Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Distribution of segmental duplications (SDs) and bundled long distance interactions in relation to acetylation of H4K8, transcriptional activity and lamina associated domains on human chromosome 7 (derived from IMR90 unless indicated otherwise). A) H4K8 acetylation profile, dark yellow: hyperacetylation of H4K8; blue: hypoacetylation of H4K8. B) the red and blue curve represent RNA-seq read counts/100 kb bin for coding and non-coding RNA, respectively (IMR91L). C) grey areas underlying the two histograms mark lamina associated domains (LADs, Tig3 cells). D) idiogram of chromosome 7, the Williams-Beuren syndrome region is highlighted in yellow beside the idiogram (at 72-74 Mb, hg18). E) transparent blue shading of the idiogram illustrates the inversion-affected segments of chromosome 7 depicted in Figure A-C. Bundled long distance interactions (F) and segmental duplications (G) are depicted in the inner circle; green ribbons: long distance interactions between genomic regions; grey: SDs with sequence similarity <98%; yellow: SDs with sequence similarity 98-99%; orange: SDs with sequence similarity >99%.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Activity Assay, Derivative Assay, RNA Sequencing, Sequencing

Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Higher order chromatin organisation and SD localisation around the Williams-Beuren syndrome region. All data are referring to genome release hg19 and are derived from IMR90 unless indicated otherwise. The proximal, central and distal SD clusters (P, C, D) of the 7q11 segment encompassing 4.8 Mb are highlighted in green within the chromosome banding track. A-C) localisation of SDs; colouring according to sequence similarity; grey: <98%, yellow: 98%-99%; orange: >99%; D) genomic interval commonly deleted in WBS and the distal 7q11.23 deletion syndrome; E) topological domains as defined by Dixon et al. ; F) topological domains identified in the corresponding region in mouse after conversion to human hg19. Note that the murine topological domain homologous to sequences deleted in the distal 7q11.23 syndrome is not fully represented due to a break of synteny within this genomic interval. See Figure for details; G-H) heatmap and arc view of CTCF binding sites as detected by ChIA-PET in MCF7; I) number of G4 motifs/100 kb bins; J) average GC-content within 100 kb bins; K) number of Alu repeats/100 kb bin; L) number of structural variants as annotated by Database of Genomic Variance (DGV) , *maximum of 1080 CNVs not shown; M) log2 ratio scores of the LaminB1 DamID Map (Tig3 cells) as reported by Guelen et al. ; N) log2 ratio scores of DNA regions prone to early apoptotic DNA degradation in 20 kb windows, turquoise: degraded DNA segments; O) log2 ratio scores of H4K8 acetylation profile in 20 kb windows, blue: hyperacetylation, grey: hypoacetylation; P) red curve representing the sum of all intrachromosomal interaction counts/bin divided by the median number of interactions for all bins of chromosome 7; Q) percentage of interactions categorised according to their interaction span size ; light grey: <0.5 Mb, grey: 0.5-1 Mb, light blue: 1–5 Mb, light brown: 5–10 Mb, dark grey: 10–25 Mb, black: ≥25 Mb. Gaps in this plot are due to alignment problems of Hi-C data in regions harbouring SDs with high sequence similarity.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Derivative Assay, Sequencing, Binding Assay, ChIA Pet Assay, Hi-C

Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Cross-species comparison showing that SDs next to the WBS locus have inserted at topological domain borders. Hi-C interactions and topological domains in the human fetal fibroblast cell line IMR90 are shown in dark green in the upper part as triangle view and bars, respectively. SDs with sequence similarity of 98%-99% and above 99%, respectively, (shown in yellow and orange in the SDs track) coincide with gaps within the Hi-C data. SD distribution and Hi-C data of the corresponding region in mouse are given in the lower part of the image. The position of FKBP6 and WBSCR16 , the human orthologues of the two genes next to the murine topological domain borders are highlighted in green and red, respectively. The intervals commonly affected in WBS and the distal 7q11.23 syndrome are indicated by pale red bars. Note that the region distal to SRRM3 including the distal SD block are homologous to a different mouse chromosome.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Comparison, Hi-C, Sequencing, Blocking Assay

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

doi: 10.1073/pnas.1520113113

Figure Lengend Snippet: Naïve human lymphocytes lack canonical XIST RNA clouds on the Xi. (A) RNA FISH analysis for XIST RNA and COT1 RNA, for naïve T cells and female fibroblast cell line (IMR-90). (B) XIST (red) and COT1 (green) RNA FISH for sorted mature naïve lymphocytes from human males and females. (C) Diversity of XIST RNA localization patterns (types I, II, III, IV) in naïve human lymphocytes. Sequential RNA FISH (for XIST RNA) followed by DNA FISH (to identify the two X chromosomes) at single-cell resolution. Arrows denote the inactive X chromosome. (D) Quantification of each type of XIST RNA localization pattern for naïve CD4+ and CD8+ T cells. (E) XIST RNA localization patterns for naïve B cells. (F) Quantification of total fluorescence for XIST RNA FISH using exon 1 probe for 12 nuclei for each cell type.

Article Snippet: Two different female fibroblast cell lines are included as positive controls: fetal lung (IMR-90) and an adult fibroblast line (Coriell Institute; GM03956).

Techniques: Fluorescence

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

doi: 10.1073/pnas.1520113113

Figure Lengend Snippet: Xist RNA FISH analysis of activated mouse T cells and quantification of human XIST RNA expression during human T-cell stimulation. (A) Representative Xist (red) and COT1 (green) RNA FISH images of mouse T cells activated for 3, 4, and 5 d. (B) Human XIST RNA expression profiling in naïve CD4+ and CD8+ T cells and activated bulk T cells from the same donor (ND340). RNA samples were normalized for total RNA before cDNA synthesis. Two different female fibroblast cell lines are included as positive controls: fetal lung (IMR-90) and an adult fibroblast line (Coriell Institute; GM03956). Two different XIST intron-spanning primer sets were used (blue: exon 1 and exon 3; red: exon 5 and exon 6) and yielded similar results.

Article Snippet: Two different female fibroblast cell lines are included as positive controls: fetal lung (IMR-90) and an adult fibroblast line (Coriell Institute; GM03956).

Techniques: RNA Expression, Cell Stimulation, cDNA Synthesis

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

doi: 10.1073/pnas.1520113113

Figure Lengend Snippet: XIST/Xist RNA quantification (using qPCR) in human and mouse lymphocytes. (A) Quantification of XIST RNA expression in female fibroblasts (fibro), and FACS-sorted CD4+, CD8+ T cells, and mature naïve B cells from human male and female donors. Two different XIST intron-spanning primer sets were used (blue: exon 1 and exon 3; red: exon 5 and exon 6) and yielded similar results. (B) Quantification of Xist RNA expression in splenic B cells after in vitro stimulation with LPS or CpG. Results from the same female mouse are shown; replicate experiments yielded similar results. (C) Quantification of Xist RNA transcripts in mature naïve T cells (mice) and 7 d after in vitro stimulation. (D) Comparison of different quantification methods to assess steady-state levels of mouse Xist RNA in naïve and activated (day 1) T cells. Equal amounts of total RNA (for cDNA synthesis) or total cell numbers were used. (E) Northern blot analysis of 20 μg of total RNA from female naïve and activated T cells hybridized using a probe for Xist (5′ end), and RNA Pol II was a loading control.

Article Snippet: Two different female fibroblast cell lines are included as positive controls: fetal lung (IMR-90) and an adult fibroblast line (Coriell Institute; GM03956).

Techniques: RNA Expression, In Vitro, Comparison, cDNA Synthesis, Northern Blot, Control

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

doi: 10.1073/pnas.1520113113

Figure Lengend Snippet: Allele-specific expression of CXCR3, CD40LG, and ATRX in naïve human male and female T cells using RNA FISH. (A) Representative RNA FISH images and counts of monoallelic and biallelic expression for each X-linked gene. Signals overlapping an X chromosome were counted. White arrow denotes nascent transcription from the X chromosome. XIST RNA (green) was used as a negative control. (B) Same as A, but for female naïve cells. Counts for female naïve T cells are shown in Fig. 3. (C) Comparison of differentially expressed genes from female and male fetal lung fibroblasts. The NES and FDR q values are shown for chrX q13 region, which had the greatest expression difference between samples. The heatmap lists the overexpressed genes in SLE samples from region chrX.q13 and FC values for the genes enriched at the leading edge for female samples.

Article Snippet: Two different female fibroblast cell lines are included as positive controls: fetal lung (IMR-90) and an adult fibroblast line (Coriell Institute; GM03956).

Techniques: Expressing, Negative Control, Comparison

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

doi: 10.1073/pnas.1520113113

Figure Lengend Snippet: Expression of X-linked genes in human B-cell lines (healthy female and female SLE patients) and sex-specific fetal lung fibroblasts. (A) Relative expression of XIST RNA in SLE patient B-cell lines (2411, 9383, 2190, 6109) and two age-matched healthy control cell lines (6141, 2747) determined using qPCR. (B) qRT-PCR analysis of XIST RNA levels after hnRNP U and YY1 knockdown in naïve and activated female T cells.

Article Snippet: Two different female fibroblast cell lines are included as positive controls: fetal lung (IMR-90) and an adult fibroblast line (Coriell Institute; GM03956).

Techniques: Expressing, Control, Quantitative RT-PCR, Knockdown