@Article{pmid25077608,
   Author="Hosid, S.  and Ioshikhes, I. ",
   Title="{{A}poptotic lymphocytes of {H}. sapiens lose nucleosomes in {G}{C}-rich promoters}",
   Journal="PLoS Comput. Biol.",
   Year="2014",
   Volume="10",
   Number="7",
   Pages="e1003760",
   Month="Jul",
   Abstract={We analyzed two sets of human CD4+ nucleosomal DNA directly sequenced by Illumina (Solexa) high throughput sequencing method. The first set has ∼40 M sequences and was produced from the normal CD4+ T lymphocytes by micrococcal nuclease. The second set has ∼44 M sequences and was obtained from peripheral blood lymphocytes by apoptotic nucleases. The different nucleosome sets showed similar dinucleotide positioning AA/TT, GG/CC, and RR/YY (R is purine, Y--pyrimidine) patterns with periods of 10-10.4 bp. Peaks of GG/CC and AA/TT patterns were shifted by 5 bp from each other. Two types of promoters in H. sapiens: AT and GC-rich were identified. AT-rich promoters in apoptotic cell had +1 nucleosome shifts 50-60 bp downstream from those in normal lymphocytes. GC-rich promoters in apoptotic cells lost 80% of nucleosomes around transcription start sites as well as in total DNA. Nucleosome positioning was predicted by combination of {AA, TT}, {GG, CC}, {WW, SS} and {RR, YY} patterns. In our study we found that the combinations of {AA, TT} and {GG, CC} provide the best results and successfully mapped 33% of nucleosomes 147 bp long with precision ±15 bp (only 31/147 or 21% is expected).},
   Note={[PubMed Central:\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117428}{PMC4117428}] [DOI:\href{https://dx.doi.org/10.1371/journal.pcbi.1003760}{10.1371/journal.pcbi.1003760}] [PubMed:\href{https://www.ncbi.nlm.nih.gov/pubmed/25077608}{25077608}] }
}

% 24946904

{"_id":"DXo2qrhmE5MFniFkD","bibbaseid":"hosid-ioshikhes-apoptoticlymphocytesofhsapienslosenucleosomesingcrichpromoters-2014","downloads":0,"creationDate":"2017-03-30T17:08:34.534Z","title":"Apoptotic lymphocytes of H. sapiens lose nucleosomes in GC-rich promoters","author_short":["Hosid, S.","Ioshikhes, I."],"year":2014,"bibtype":"article","biburl":"http://adam.med.uottawa.ca/BibBase/Publications.Dr.Ioshikhes.bib","bibdata":{"bibtype":"article","type":"article","author":[{"propositions":[],"lastnames":["Hosid"],"firstnames":["S."],"suffixes":[]},{"propositions":[],"lastnames":["Ioshikhes"],"firstnames":["I."],"suffixes":[]}],"title":"Apoptotic lymphocytes of H. sapiens lose nucleosomes in GC-rich promoters","journal":"PLoS Comput. Biol.","year":"2014","volume":"10","number":"7","pages":"e1003760","month":"Jul","abstract":"We analyzed two sets of human CD4+ nucleosomal DNA directly sequenced by Illumina (Solexa) high throughput sequencing method. The first set has ∼40 M sequences and was produced from the normal CD4+ T lymphocytes by micrococcal nuclease. The second set has ∼44 M sequences and was obtained from peripheral blood lymphocytes by apoptotic nucleases. The different nucleosome sets showed similar dinucleotide positioning AA/TT, GG/CC, and RR/YY (R is purine, Y--pyrimidine) patterns with periods of 10-10.4 bp. Peaks of GG/CC and AA/TT patterns were shifted by 5 bp from each other. Two types of promoters in H. sapiens: AT and GC-rich were identified. AT-rich promoters in apoptotic cell had +1 nucleosome shifts 50-60 bp downstream from those in normal lymphocytes. GC-rich promoters in apoptotic cells lost 80% of nucleosomes around transcription start sites as well as in total DNA. Nucleosome positioning was predicted by combination of AA, TT, GG, CC, WW, SS and RR, YY patterns. In our study we found that the combinations of AA, TT and GG, CC provide the best results and successfully mapped 33% of nucleosomes 147 bp long with precision ±15 bp (only 31/147 or 21% is expected).","note":"[PubMed Central:\\hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117428PMC4117428] [DOI:\\hrefhttps://dx.doi.org/10.1371/journal.pcbi.100376010.1371/journal.pcbi.1003760] [PubMed:\\hrefhttps://www.ncbi.nlm.nih.gov/pubmed/2507760825077608] ","bibtex":"@Article{pmid25077608,\n Author=\"Hosid, S. and Ioshikhes, I. \",\n Title=\"{{A}poptotic lymphocytes of {H}. sapiens lose nucleosomes in {G}{C}-rich promoters}\",\n Journal=\"PLoS Comput. Biol.\",\n Year=\"2014\",\n Volume=\"10\",\n Number=\"7\",\n Pages=\"e1003760\",\n Month=\"Jul\",\n Abstract={We analyzed two sets of human CD4+ nucleosomal DNA directly sequenced by Illumina (Solexa) high throughput sequencing method. The first set has ∼40 M sequences and was produced from the normal CD4+ T lymphocytes by micrococcal nuclease. The second set has ∼44 M sequences and was obtained from peripheral blood lymphocytes by apoptotic nucleases. The different nucleosome sets showed similar dinucleotide positioning AA/TT, GG/CC, and RR/YY (R is purine, Y--pyrimidine) patterns with periods of 10-10.4 bp. Peaks of GG/CC and AA/TT patterns were shifted by 5 bp from each other. Two types of promoters in H. sapiens: AT and GC-rich were identified. AT-rich promoters in apoptotic cell had +1 nucleosome shifts 50-60 bp downstream from those in normal lymphocytes. GC-rich promoters in apoptotic cells lost 80% of nucleosomes around transcription start sites as well as in total DNA. Nucleosome positioning was predicted by combination of {AA, TT}, {GG, CC}, {WW, SS} and {RR, YY} patterns. In our study we found that the combinations of {AA, TT} and {GG, CC} provide the best results and successfully mapped 33% of nucleosomes 147 bp long with precision ±15 bp (only 31/147 or 21% is expected).},\n Note={[PubMed Central:\\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117428}{PMC4117428}] [DOI:\\href{https://dx.doi.org/10.1371/journal.pcbi.1003760}{10.1371/journal.pcbi.1003760}] [PubMed:\\href{https://www.ncbi.nlm.nih.gov/pubmed/25077608}{25077608}] }\n}\n\n% 24946904 \n","author_short":["Hosid, S.","Ioshikhes, I."],"key":"pmid25077608","id":"pmid25077608","bibbaseid":"hosid-ioshikhes-apoptoticlymphocytesofhsapienslosenucleosomesingcrichpromoters-2014","role":"author","urls":{},"downloads":0},"search_terms":["apoptotic","lymphocytes","sapiens","lose","nucleosomes","rich","promoters","hosid","ioshikhes"],"keywords":[],"authorIDs":[],"dataSources":["LXvCTosf85HrNdiXJ"]}