NDLI: Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.

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Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Cooper, Sara J. Trinklein, Nathan D. Anton, Elizabeth D. Nguyen, Loan Myers, Richard M.
Description	Country affiliation: United States Author Affiliation: Cooper SJ ( Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA.)
Abstract	Transcriptional promoters comprise one of many classes of eukaryotic transcriptional regulatory elements. Identification and characterization of these elements are vital to understanding the complex network of human gene regulation. Using full-length cDNA sequences to identify transcription start sites (TSS), we predicted more than 900 putative human transcriptional promoters in the ENCODE regions, representing a comprehensive sampling of promoters in 1% of the genome. We identified 387 fragments that function as promoters in at least one of 16 cell lines by measuring promoter activity in high-throughput transient transfection reporter assays. These positive functional results demonstrate widespread use of alternative promoters. We show a strong correlation between promoter activity and the corresponding endogenous RNA transcript levels, providing the first experimental quantitative estimate of promoter contribution to gene regulation. Finally, we identified functional regions within a randomly selected subset of 45 promoters using deletion analyses. These experiments showed that, on average, the sequence -300 to -50 bp of the TSS positively contributes to core promoter activity. Interestingly, putative negative elements were identified -1000 to -500 bp upstream of the TSS for 55% of genes tested. These data provide the largest and most comprehensive view of promoter function in the human genome.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
Journal	Genome Research
Issue Number	1
Volume Number	16
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2006-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Gene Expression Regulation Physiology Genome, Human Response Elements Transcription, Genetic Hela Cells Research Support, N.i.h., Extramural
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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