Clustering of DNA sequences in human promoters
We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and mo...
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Veröffentlicht in: | Genome research 2004-08, Vol.14 (8), p.1562-1574 |
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creator | FitzGerald, Peter C Shlyakhtenko, Andrey Mir, Alain A Vinson, Charles |
description | We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression. |
doi_str_mv | 10.1101/gr.1953904 |
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A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.</description><identifier>ISSN: 1088-9051</identifier><identifier>DOI: 10.1101/gr.1953904</identifier><identifier>PMID: 15256515</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Base Sequence ; Cluster Analysis ; Computational Biology - methods ; Consensus Sequence ; Humans ; Letters ; Models, Genetic ; Molecular Sequence Data ; Promoter Regions, Genetic ; Transcription Initiation Site</subject><ispartof>Genome research, 2004-08, Vol.14 (8), p.1562-1574</ispartof><rights>Copyright 2004 Cold Spring Harbor Laboratory Press ISSN</rights><rights>Copyright © 2004, Cold Spring Harbor Laboratory Press 2004</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c439t-14a3d518790b5814685eed648b89b46c72c048d7d164f67b2834cb8e2efc8053</citedby><cites>FETCH-LOGICAL-c439t-14a3d518790b5814685eed648b89b46c72c048d7d164f67b2834cb8e2efc8053</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC509265/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC509265/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15256515$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>FitzGerald, Peter C</creatorcontrib><creatorcontrib>Shlyakhtenko, Andrey</creatorcontrib><creatorcontrib>Mir, Alain A</creatorcontrib><creatorcontrib>Vinson, Charles</creatorcontrib><title>Clustering of DNA sequences in human promoters</title><title>Genome research</title><addtitle>Genome Res</addtitle><description>We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.</description><subject>Base Sequence</subject><subject>Cluster Analysis</subject><subject>Computational Biology - methods</subject><subject>Consensus Sequence</subject><subject>Humans</subject><subject>Letters</subject><subject>Models, Genetic</subject><subject>Molecular Sequence Data</subject><subject>Promoter Regions, Genetic</subject><subject>Transcription Initiation Site</subject><issn>1088-9051</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkLtOwzAUhj2AaCksPADKxICUYseX2AND1XKTKli6W45zkgYldrETJN6eVo24TGc4338uH0JXBM8JweSuDnOiOFWYnaApwVKmCnMyQecxvmOMKZPyDE0Iz7jghE_RfNkOsYfQuDrxVbJ6XSQRPgZwFmLSuGQ7dMYlu-A7v6fiBTqtTBvhcqwztHl82Cyf0_Xb08tysU4to6pPCTO05ETmChdcEiYkBygFk4VUBRM2zyxmssxLIlgl8iKTlNlCQgaVlZjTGbo_jt0NRQelBdcH0-pdaDoTvrQ3jf7fcc1W1_5Tc6wyccjfjPng98_EXndNtNC2xoEfohYiF1SqA3h7BG3wMQaofnYQrA9CdR30KHQPX_-96hcdbdJvu9Vylw</recordid><startdate>20040801</startdate><enddate>20040801</enddate><creator>FitzGerald, Peter C</creator><creator>Shlyakhtenko, Andrey</creator><creator>Mir, Alain A</creator><creator>Vinson, Charles</creator><general>Cold Spring Harbor Laboratory Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20040801</creationdate><title>Clustering of DNA sequences in human promoters</title><author>FitzGerald, Peter C ; Shlyakhtenko, Andrey ; Mir, Alain A ; Vinson, Charles</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c439t-14a3d518790b5814685eed648b89b46c72c048d7d164f67b2834cb8e2efc8053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Base Sequence</topic><topic>Cluster Analysis</topic><topic>Computational Biology - methods</topic><topic>Consensus Sequence</topic><topic>Humans</topic><topic>Letters</topic><topic>Models, Genetic</topic><topic>Molecular Sequence Data</topic><topic>Promoter Regions, Genetic</topic><topic>Transcription Initiation Site</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>FitzGerald, Peter C</creatorcontrib><creatorcontrib>Shlyakhtenko, Andrey</creatorcontrib><creatorcontrib>Mir, Alain A</creatorcontrib><creatorcontrib>Vinson, Charles</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>FitzGerald, Peter C</au><au>Shlyakhtenko, Andrey</au><au>Mir, Alain A</au><au>Vinson, Charles</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Clustering of DNA sequences in human promoters</atitle><jtitle>Genome research</jtitle><addtitle>Genome Res</addtitle><date>2004-08-01</date><risdate>2004</risdate><volume>14</volume><issue>8</issue><spage>1562</spage><epage>1574</epage><pages>1562-1574</pages><issn>1088-9051</issn><abstract>We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>15256515</pmid><doi>10.1101/gr.1953904</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Base Sequence Cluster Analysis Computational Biology - methods Consensus Sequence Humans Letters Models, Genetic Molecular Sequence Data Promoter Regions, Genetic Transcription Initiation Site |
title | Clustering of DNA sequences in human promoters |
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