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Keywords {🔍}

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Topics {✒️}

cell-free circulating dna circulating cell-free dna open access license cell-free dna fragmentomics apply low-pass filter low-pass filter applied cell-free dna level exon v4+utrs kit /bmcgenomics/supplements/16/s13 article number s1 classic log-normal shape high-resolution data shows universal sequence-dictated positioning open biomed eng article download pdf immune complexes cic-c3d free circulating dna cell-free dna nucleosome-guided fragmentation patterns full size image full access nucleosome free region bmc med genomics o'leary jj privacy choices/manage cookies apoptotic dna fragmentation resolution score distributions nucleosome occupancy pattern resolution score equals single nucleosome size epigenetic regulation marks intrinsic nucleosome occupancy related subjects dna fragmentation pattern nucleosome fragmentation pattern short nucleotide fragments regions immediately upstream circulating tumor dna nucleosome-guided periodicity observed circulating nucleic acids biochem cell biol trends cell biol cell death differ mnase-seq assays average resolution score dinucleosome fragmentation pattern circulating tumor cells cfdna patterning reflects transcription start sites nucleosome position stringencies

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WebPage:
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         headline:Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation
         description:The assessment of cell-free circulating DNA fragments, also known as a "liquid biopsy" of the patient's plasma, is an important source for the discovery and subsequent non-invasive monitoring of cancer and other pathological conditions. Although the nucleosome-guided fragmentation patterns of cell-free DNA (cfDNA) have not yet been studied in detail, non-random representation of cfDNA sequencies may reflect chromatin features in the tissue of origin at gene-regulation level. In this study, we investigated the association between epigenetic landscapes of human tissues evident in the patterns of cfDNA in plasma by deep sequencing of human cfDNA samples. We have demonstrated that baseline characteristics of cfDNA fragmentation pattern are in concordance with the ones corresponding to cell lines-derived. To identify the loci differentially represented in cfDNA fragment, we mapped the transcription start sites within the sequenced cfDNA fragments and tested for association of these genomic coordinates with the relative strength and the patterns of gene expressions. Preselected sets of house-keeping and tissue specific genes were used as models for actively expressed and silenced genes. Developed measure of gene regulation was able to differentiate these two sets based on sequencing coverage near gene transcription start site. Experimental outcomes suggest that cfDNA retains characteristics previously noted in genome-wide analysis of chromatin structure, in particular, in MNase-seq assays. Thus far the analysis of the DNA fragmentation pattern may aid further developing of cfDNA based biomarkers for a variety of human conditions.
         datePublished:2015-12-16T00:00:00Z
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            Nucleosome Position
            Nucleosome Occupancy
            Peak Histogram
            Resolution Score
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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ScholarlyArticle:
      headline:Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation
      description:The assessment of cell-free circulating DNA fragments, also known as a "liquid biopsy" of the patient's plasma, is an important source for the discovery and subsequent non-invasive monitoring of cancer and other pathological conditions. Although the nucleosome-guided fragmentation patterns of cell-free DNA (cfDNA) have not yet been studied in detail, non-random representation of cfDNA sequencies may reflect chromatin features in the tissue of origin at gene-regulation level. In this study, we investigated the association between epigenetic landscapes of human tissues evident in the patterns of cfDNA in plasma by deep sequencing of human cfDNA samples. We have demonstrated that baseline characteristics of cfDNA fragmentation pattern are in concordance with the ones corresponding to cell lines-derived. To identify the loci differentially represented in cfDNA fragment, we mapped the transcription start sites within the sequenced cfDNA fragments and tested for association of these genomic coordinates with the relative strength and the patterns of gene expressions. Preselected sets of house-keeping and tissue specific genes were used as models for actively expressed and silenced genes. Developed measure of gene regulation was able to differentiate these two sets based on sequencing coverage near gene transcription start site. Experimental outcomes suggest that cfDNA retains characteristics previously noted in genome-wide analysis of chromatin structure, in particular, in MNase-seq assays. Thus far the analysis of the DNA fragmentation pattern may aid further developing of cfDNA based biomarkers for a variety of human conditions.
      datePublished:2015-12-16T00:00:00Z
      dateModified:2015-12-16T00:00:00Z
      pageStart:1
      pageEnd:12
      license:http://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/1471-2164-16-S13-S1
      keywords:
         Fragmentation Pattern
         Nucleosome Position
         Nucleosome Occupancy
         Peak Histogram
         Resolution Score
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      name:Atlas Oncology Diagnostics, ltd, Moscow, Russia
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      name:Research Centre for Medical Genetics, Moscow, Russia
      name:School of Systems Biology, George Mason University, Fairfax, USA
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      name:Knight Cancer Institute, Oregon Health & Sciences University, Portland, USA
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      name:Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
      name:Atlas Oncology Diagnostics, ltd, Moscow, Russia

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