Journal: Cancer Cell International

Article Title: LncRNA NKILA as a key regulator in cancer pathogenesis: insights into its mechanisms and clinical implications

doi: 10.1186/s12935-025-04115-z

Figure Lengend Snippet: Schematic representation of the lncRNA NKILA transcript and its genomic location on chromosome 20q13.31. A . Genomic location of the NKILA gene, as extracted from the GeneCards database ( https://www.genecards.org/cgi-bin/carddisp.pl?gene=NKILA&keywords=nkila ). B . Genomic context of NKILA, based on information derived from the National Center for Biotechnology Information (NCBI) database ( https://www.ncbi.nlm.nih.gov/gene/105416157 )

Article Snippet: B . Genomic context of NKILA, based on information derived from the National Center for Biotechnology Information (NCBI) database ( https://www.ncbi.nlm.nih.gov/gene/105416157 ) Fig. 2 The localization of NKILA in common cell lines is mainly located in the cytoplasm (bar plot from lncATLAS analysis; https://lncatlas.crg.eu/ ) Fig. 3 (A) The expression profile of NKILA in various cancer tissues and normal tissues was obtained according to the GEPIA database analysis. (B) GEPIA2 ( http://gepia2.cancer-pku.cn/#survival ) figure displaying overall survival in cancer patients with low NKILA expression using The Cancer Genome Atlas (TCGA) database. (C) GEPIA2 ( http://gepia2.cancer-pku.cn/#survival ) figure displaying disease-free surviva in cancer patients with low NKILA expression using The Cancer Genome Atlas (TCGA) database.

Techniques: Derivative Assay

Journal: Cell reports

Article Title: Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2.

doi: 10.1016/j.celrep.2023.112748

Figure Lengend Snippet: Figure 3. While displaying opposite kinetics, FOXA1 and SOX2 both perform a dense scan- ning of compact regions (A) Simulating chromatin-scanning trajectories for 1,000 steps: after one step of nucleoplasmic diffu- sion (green), the probability to diffuse again (Pdiffusion, green) or interact with chromatin (Pinteraction, red) is inferred from diffusion coefficients. If chromatin interaction occurs, the probability to interact with a site in low- (Pcompact, black) versus high-mobility (Popen, orange) chromatin is inferred from radius of confinements and average displacements. (B–D) Representative scanning trajectories by a single molecule of FOXA1 (B), SOX2 (C), and HNF4A (D) exploring 1,000 chromatin sites. Each step of diffusion is set to occur in a random direction. Red dots: binding to low-mobility, compact chromatin. White dots: binding to high-mobility, open chro- matin. (E and F) Total time of chromatin interaction (E) or nucleoplasmic diffusion (F) during the exploration of 1,000 sites. (G) Average areas (mm2) after Delaunay triangulation of low-mobility chromatin interaction spatial co- ordinates for 10,000 simulated scanning trajectories. For all panels, ***p < 0.0001, n.s., non-significant differences (p > 0.05) as determined by one-way ANOVA.

Article Snippet: Gel extraction kit QIAGEN 28706 Gibson Assembly kit NEB E5510 NEBNext UltraTM II for DNA Library Prep NEB E7645 CUTANATM pAG-MNase Epicypher 15–1016 Deposited data FOXA1-HALO ChIP-seq This paper GSE220570 HNF4A-HALO ChIP-seq This paper GSE220570 H2B-HALO 0h CHIP-seq This paper GSE220570 H2B-HALO 6h ChIP-seq This paper GSE220570 MNase-seq This paper GSE220570 SOX2-DBD-V5 CUT&RUN This paper GSE220570 FOXA1-NHAA-HALO ChIP-seq This paper GSE220570 FOXA1-RRAA-HALO ChIP-seq This paper GSE220570 FOXA1-DBD-HALO ChIP-seq This paper GSE220570 SOX2-V5 CUT&RUN This paper GSE220570 FOXA2 ChIP-seq GEO GSE90456 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE90456 SOX2 ChIP-seq GEO GSE36570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE36570 DNase-I hypersensitivity ENCODE Portal ENCFF737YIY https://www.encodeproject.org/files/ ENCFF737YIY/ Experimental models: Cell lines DH5A competent cells Invitrogen 18265017 Human BJ fibroblasts ATCC CRL-2522 (Continued on next page) 14 Cell Reports 42, 112748, July 25, 2023

Techniques: Diffusion-based Assay, Binding Assay

Journal: Cell reports

Article Title: Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2.

doi: 10.1016/j.celrep.2023.112748

Figure Lengend Snippet: Figure 6. Non-DBD protein regions provide an essential contribution to the targeting and scanning of silent, compact chromatin by FOXA1 and SOX2 (A and B) SOX2- (A) and FOXA1-HALO/V5 (B) constructs and corresponding DBD truncations. (C and D) ChIP-seq and DNase-seq signals for SOX2, SOX2-DBD (C), and FOXA1, FOXA1-DBD (D), at shared peaks (top panel) or peaks bound only by the full-length proteins. (E) SMT measurement of scanning of low-mobility, compact chromatin by HALO-tagged SOX2 and FOXA1 full-length and DBD truncations. (F) Representative scanning trajectories by a single molecule of SOX2-DBD and FOXA1-DBD. (G and H) Average areas (mm2) after Delaunay triangulation of low-mobility, compact chromatin interactions spatial coordinates for 10,000 simu- lated scanning trajectories of full-length or DBD truncations of SOX2 (G) and FOXA1 (H). ***p < 0.0001, n.s., non-significant differences (p > 0.05) as determined by one-way ANOVA.

Article Snippet: Gel extraction kit QIAGEN 28706 Gibson Assembly kit NEB E5510 NEBNext UltraTM II for DNA Library Prep NEB E7645 CUTANATM pAG-MNase Epicypher 15–1016 Deposited data FOXA1-HALO ChIP-seq This paper GSE220570 HNF4A-HALO ChIP-seq This paper GSE220570 H2B-HALO 0h CHIP-seq This paper GSE220570 H2B-HALO 6h ChIP-seq This paper GSE220570 MNase-seq This paper GSE220570 SOX2-DBD-V5 CUT&RUN This paper GSE220570 FOXA1-NHAA-HALO ChIP-seq This paper GSE220570 FOXA1-RRAA-HALO ChIP-seq This paper GSE220570 FOXA1-DBD-HALO ChIP-seq This paper GSE220570 SOX2-V5 CUT&RUN This paper GSE220570 FOXA2 ChIP-seq GEO GSE90456 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE90456 SOX2 ChIP-seq GEO GSE36570 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE36570 DNase-I hypersensitivity ENCODE Portal ENCFF737YIY https://www.encodeproject.org/files/ ENCFF737YIY/ Experimental models: Cell lines DH5A competent cells Invitrogen 18265017 Human BJ fibroblasts ATCC CRL-2522 (Continued on next page) 14 Cell Reports 42, 112748, July 25, 2023

Techniques: Construct, ChIP-sequencing