MOESM1 of Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing
Creators: name: Jiji Kurup
name: Campeanu, Ion
name: Kidder, Benjamin
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Figure S1. Expression of KDM5 family members in KDM5B-depleted ES cells. (A) Quantitative real-time Q-RT-PCR expression analysis of KDM5 family members in control and KDM5B-depleted ES cells. Figure S2. Characterization of altered nucleosome distributions in KDM5B depleted ES cells. (A–B) Schema of −1 nucleosomes relative to transcriptional start sites (TSS) shifted (A) downstream or (B) upstream. (C) Average profiles of nucleosomes around TSS of genes with −1 nucleosomes shifted downstream in KDM5B-depleted ES cells (shift distance: 0, 1–9, 10–50, 51–100, 101–150, 151–200 bp). Note the altered nucleosome densities and asynchronous array of nucleosomes in KDM5B-depleted ES cells relative to control ES cells. (D) Two-dimensional (2D) occupancy plot of nucleosomes around TSS of genes with −1 nucleosomes shifted upstream in KDM5B-depleted ES cells. Plot2DO(31) was used to show relative nucleosome occupancy and fragment length in a heatmap matrix. Average profile of nucleosome occupancy is shown above the heatmap plot. X-axis: position relative to center of nucleosome; y-axis: fragment length (bp). (E) Average profiles (relative to TSS) of −1 nucleosomes shifted upstream. (F) Two-dimensional (2D) occupancy plot of nucleosomes around TSS of genes with −1 nucleosomes shifted upstream in KDM5B-depleted ES cells. Figure S3. Variant nucleosomes are associated with distinct regulatory elements and genic features in the KDM5B depleted ES cells. (A–B) Schema of −1 nucleosomes relative to transcriptional start site (TSS) shifted (A) downstream or (B) upstream. (C–F) HOMER (40) functional annotation of regions enriched with (C, E) downstream or (D, F) upstream shifted nucleosomes in KDM5B-depleted ES cells. Figure S4. DNA shape and sequence features of variant nucleosomes in KDM5B depleted ES cells. Average profiles of DNA shape and sequence features of regions with variant (A–D) +1 nucleosomes in KDM5B-depleted ES cells (nucleosome shift distance: 0, 1–9, 10–50, 51–100, 101–150, 151–200 bp). (A–B) Propeller Twist and (C-D) Opening (A, C) average profiles and (B, D) boxplots of sequences with downstream (top) or upstream (bottom) shifted +1 nucleosomes (black line, 0 bp; blue, 10–50 bp; green, 51–100 bp; orange, 101–150 bp; red, 151–200 bp shift). Note that 151–200 bp shifted nucleosomes in KDM5B-depleted ES cells exhibit altered Propeller Twist and Opening relative to control ES cells. Schematic representations of Propeller Twist and Opening DNA shape features are also shown(49). Figure S5. Electrostatic potential and slide DNA shape and sequence features of variant nucleosomes in KDM5B depleted ES cells. Average profiles of DNA shape and sequence features of regions with variant +1 or −1 nucleosomes in KDM5B-depleted ES cells (nucleosome shift distance: 0, 1–9, 10-50, 51–100, 101–150, 151–200 bp). (A–D) Electrostastic potential (EP) and (E–H) slide (A, C, E, G) average profiles and (B, D, F, H) boxplots of sequences with downstream (top) or upstream (bottom) shifted +1 or −1 nucleosomes (black line, 0 bp; blue, 10–50 bp; green, 51–100 bp; orange, 101–150 bp; red, 151–200 bp shift). Note that 151–200 bp shifted nucleosomes in KDM5B-depleted ES cells exhibit altered electrostatic potential and slide relative to control ES cells. Figure S6. Stagger and helix twist DNA shape and sequence features of variant nucleosomes in KDM5B depleted ES cells. Average profiles of DNA shape and sequence features of regions with variant +1 or −1 nucleosomes in KDM5B-depleted ES cells (nucleosome shift distance: 0, 1–9, 10–50, 51–100, 101–150, 151–200 bp). (A–D) Stagger and (E–H) helix twist (A, C, E, G) average profiles and (B, D, F, H) boxplots of sequences with downstream (top) or upstream (bottom) shifted +1 or −1 nucleosomes (black line, 0 bp; blue, 10–50 bp; green, 51–100 bp; orange, 101–150 bp; red, 151–200 bp shift). Note that 151–200 bp shifted nucleosomes in KDM5B-depleted ES cells exhibit altered stagger and helix twist relative to control ES cells.