Journal: The Journal of Biological Chemistry

Article Title: A distal super enhancer mediates estrogen-dependent mouse uterine–specific gene transcription of Igf1 ( insulin-like growth factor 1 )

doi: 10.1074/jbc.RA119.008759

Figure Lengend Snippet: Enhancer-associated characteristics of a region 50–70 kb 5′ of Igf1 TSSs. A, screen shot (Wash U Epi Genome Browser) of the potential distal enhancer region. Tracks include SMC1a ChIP-seq of mouse uterus from V- or E2-treated samples and five E2-induced peaks of RNA PolII ChIP-seq that co-localize with E2-induced H3K27Ac and ERα ChIP-seq enrichment. The peaks are numbered 1–5. Stranded total RNA-seq from total mouse uterus RNA with E2-induced positive strand eRNA transcribed from peaks 3, 4, and 5 are noted. In the HiC heat map, the arrows indicate interactions between enhancer and TSS. See also Fig. S1 (A and B). B, focus on ERα ChIP-seq and H3K27Ac at each enhancer peak, 1–5. C, ranked H3K27Ac signal at 4600 ERα-binding regions. Red points beyond the elbow of the signal curve where slope = 1 are classified as super enhancers. The box plot shows normalized H3K27Ac signal at typical versus super enhancers, with mean indicated. D, signal strength (FPKM) of + strand RNA-seq from PolII local maximum to 1500 nt 3′, at enhancer peaks 1–5. The data are represented as means ± S.E. (n = 3/peak) and at five control regions between peaks (n = 15) of V or E2 6-h samples. Data were analyzed using ANOVA with Fisher's False Discovery Rate (FDR) post test. +, p < 0.01 versus control region. See also Fig. S1B.

Article Snippet: SMC1a ChIP-seq libraries were sequenced as single-end 75-mers by Active Motif on an Illumina NextSeq500.

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

Journal: The Journal of Biological Chemistry

Article Title: A distal super enhancer mediates estrogen-dependent mouse uterine–specific gene transcription of Igf1 ( insulin-like growth factor 1 )

doi: 10.1074/jbc.RA119.008759

Figure Lengend Snippet: Deletion of Igf1 enhancer 4 prevents SMC1a binding to Igf1 enhancer and TSS regions. A, SMC1a (cohesin subunit) binding to the IGF1 enhancer region and to TSSs was evaluated using ChIP-PCR of chromatin isolated from uterus samples of ovariectomized mice that were collected 1 h after injection of saline (V) or E2. The samples were taken from mice with deletion of IGF1enh4 (IGF1enh4KO) or their WT littermates. Baseline values are from Untr6, a gene desert on chromosome 6. Enrichment is calculated as binding events/1000 cells, as described under “Experimental procedures.” The data are represented as means ± S.D. A pool of three uteri was used for each condition and tested in triplicate assays. V versus E2 (E) values were tested using two-way ANOVA with Fisher's LSD post test. *, p < 0.001 versus V; + <0.0001 versus WT; #, p < 0.05 versus Untr6. B, interaction between IGF1enh4 and TSS was demonstrated using 3C-PCR. A 300-bp fragment (*) formed by ligation of BsrGI fragments was detected in WT samples and increased after E2 treatment. M indicates size markers, with sizes in bp. Graph of ratio of ligation band versus a control region band. C, sequencing the fragment confirmed that the band is a ligation product of fragments from the enhancer and TSS (underlined) regions ligated together at the BsrGI site (shaded gray). BLAST alignment of each part of fragment with mm10 coordinates is indicated.

Article Snippet: SMC1a ChIP-seq libraries were sequenced as single-end 75-mers by Active Motif on an Illumina NextSeq500.

Techniques: Binding Assay, Isolation, Injection, Saline, Ligation, Control, Sequencing

Journal: The EMBO Journal

Article Title: LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

doi: 10.15252/embj.2022110921

Figure Lengend Snippet:

Article Snippet: ChIP‐seq Library Prep Kit , BD (Becton Dickinson) , NOVA‐5143‐02.

Techniques: Recombinant, Plasmid Preparation, Sequencing, Protease Inhibitor, Software, Reverse Transcription, Immunoprecipitation, Magnetic Beads, Fluorescence, Microscopy, Agarose Gel Electrophoresis

Journal: The Journal of Biological Chemistry

Article Title: Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression–regulating NSL complexes

doi: 10.1016/j.jbc.2022.101588

Figure Lengend Snippet: PHF20 and PHF20L1 bind to the promoters of highly expressed genes. A , Venn diagram indicating the numbers and the overlap of 3xHA PHF20 and 3xHA PHF20L1 ChIP-Seq peaks. B , pie chart of the genomic distribution of 3xHA PHF20-binding ( left ) and 3xHA PHF20L1-binding sites. C , average normalized input and HA ChIP-Seq profiles of 3xHA PHF20 ( left ) and 3xHA PHF200L1 ( right ) across transcription start sites (TSSs). D , Venn diagram indicating the numbers and overlap of 3xHA PHF20, 3xHA PHF20L1, and KANSL3 ChIP-Seq peaks. E , boxplot showing the expression of genes that do not have PHF20 or PHF20L1 binding to their promoters (nonbound), genes that have both PHF20 and PHF20L1 binding to their promoters (dual targets), or genes that have only PHF20 binding to their promoters (PHF20_only targets) in U2OS cells. ∗∗∗∗ p (by two-sided t test) <0.0001. ChIP-Seq, chromatin immunoprecipitation sequencing; HA, hemagglutinin; PHF20, plant homeodomain finger protein 20; PHF20L1, PHF20-like protein 1.

Article Snippet: HA-ChIPs and library preparation for sequencing PHF20-bound and PHF20L-bound DNA (ChIP-Seq) were performed at MD Anderson Epigenomics Profiling Core as described earlier ( ).

Techniques: ChIP-sequencing, Binding Assay, Expressing