( c ). PCHiC data in fetal thymocytes and in naïve CD8 cells suggests that rs138300818 interacts with both PTPRK and THEMIS transcription start sites. The genetic association signal for early-onset T1D is colocalized with eQTL signal for THEMIS in human whole blood; rs138300818 reference allele—which forms the RFX7/5 binding motif—is associated with higher THEMIS expression ( d ).

    Techniques Used: Binding Assay, Expressing

    Related Articles

    other:

    Article Title: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability
    Article Snippet: The pre-trained 18 state chromHMM model based on the six histone marks was applied to the binarized bed files, using the MakeSegmentation script provided and the model parameters downloaded from the Roadmap Epigenomics web portal.

    Article Title: Rare germline structural variants increase risk for pediatric solid tumors
    Article Snippet: Enhancer, genic enhancer, bivalent enhancer, and flanking active transcription start site annotations were used from the Roadmap Epigenomics Project 15-state ChromHMM model (24).

    Article Title: An RNA-informed dosage sensitivity map reflects the intrinsic functional nature of genes.
    Article Snippet: All chromatin features were based on the Roadmap Epigenomics Project32 using the core 15-state ChromHMM33 model, where 27 Roadmap tissues were mapped to 26 GTEx tissues.

    Article Title: Autism Spectrum Disorder: Understanding the Impact of SNPs on Biological Pathways in the Fetal and Adult Cortex
    Article Snippet: Enrichment within active regulatory elements and histone modi cation marks was identi ed using the Roadmap Epigenomics Project 15- state ChromHMM models28,70 for adult dorsolateral prefrontal cortex (E073_15_coreMarks_hg38lift_mnemonics.bed.gz) and fetal brain (E081_15_coreMarks_hg38lift_mnemonics.bed.gz) (downloaded from https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/ nal/, 22/11/2020) (Supplementary Table 1).

    Modification:

    Article Title: Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants
    Article Snippet: .. Roadmap Epigenomics fetal thymus ChromHMM model —based on histone modification data—predicted strong transcription overlapping rs138300818 (Fig. ). ..

    Derivative Assay:

    Article Title: Genetic analyses in multiplex families confirms chromosome 5q35 as a risk locus for Alzheimer's Disease in individuals of African Ancestry.
    Article Snippet: .. These annotation datasets included; The RoadMap Epigenome Project (Roadmap Epigenomics Consortium et al., 2015) primary chromHMM models in AD relevant cell types (H1 derived Neuronal progenitor cells, H9 derived neuron cultured cells, brain prefrontal cortex, brain hippocampus, brain cingulate gyrus, brain mid frontal lobe), promoter capture C conformational data from neurons (Chesi et al., 2019) directly identifying interactions between genomic regions and the promoter they putatively act upon, and Hi-C conformational data from brain adult cortex providing a higher level identification of regional interactions (Lu et al., 2020). ..

    Cell Culture:

    Article Title: Genetic analyses in multiplex families confirms chromosome 5q35 as a risk locus for Alzheimer's Disease in individuals of African Ancestry.
    Article Snippet: .. These annotation datasets included; The RoadMap Epigenome Project (Roadmap Epigenomics Consortium et al., 2015) primary chromHMM models in AD relevant cell types (H1 derived Neuronal progenitor cells, H9 derived neuron cultured cells, brain prefrontal cortex, brain hippocampus, brain cingulate gyrus, brain mid frontal lobe), promoter capture C conformational data from neurons (Chesi et al., 2019) directly identifying interactions between genomic regions and the promoter they putatively act upon, and Hi-C conformational data from brain adult cortex providing a higher level identification of regional interactions (Lu et al., 2020). ..

    Capture-C:

    Article Title: Genetic analyses in multiplex families confirms chromosome 5q35 as a risk locus for Alzheimer's Disease in individuals of African Ancestry.
    Article Snippet: .. These annotation datasets included; The RoadMap Epigenome Project (Roadmap Epigenomics Consortium et al., 2015) primary chromHMM models in AD relevant cell types (H1 derived Neuronal progenitor cells, H9 derived neuron cultured cells, brain prefrontal cortex, brain hippocampus, brain cingulate gyrus, brain mid frontal lobe), promoter capture C conformational data from neurons (Chesi et al., 2019) directly identifying interactions between genomic regions and the promoter they putatively act upon, and Hi-C conformational data from brain adult cortex providing a higher level identification of regional interactions (Lu et al., 2020). ..

    Hi-C:

    Article Title: Genetic analyses in multiplex families confirms chromosome 5q35 as a risk locus for Alzheimer's Disease in individuals of African Ancestry.
    Article Snippet: .. These annotation datasets included; The RoadMap Epigenome Project (Roadmap Epigenomics Consortium et al., 2015) primary chromHMM models in AD relevant cell types (H1 derived Neuronal progenitor cells, H9 derived neuron cultured cells, brain prefrontal cortex, brain hippocampus, brain cingulate gyrus, brain mid frontal lobe), promoter capture C conformational data from neurons (Chesi et al., 2019) directly identifying interactions between genomic regions and the promoter they putatively act upon, and Hi-C conformational data from brain adult cortex providing a higher level identification of regional interactions (Lu et al., 2020). ..

    Sequencing:

    Article Title: Thymocyte regulatory variant alters transcription factor binding and protects from type 1 diabetes in infants.
    Article Snippet: .. Roadmap Epigenomics fetal thymus ChromHMM model28—based on histone Figure 2. rs138300818 G insertion allele significantly increases sequence similarity with a thymocyte H3K27ac motif in CD4+αß cells. (a) Overlap between a thymocyte H3K27ac motif and rs138300818 alternative G allele (highlighted with star) and reference null allele flanking sequence. ..



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