Neoplasia, Год журнала: 2024, Номер 58, С. 101071 - 101071
Опубликована: Окт. 13, 2024
Язык: Английский
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown
Опубликована: Янв. 15, 2025
3D genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome linked these to gene regulation. However, only measure interaction probabilities on a relative scale. Here, we overcome this limitation by using live imaging data calibrate in mouse embryonic stem cells, thus obtaining absolute looping for 36,804 genome. We find that looped state is generally rare, with mean probability of 2.3% maximum 26% quantified loops. On average, CTCF-CTCF are stronger than between cis-regulatory elements (3.2% vs. 1.1%). Our findings can be extended human cells differentiated under certain assumptions. Overall, establish an approach genome-wide loop quantification report occur low probabilities, generalizing recent results whole
Язык: Английский
Процитировано
1
Journal of the Science of Food and Agriculture, Год журнала: 2025, Номер unknown
Опубликована: Май 23, 2025
Abstract BACKGROUND Menaquinone‐7 (MK‐7), a type of vitamin K 2 (VK ), is considered to be health‐promoting functional ingredient in the current recommended dietary supply. However, it challenge isolate high‐yield MK‐7‐producing strains with reasonable safety from natural food, which further limits their use as starter culture. RESULTS In this study, an MK‐7 production strain derived commercial natto yield 2.33 ± 0.06 mg L −1 , Bacillus subtilis 4‐b4, was screened using selective medium containing rotenone combined VK enzyme‐linked immunosorbent assay kit, and high‐performance liquid chromatography. This exhibited excellent no hemolysis, antioxidant activity, sensitivity antibiotics. Furthermore, its fermentation strategies (fermentation condition supply key precursor substances) were optimized improve biosynthesis. As result, increased 3.31‐fold, reaching 7.70 0.24 at shake flask level. After scaling up through fed‐batch fermentation, 23.43 0.41 5 bioreactor. CONCLUSION The study developed good antibiotic for producing MK‐7, improved biosynthesis process, laying foundation availability biologically active fermented food industry. © 2025 Society Chemical Industry.
Язык: Английский
Процитировано
0
BMC Bioinformatics, Год журнала: 2025, Номер 26(1)
Опубликована: Янв. 23, 2025
Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of sequences and assembly DNA from oligonucleotides, require specialized software. In this article, we present program with graphical interface that allows non-bioinformatics to perform tasks needed in genomics. We developed BAC-browser v.2.1. It helps nucleotide features following tools: generate sequence amino acid using codon frequency table for specific organism, well visualization restriction sites, GC composition, skew secondary structure. To assemble sequences, fragmentation tool was created: regular breakdown into oligonucleotides certain length thermodynamic alignment. demonstrate possibility fragments assemblies designed different modes BAC-browser. The has large number tools working field systemic freely available at link direct https://sysbiomed.ru/upload/BAC-browser-2.1.zip .
Язык: Английский
Процитировано
0
Опубликована: Май 16, 2025
Abstract Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, transcription occurs sporadic bursts, transcriptional coordination has been observed between proximal but how folding of mammalian chromosomes influences coregulation cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent from three adjacent located around a strong contact insulation site FOS locus, during estrogen response human breast cancer cells. To interpret this data, developed two new analysis approaches dissect sources (co)variation activities: one separate allele-extrinsic, allele-intrinsic, gene-autonomous components; another quantify contributions burst co-occurrence size correlations. We find that variability largely gene-autonomous, yet correlations display distinct patterns occur almost exclusively cis. Correlations stronger less insulated genes. However, unexpectedly, substantial also and, under certain on same side can exhibit uncorrelated occurrences. By disentangling correlations, reveal coregulatory influenced by chromosome folding.
Язык: Английский
Процитировано
0
Опубликована: Май 16, 2025
Abstract Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, transcription occurs sporadic bursts, transcriptional coordination has been observed between proximal but how folding of mammalian chromosomes influences coregulation cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent from three adjacent located around a strong contact insulation site FOS locus, during estrogen response human breast cancer cells. To interpret this data, developed two new analysis approaches dissect sources (co)variation activities: one separate allele-extrinsic, allele-intrinsic, gene-autonomous components; another quantify contributions burst co-occurrence size correlations. We find that variability largely gene-autonomous, yet correlations display distinct patterns occur almost exclusively cis. Correlations stronger less insulated genes. However, unexpectedly, substantial also and, under certain on same side can exhibit uncorrelated occurrences. By disentangling correlations, reveal coregulatory influenced by chromosome folding.
Язык: Английский
Процитировано
0
Neoplasia, Год журнала: 2024, Номер 58, С. 101071 - 101071
Опубликована: Окт. 13, 2024
Язык: Английский
Процитировано
2