Journal: Nucleic Acids Research

Article Title: Sequence and expression analysis of gaps in human chromosome 20

doi: 10.1093/nar/gks302

Figure Lengend Snippet: Chromatin distribution and DNA methylation profile across human chr 20-gap regions. ( A ) H3K27me3 is distributed across all three human chr-20 gap regions in EBV-PBLs. ( B ) MRE-Seq (hypomethylated) and MBD-Seq (hypermethylated) aligned peak reads within gaps 1 and 3. Methylation distribution is similar in PBL and human cerebellum for both gaps 1 and 3. ( C ) Methylation profile of gap 2 shows it to be enriched for both hypomethylated and hypermethylated CpGs, respectively. CpG island 4/1a (red rectangle) is enriched for both MBD-Seq and MRE-Seq reads suggesting it to be a differentially methylated locus. CpG islands 2–6 were annotated using the classification: 500-bp region of genomic DNA with ≥50% CG content and an observed CpG to expected CpG ratio of 0.6. CpG islands 1a–3a were classified based on a CpG island being a 500-bp region of genomic DNA with ≥55% CG content and an observed CpG to expected CpG ratio of 0.65. Images are drawn to scale. ( D ) Differentially methylated and paternally hypermethylated CpGs island 4/1a within gap 2 using bisulfite allelic sequencing and gDNA from mouse–human cell hybrid cell lines or diploid human cells.

Article Snippet: In situ hybridizations were performed using purchased control human cerebellum brain sections (70-year-old female donor, Cat # TCB-4089 Capital Biosciences) as previously published ( ) using Fluorescein -labeled oligos ( Supplementary Table S7 ).

Techniques: DNA Methylation Assay, Methylation, Sequencing

Journal: Nucleic Acids Research

Article Title: Sequence and expression analysis of gaps in human chromosome 20

doi: 10.1093/nar/gks302

Figure Lengend Snippet: De novo prediction and experimental verification of structured ncRNAs within human chr 20 gaps. ( A ) Expression confirmation of ncRNAs predicted by CMfinder using total universal reference RNA. ( B ) Expression of candidate ncRNAs in a human multi-tissue RNA panel. ( C ) Elevated expression of candidate ncRNAs: 5, 6, 9 and 12 in a human multi-region brain panel. ( D ) RNA structure of ncRNA numbers: 5, 6, 9 predicted using INFERNAL. The Vienna RNA conservation coloring scheme highlights the mutational pattern with respect to the structure and a circle around a variable base(s) marks consistent and compensatory mutations. The color coding is explained in a color scheme legend. There are six different canonical base pairs (G-C, C-G, A-U, U-A, G-U, U-G) described by the different colors ( x -axis), and if the base pair is not supported in a sequence of the alignment the color shading gets lighter ( y -axis, incompatible pairs). ( E ) Candidate ncRNA number 5 is specifically expressed in the nucleus of Purkinje cells in the human cerebellum. ( F ) Localized view of the DLGAP4 promoter (chr 20:34,355,500–34,385,499, hg18 + chr 20 gaps) showing candidate ncRNAs in gap 1. RNA-Seq tracks show forward and reverse aligned reads in blue and green, respectively.

Article Snippet: In situ hybridizations were performed using purchased control human cerebellum brain sections (70-year-old female donor, Cat # TCB-4089 Capital Biosciences) as previously published ( ) using Fluorescein -labeled oligos ( Supplementary Table S7 ).

Techniques: Expressing, Sequencing, RNA Sequencing