dnase i hotspot data from encode, blueprint, and consolidated and unconsolidated roadmap  (Epigenomics ag)

Journal: American journal of human genetics

Article Title: Monoallelic loss-of-function variants in ZNF536 are associated with a neurodevelopmental disorder with prominent behavioral features

doi: 10.1016/j.ajhg.2026.08.013

Figure Lengend Snippet: (A) Strategy for generating Zfp536 p.(Gln169Ter) KI mice using CRISPR/Cas9-mediated genome editing within exon 4. Mouse NM_172385.3 has six exons, and the lower panel is a zoomed in view of exon 4 where the mutation encoding p.(Gln169Ter) is located. (B) Representative Sanger sequencing chromatograms of PCR products from tail DNA, showing WT, HET, and HOM genotypes. (C) Distribution of offspring genotypes from HET × HET crosses. (D) Survival curves of WT, HET, and HOM mice within the first 40 postnatal days. (E) Three-chamber social interaction test. Time spent with an object (O) versus stranger 1 (S1), and stranger 1 (S1) versus stranger 2 (S2), is shown. Preference indexes (S1:O and S2:S1) are compared between WT and HET mice. (F) Repetitive behavior assessment. Statistical comparison of grooming duration, digging duration, and rearing frequency between WT and HET mice. (G) Novel object recognition test. Exploration time with old versus novel objects is compared within each genotype, and discrimination indexes are compared between WT and HET mice. (H) Light–dark box test. Time spent in the light compartment and number of light box entries are compared between WT and HET mice. (I) Open field test. Total distance traveled and time spent in the central zone are compared between WT and HET mice. (J) Elevated plus maze test. Duration and distance traveled in the open and closed arms are compared between WT and HET mice. All data are presented as mean ± SEM. Statistical analyses were performed using Student’s t-test. ns, not significant; *p < 0.05, **p < 0.01. WT, wild type; HET, heterozygous; HOM, homozygous.

Article Snippet: KI mice harboring the Zfp536 p.Gln169Ter-encoding mutation were bred and maintained under specific pathogen-free (SPF) conditions at the Cyagen animal facility.

Techniques: CRISPR, Mutagenesis, DNA Sequencing, Comparison

Journal: American journal of human genetics

Article Title: Monoallelic loss-of-function variants in ZNF536 are associated with a neurodevelopmental disorder with prominent behavioral features

doi: 10.1016/j.ajhg.2026.08.013

Figure Lengend Snippet: (A) Representative images of E18.5 mouse brains and quantification of brain weight, cortical anterior–dorsal (A–D) length, anterior–posterior (A–P) length, and cortical surface area. Scale bar, 2 mm. (B) Representative DAPI staining of the E18.5 cerebral cortex. Scale bar, 100 μm. (C) Quantification of total cortical thickness based on DAPI staining. (D) Quantification of cortical plate (CP), intermediate zone (IZ), and ventricular/subventricular zone (VZ/SVZ) thickness. (E) Representative immunofluorescence staining of SATB2, CTIP2, and TBR1 in the E18.5 cortex. SATB2 marks upper-layer neurons (layers 2–4), CTIP2 marks layer 5 neurons, and TBR1 marks layer 6 neurons. Scale bar, 100 μm. (F) Quantification of layer thickness across genotypes. (G) Representative high-magnification images of SATB2+, CTIP2+, and TBR1+ neurons within 5000 μm 2 cortical regions. Scale bar, 20 μm. (H) Quantification of neuronal density across cortical layers (SATB2+ in L2–4, CTIP2+ in L5, TBR1+ in L6). All data are presented as mean ± SEM. Statistical analyses were performed using Student’s t-test. ns, not significant; *p < 0.05, **p < 0.01. WT, wild type; HET, heterozygous; HOM, homozygous.

Article Snippet: KI mice harboring the Zfp536 p.Gln169Ter-encoding mutation were bred and maintained under specific pathogen-free (SPF) conditions at the Cyagen animal facility.

Techniques: Mutagenesis, Staining, Immunofluorescence

Journal: Synthetic and Systems Biotechnology

Article Title: Metabolic engineering and adaptive laboratory evolution enhance squalene production in Yarrowia lipolytica

doi: 10.1016/j.synbio.2026.01.017

Figure Lengend Snippet: Schematic of constructing engineered Y. lipolytica strain for squalene production. I indicate lipid droplet engineering to modulate triacylglycerols synthesis and increase squalene storage capacity. II indicates modulation of the MVA pathway to promote squalene synthesis flux. III indicates enzyme fusion engineering to promote catalytic efficiency between ERG20 and SQS. IV indicates iterative copy numbering of the ScHMG1 gene. V indicates adaptive evolutionary engineering strategies. Red font represents endogenous genes, and blue font represents heterologous genes. DGA1, Diacylglycerol acyltransferase; LRO1, Phospholipid: diacylglycerol acyltransferase; ERG10, Acetyl-CoA acetyltransferase; ERG13, HMG-CoA synthase; ScHMG1, 3-hydroxy-3-methyl glutaryl coenzyme A reductase of S. cerevisiae origin; ERG20, farnesyl diphosphate synthase; SQS, squalene synthase.

Article Snippet: The 3-hydroxy-3-methylglutaryl-CoA reductase encoding gene ScHMG1 (GenBank ID: 854900) from S. cerevisiae was codon-optimized and synthesized (Genewiz, Suzhou, China).

Techniques:

Journal: Synthetic and Systems Biotechnology

Article Title: Metabolic engineering and adaptive laboratory evolution enhance squalene production in Yarrowia lipolytica

doi: 10.1016/j.synbio.2026.01.017

Figure Lengend Snippet: Enhancing the expression of ScHMG1 to boost squalene synthesis . (A) Schematic design of overexpressing ScHMG1 at the IntC locus. (B) Effects of enhanced ScHMG1 expression on squalene and lipid synthesis in the engineered Y. lipolytica strain. (C) The pH, biomass, and glucose consumption of the engineered strains after 72 h of fermentation.

Article Snippet: The 3-hydroxy-3-methylglutaryl-CoA reductase encoding gene ScHMG1 (GenBank ID: 854900) from S. cerevisiae was codon-optimized and synthesized (Genewiz, Suzhou, China).

Techniques: Expressing