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Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

ABSTRACT: Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

PROVIDER: PRJNA836112 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19135478_1.fastq.gz	Fastqsanger.gz
	SRR19135478_2.fastq.gz	Fastqsanger.gz
	SRR19135479_1.fastq.gz	Fastqsanger.gz
	SRR19135479_2.fastq.gz	Fastqsanger.gz
	SRR19135480_1.fastq.gz	Fastqsanger.gz

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Genome-wide maps and functional peak analysis of ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) in human plasma

Project description:We report the application of an uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma. The uscfDNA sequencing pipeline include two uscfDNA-optimized extraction methods (QiaM and SPRI) and one control extraction method (QiaC). Final libraries are made with a single-stranded library prepartion kit. We generate genome-wide maps revealing the presence of an uscfDNA population (25-99bp) in addition to the mncfDNA (100-250bp).

2022-05-10 | GSE202430 | GEO

Single-stranded Pre-methylated 5mC Adapters Uncover the Methylation Profile of Plasma Ultrashort Single-stranded Cell-free DNA

Project description:Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ~50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the “5mCAdpBS-Seq” workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (~15%) and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment positively affected gene expression of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.

2024-03-28 | GSE252088 | GEO

Effect of Oral Administration of Methylene Blue MMX Tablets on Double Stranded DNA

Project description:Single Centre, open label assignment phase II clinical study. To evaluate the effect of oral 200mg Methylene Blue tablets (administered 8x25mg) prior to endoscopy on double stranded DNA breaks in colonic biopsy samples assessed by histone gamma H2AX analysis, compared to control biopsies.

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Strand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes

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Protein UFMylation regulates ribosomal DNA double-stranded break repair

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Novel insight into the composition of human single-stranded DNA-binding protein 1 (hSSB1)-containing protein complexes

Project description:Single-stranded DNA-binding proteins are essential cellular components required for the protection, metabolism and processing of single-stranded DNA. Human single-stranded DNA-binding protein 1 (hSSB1) is one such protein, with described roles in genome stability maintenance and transcriptional regulation. As yet, however, the mechanisms through which hSSB1 functions and the binding partners with which it interacts remain poorly understood. In this work, hSSB1 was immunoprecipitated from cell lysate samples that had been enriched for non-soluble nuclear proteins and hSSB1-associating proteins identified by mass spectrometry. In doing so, 334 potential hSSB1-associating proteins were identified, with known roles in a range of distinct biological processes. Unexpectedly, whilst hSSB1 has largely been studied in a genome stability context, few other DNA repair or replication proteins were detected. By contrast, a large number of proteins were identified with roles in mRNA metabolism, reflecting a currently emerging area of hSSB1 study. In addition, numerous proteins were detected that comprise various chromatin-remodelling complexes. These findings provide new insight into the binding partners of hSSB1 and will likely function as a platform for future research.

2016-12-22 | PXD004686 | Pride

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