Journal: Biophysical Journal

Article Title: Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C

doi: 10.1016/j.bpj.2019.06.032

Figure Lengend Snippet: The pipeline of the HLM. (A) Contact probability matrix P of a 10-Mb genomic region of chr5 in GM12878 cells is shown. (B) Z matrix calculated from Eq. 7 is shown above the diagonal. The significant contacts selected from Z are shown below the diagonal. The sign of the first principal component of Z is provided on the left-hand side of the panel, and we divide the whole chromosome domain into “L” (purple), “M” (green), and “N” (orange) accordingly. (C) The interaction strength matrix K˜ calculated by the constrained optimization is shown. (D) The conformational ensemble of chromosomes generated from HLM potential defined by K˜ and Z (Eq. 1) is illustrated with the L, M, and N domains colored in purple, green, and orange, respectively, following the domain labels assigned in (B). (E) shows P˜-matrix calculated using a conformational ensemble produced from molecular dynamics simulations. The PC between P (A) and P˜ (E) is 0.96. To see this figure in color, go online.

Article Snippet: We simulated chr5 of GM12878 cells at 50-kb resolution with MiChroM ( Fig. S13 G ) and compared PC( s ) of a 10-Mb region based on both models ( Fig. S13 H ).

Techniques: Generated, Produced

Journal: Biophysical Journal

Article Title: Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C

doi: 10.1016/j.bpj.2019.06.032

Figure Lengend Snippet: Genomic Regions Simulated in This Work

Article Snippet: We simulated chr5 of GM12878 cells at 50-kb resolution with MiChroM ( Fig. S13 G ) and compared PC( s ) of a 10-Mb region based on both models ( Fig. S13 H ).

Techniques:

Journal: Immunity

Article Title: Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma

doi: 10.1016/j.immuni.2014.12.021

Figure Lengend Snippet: A) Number of TSSs with chromatin fold-change that is concordant with nearby variable DREs (within 500kb). B) Mean transcript abundance as determined by RNA-Seq for genes linked to augmented, unchanged or attenuated DREs and located within the distances shown from the DREs. Statistical significance (Mann-Whitney test): *p≤ 0.05 ** p≤ 0.01, **** p≤ 0.0001. C) UCSC Genome Browser views of H3K27ac ChIP-seq data, showing augmented DREs (highlighted in blue). RNA-seq data depict the corresponding up-regulation of mRNA from DRE target genes. The bottom track shows significant spatial interactions in GM12878 B cells (ENCODE, 5C data) between restriction fragments encompassing the DREs and restriction fragments near the target gene TSSs (Sanyal et al., 2012).

Article Snippet: Published 5C data for the B lymphoblastoid cell line GM12878 confirms interactions between these DREs and regions proximal to many of the TSSs ( Sanyal et al., 2012 ).

Techniques: RNA Sequencing, MANN-WHITNEY, ChIP-sequencing

Journal: Immunity

Article Title: Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma

doi: 10.1016/j.immuni.2014.12.021

Figure Lengend Snippet: A) Heatmap representation of enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways identified from down-regulated genes within 500kb of attenuated DREs. B) Expression profiles (microarray) for TFs predicted to bind motifs in attenuated DREs. Refer to Table S6 for expression values. C) SPIB transcripts, as measured by qPCR, in GM12878 cells transfected with either control or SPIB shRNA. Results represent the mean ± SEM of three independent experiments. D) H3K27ac ChIP assays in GM12878 cells transfected with control or SPIB-specific shRNA. Associated DNA was analyzed via qPCR using primers spanning DREs harboring SPIB binding sites. Results represent the mean ± SEM of three independent experiments. E) Transcript levels for DRE target genes, as measured by qPCR, in GM12878 cells transfected with either control or SPIB-specific shRNA. Results represent the mean ± SEM of three independent experiments. Statistical significance (unpaired t-test): * p≤ 0.05.

Article Snippet: Published 5C data for the B lymphoblastoid cell line GM12878 confirms interactions between these DREs and regions proximal to many of the TSSs ( Sanyal et al., 2012 ).

Techniques: Expressing, Microarray, Transfection, Control, shRNA, Binding Assay

Journal: Immunity

Article Title: Enhancer Sequence Variants and Transcription Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B Cell Lymphoma

doi: 10.1016/j.immuni.2014.12.021

Figure Lengend Snippet: A) UCSC Genome Browser views of H3K27ac ChIP-seq data illustrating attenuated DREs harboring the indicated sequence variants in FL and the reference sequence in CC (upper 2 tracks). The bottom track shows ChIP-seq data for the indicated TFs performed in the GM12878 B cell line (Neph et al., 2012). Arrows indicate the variant sequence and location in PWMs for each TF. B) Expression of the DRE target genes quantified by microarray analysis. C) Oligonucleotide precipitation assays demonstrate reduced TF binding in variant-containing compared to reference sequences. Western blots were probed with antibodies specific to the TF of interest (representative of three experimental replicates). D) Luciferase reporter assays performed in lymphoma cell lines demonstrate significantly reduced activity for the variant-containing compared to reference sequences in the attenuated DREs. Luciferase activity is presented as a fold change for the enhancer vector relative to a reporter containing only the SV40 promoter (set to a value of 1.0). Results represent the mean ± SEM of three independent experiments. Statistical significance (paired t-test): * p≤ 0.05.

Article Snippet: Published 5C data for the B lymphoblastoid cell line GM12878 confirms interactions between these DREs and regions proximal to many of the TSSs ( Sanyal et al., 2012 ).

Techniques: ChIP-sequencing, Sequencing, Variant Assay, Expressing, Microarray, Binding Assay, Western Blot, Luciferase, Activity Assay, Plasmid Preparation

Journal: The Journal of Molecular Diagnostics : JMD

Article Title: Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors

doi: 10.1016/j.jmoldx.2017.05.006

Figure Lengend Snippet: Potential clinical applications of OSU-SpARKFuse. A: Venn diagram representing concordance of variant calls from OSU-SpARKFuse and high-confidence variant calls from National Institute of Standards and Technology (NIST) for the GM12878 cell line. B: Genome Browser screen shot depicting C to G bp substitution, resulting in a C481S mutation in a patient with chronic lymphocytic leukemia resistant to treatment with ibrutinib. C: Mean exon-level read depth for indicated MET exons (https://www.ncbi.nlm.nih.gov/refseq; accession number NM_001127500). Red text indicates skipped exon. Asterisk represents untranslated region not covered by OSU-SpARKFuse probes.

Article Snippet: To gauge the accuracy of identifying SNPs from RNAseq data, we used the HapMap cell line GM12878 that was extensively characterized by the National Institute of Standards and Technology (NIST) and has publically available data for high-confidence SNP calls based on various DNAseq methods.

Techniques: Variant Assay, Mutagenesis

Journal: Scientific Reports

Article Title: Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

doi: 10.1038/s41598-022-12568-9

Figure Lengend Snippet: iPALM imaging of a target chromatin loop region. ( A ) GM12878 Hi-C (top left) and CTCF and RNAPII merged ChIA-PET (top right) contact map for the target region chromosome 14: 23.016–23.049 Mb (hg19, 1 Kb resolution with balanced normalization), as well as ChIA-PET genome browser view for the same region (bottom). ChIA-PET loops (green for CTCF and blue for RNAPII) are also presented on top of the upper diagonal area of the contact maps. In the browser view, CTCF loops and peaks (green), RNAPII loops and peaks (blue), and genes localized in the target region are presented. ( B ) Schematic of the target loop region inferred by ChIA-PET data with attached oligopaint probe. ( C ) Schematic of the iPALM method. The probe set contains 336 DNA oligos tagged with Atto647N designed to stain along the target chromatin region ( D ) Representative images of the target region from 6 different cells obtained by iPALM.

Article Snippet: To compare our results with higher resolution genomic data we processed publicly available GM12878 Micro-C data from Dovetail Genomics.

Techniques: Imaging, Hi-C, ChIA Pet Assay, Staining