Journal: Nucleic Acids Research

Article Title: Analysis of epigenetic features characteristic of L1 loci expressed in human cells

doi: 10.1093/nar/gkac013

Figure Lengend Snippet: Promoters of L1 loci expressed in MCF7 cells are hypomethylated. Analysis of CpG methylation at promoters of expressed loci ( n = 160, orange), unexpressed loci ( n = 2,885, blue), total loci ( n = 4,815, purple), expressed loci with an ATAC peak ( n = 132), expressed loci without an ATAC peak ( n = 28), unexpressed loci with an ATAC peak ( n = 279), and unexpressed loci without an ATAC peak ( n = 2,606). A total of 158 loci were unmapped following bisulfite sequencing and thus excluded from this analysis. Significance between different groups of L1 loci was determined by Student's t -test (**** P < 0.0001).

Article Snippet: ATAC library preparation and PE sequencing were done by the Tulane Center for Translational Research in Infection and Inflammation NextGen Sequencing core according to their standard protocols seeding 2 million cells.

Techniques: CpG Methylation Assay, Methylation Sequencing

Journal: Nucleic Acids Research

Article Title: Analysis of epigenetic features characteristic of L1 loci expressed in human cells

doi: 10.1093/nar/gkac013

Figure Lengend Snippet: Long-distance interactions of specific L1-loci in MCF7 cells. Screenshots of Integrated Genomics Viewer of L1-2830 ( A ), L1-0650 ( B ) and L1-0238 ( C ) in MCF7 cells. L1-2830 is an expressed locus with the most mapped RNA-Seq reads in MCF7. L1-0650 is a ‘transitional’ locus, i.e. unexpressed locus with the second most ATAC-sequencing reads mapped. L1-0238 is a randomly-selected unexpressed locus. Information regarding the locus location (chromosome, start site, end site and orientation), RNA-Seq reads, presence of an ATAC peak, L1 sub-family, and number of reads from ATAC sequencing is shown in a table format at the top. Loops indicate CTCF binding sites (purple, shaded) within 500 kb of the L1 start site (black arrow). RNA polymerase II (Pol II) loops (red) are only shown if the pol II binding site overlaps within 500 bp of the L1 start site. Red arrows indicate magnification of the indicated genomic region that includes analysis of the activating histone marks from previously described CHIP-Seq data (Figure ). The status of each histone mark is examined in two experiments.

Article Snippet: ATAC library preparation and PE sequencing were done by the Tulane Center for Translational Research in Infection and Inflammation NextGen Sequencing core according to their standard protocols seeding 2 million cells.

Techniques: RNA Sequencing, Sequencing, Binding Assay, ChIP-sequencing

Journal: Nucleic Acids Research

Article Title: Analysis of epigenetic features characteristic of L1 loci expressed in human cells

doi: 10.1093/nar/gkac013

Figure Lengend Snippet: Comparative analysis of full-length L1 loci identified within the TTC28 gene. ( A ) Schematic of the TTC28 gene (black) and exons (heavy black bars) transcription start site (green arrow), seven full-length L1 loci (blue arrows reflecting L1 orientation relative to the gene), and a CTCF binding site (orange box). The chart below the schematic contains information regarding each of the seven loci: L1-5212, L1-5214, L1-5215, L1-5216, L1-5217, L1-5218 and L1-5219. The information provided is L1 sub-family, RNA-Seq reads for expressed loci (Illumina or PacBio technologies ), and sequence status of YY1 and RUNX3 binding sites . Reads mapped to L1-5217 in HEK293 cells were manually determined not to primarily originate from an L1 promoter. ( B ) 3D interactions and epigenetic marks identified at L1 loci within the TTC28 gene in MCF7 cells. Loops indicate CTCF binding sites (purple, shaded) within 500 kb of the L1-5219 start site (black arrow). RNA polymerase II (Pol II) loops (red) are only shown if the pol II binding site directly overlaps with an L1 start site. DNAse Hypersensitivity Site (DHS) linkages (light red lines) and the surrounding genomic sequences (blue) are shown as well . A CTCF binding site 5′ of the L1-5219 is marked in red. Red arrows indicate magnification of the L1-5219 element and the associated enhancer region, respectively, showing the presence of activating histone marks at each genomic region as determined by previously described CHIP-Seq data (Figure ). The status of each histone mark is shown from two experiments.

Article Snippet: ATAC library preparation and PE sequencing were done by the Tulane Center for Translational Research in Infection and Inflammation NextGen Sequencing core according to their standard protocols seeding 2 million cells.

Techniques: Binding Assay, RNA Sequencing, Sequencing, Genomic Sequencing, ChIP-sequencing

Journal: Current opinion in immunology

Article Title: Serology in the 21 st Century: The Molecular-Level Analysis of the Serum Antibody Repertoire

doi: 10.1016/j.coi.2015.06.009

Figure Lengend Snippet: Isolated B cells are sorted into several subsets based on expressed cell markers that correspond to the developmental stage of the B cell. These populations can be further processed for high-throughput sequencing to generate the antibody repertoire encoded by B cells (cellular repertoire, left side of the figure). The corresponding serum immunoglobulins are isolated from the samples and can be analyzed by various methods including well established technologies such as 2D gels or by recently established methodologies such as high resolution shotgun proteomics (serological repertoire, left side of the figure). The methodologies for serological immunoglobulin analysis can be broadly based upon the phenotype of an antibody subpopulation (e.g., ELISA titer of antigen-specific fraction) or upon decipherment of the molecular identity and sequence determination of an antibody subpopulation (e.g., LC-MS/MS immunoglobulin sequencing, Ig-seq).

Article Snippet: Somatic variants of antibodies having the same CDR-H3 are determined based on the NextGen sequencing data but cannot be unambiguously quantified proteomically.

Techniques: Isolation, Next-Generation Sequencing, Enzyme-linked Immunosorbent Assay, Sequencing, Liquid Chromatography with Mass Spectroscopy

Journal: Chemical research in toxicology

Article Title: Establishing Linkages Among DNA Damage, Mutagenesis, and Genetic Diseases

doi: 10.1021/acs.chemrestox.2c00155

Figure Lengend Snippet: Technologies discussed in this paper. (A) Mutational spectra classically are produced by damaging the genome of a cell or vector and replicating the damaged piece of DNA in cells that have normal or disabled DNA repair status or normal or altered replicative status. Mutations are determined and plotted along the sequence of the piece of DNA as shown. (B) Often it is of value to test the hypothesis that a given mutation might have been caused by a specific DNA adduct. In that case, an oligodeoxynucleotide is synthesized with the adduct at a specific site. The oligonucleotide is spliced into the genome of a vector, usually a plasmid or viral genome, and replicated in living cells. Mutant progeny are sequenced. The type, amount and genetic requirements for mutagenesis are thereby determined, along with the potential genotoxicity of the lesion. Most of the lesions discussed in the text were evaluated by this site-specific mutagenesis strategy.

Article Snippet: Yet, at the time we wrote the original paper, we could not anticipate the discovery of an entire family of lesion bypass polymerases (the Y-family DNA polymerases), the impressive progress in mass spectrometry and high-throughput DNA sequencing (NextGen sequencing) as well as other advances that occurred to bring the field to its present state.

Techniques: Produced, Plasmid Preparation, Sequencing, Mutagenesis, Synthesized