MNase-seq (micrococcal nuclease sequencing) is used to map nucleosome positions in eukaryotic genomes to study the relationship between chromatin structure and DNA-dependent processes. Current protocols require at least two days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for and other fungi which takes only three hours. Modified protocols were developed for wild fungi and mammalian cells. This method for rapidly producing sequencing-ready nucleosome footprints from several organisms makes MNase-seq faster and easier, with less chemical waste.
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| http://dx.doi.org/10.1016/j.xpro.2021.100486 | DOI Listing |
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Gene expression profiles based on maternal plasma cfDNA nucleosome footprints indicate fetal development and maternal immunity changes during pregnancy progress.
Placenta
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Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China. Electronic address:
Background: Pregnancy significantly alters the maternal immune system, affecting fetal development. The collection of tissues from the human placenta and fetus is not ethically or practically feasible at various gestational stages, thus limiting the study of gene expression in the fetus and placenta. Recent studies have shown that plasma cell-free DNA (cfDNA) nucleosome patterns can predict gene expression in the source tissue, offering insights into an individual's health status.
View Article and Find Full Text PDFLBFextract: Unveiling transcription factor dynamics from liquid biopsy data.
Comput Struct Biotechnol J
December 2024
Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin 10178, Germany.
Motivation: The analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation, but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns.
Results: We introduce Liquid Biopsy Feature extract (LBFextract), a comprehensive package designed to streamline feature extraction from cfDNA sequencing data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies.
Single chromatin fiber profiling and nucleosome position mapping in the human brain.
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Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:
We apply a single-molecule chromatin fiber sequencing (Fiber-seq) protocol designed for amplification-free cell-type-specific mapping of the regulatory architecture at nucleosome resolution along extended ∼10-kb chromatin fibers to neuronal and non-neuronal nuclei sorted from human brain tissue. Specifically, application of this method enables the resolution of cell-selective promoter and enhancer architectures on single fibers, including transcription factor footprinting and position mapping, with sequence-specific fixation of nucleosome arrays flanking transcription start sites and regulatory motifs. We uncover haplotype-specific chromatin patterns, multiple regulatory elements cis-aligned on individual fibers, and accessible chromatin at 20,000 unique sites encompassing retrotransposons and other repeat sequences hitherto "unmappable" by short-read epigenomic sequencing.
View Article and Find Full Text PDFKAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.
Genome Res
January 2025
Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305, USA.
Article Synopsis
- Gene regulation in eukaryotes involves how DNA is organized in the genome and the activation of transcription, with open-chromatin configurations linked to active regulatory elements.
- The new method, KAS-ATAC, combines techniques to simultaneously map chromatin accessibility and active transcription, providing insights into how DNA is structured and how transcription occurs.
- Findings indicate that active transcription is lower at distal enhancers than at promoters, and while most transcription factors interact with both transcribed and non-transcribed DNA, some do not engage with single-stranded DNA, highlighting complex regulatory dynamics.
MNase-seq to Identify Genome-Wide DNA-Protein Interactions.
Methods Mol Biol
November 2024
Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ, USA.
Identification of the occupancy of transcription factors (TFs) and nucleosomes across the genome yields insights into the regulation of gene expression patterns. While several independent techniques can be performed and then analyzed in composite to reveal this chromatin landscape, the use of micrococcal nuclease (MNase) digestion can resolve the footprints of nearly all chromatin proteins simultaneously. The protocol below describes the use of MNase to identify chromatin footprints of both TFs and nucleosomes in two vastly different cell types, Mouse embryonic stem cells (mESCs) and sperm, with differing levels of chromatin compaction.
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