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Protocol to Retrieve Unknown Flanking DNA Using Fork PCR for Genome Walking.
Bio Protoc
January 2025
International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, China.
PCR-based genome walking is one of the prevalent techniques implemented to acquire unknown flanking genomic DNAs. The worth of genome walking includes but is not limited to cloning full-length genes, mining new genes, and discovering regulatory regions of genes. Therefore, this technique has advanced molecular biology and related fields.
View Article and Find Full Text PDFTwo unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain.
Genes Dev
January 2025
Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, the Netherlands;
Enhancers are tissue-specific regulatory DNA elements that can activate transcription of genes over distance. Their target genes most often are located in the same contact domain-chromosomal entities formed by cohesin DNA loop extrusion and typically flanked by CTCF-bound boundaries. Enhancers shared by multiple unrelated genes are underexplored but may be more common than anticipated.
View Article and Find Full Text PDFAAV vector transduction restriction and attenuated toxicity in hESCs via a rationally designed inverted terminal repeat.
Nucleic Acids Res
January 2025
Ophthalmology, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC 27517, USA.
Adeno-associated virus (AAV) inverted terminal repeats (ITRs) induce p53-dependent apoptosis in human embryonic stem cells (hESCs). To interrogate this phenomenon, a synthetic ITR (SynITR), harboring substitutions in putative p53 binding sites was generated and evaluated for vector production and gene delivery. Replication of SynITR flanked transgenic genome was similar compared to wild type (wt) ITR, with a modest increase in vector titers.
View Article and Find Full Text PDFAbundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation.
iScience
January 2025
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
The regulation of gene expression relies on the coordinated action of transcription factors (TFs) at enhancers, including both activator and repressor TFs. We employed deep learning (DL) to dissect HepG2 enhancers into positive (PAR), negative (NAR), and neutral activity regions. Sharpr-MPRA and STARR-seq highlight the dichotomy impact of NARs and PARs on modulating and catalyzing the activity of enhancers, respectively.
View Article and Find Full Text PDFCHH hypermethylation contributes to the early ripening of grapes revealed by DNA methylome landscape of 'Kyoho' and its bud mutant.
Hortic Res
January 2025
College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China.
DNA methylation is a stable epigenetic mark that plays a crucial role in plant life processes. However, the specific functions of DNA methylation in grape berry development remain largely unknown. In this study, we performed whole-genome bisulfite sequencing on 'Kyoho' grape and its early-ripening bud mutant 'Fengzao' at different developmental stages.
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