Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.
نویسندگان
چکیده
Fields such as genomics and systems biology are built on the synergism between computational and experimental techniques. This type of synergism is especially important in accomplishing goals like identifying all functional transcription factor binding sites in vertebrate genomes. Precise detection of these elements is a prerequisite to deciphering the complex regulatory networks that direct tissue specific and lineage specific patterns of gene expression. This review summarizes approaches for in silico, in vitro, and in vivo identification of transcription factor binding sites. A variety of techniques useful for localized- and high-throughput analyses are discussed here, with emphasis on aspects of data generation and verification.
منابع مشابه
Mapping of Transcription Factor Binding Region of Kappa Casein (CSN3) Gene in Iranian Bacterianus and Dromedaries Camels
κ-casein is a glycosilated protein in mammalian milk that plays an essential role in the milk micelles. Control of κ-casein expression reflects this essential role, although an understanding of the mechanisms involved lags behind that of the other milk protein genes. Transcriptional regulation, a first mechanism for controlling the development of organisms, is carried out by transcription facto...
متن کاملMapping of Transcription Factor Binding Region of Kappa Casein (CSN3) Gene in Iranian Bacterianus and Dromedaries Camels
κ-casein is a glycosilated protein in mammalian milk that plays an essential role in the milk micelles. Control of κ-casein expression reflects this essential role, although an understanding of the mechanisms involved lags behind that of the other milk protein genes. Transcriptional regulation, a first mechanism for controlling the development of organisms, is carried out by transcription facto...
متن کاملPositional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes
Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity are frequently unreliable. On the other hand, comprehensive experimental validation is difficult and time consuming. We introduce a simple strategy that dramatically impro...
متن کاملComputational identification of composite regulatory sites in 16s-rRNA gene promoters of Mycobacterium species
The availability of completely sequenced genomes allow the use of computational techniques to investigate cis-acting sequences controlling transcription regulation associated with groups of functionally related genes. Theoretical analysis was performed to assign functions to regulatory systems. The identification of such sites is relevant for locating a promoter at the 5' boundary of a gene. Th...
متن کاملPhyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data
The transcription of a gene from its DNA template into an mRNA molecule is the first, and most heavily regulated, step in gene expression. Especially in bacteria, regulation is typically achieved via the binding of a transcription factor (protein) or small RNA molecule to the chromosomal region upstream of a regulated gene. The protein or RNA molecule recognizes a short, approximately conserved...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Genome research
دوره 16 12 شماره
صفحات -
تاریخ انتشار 2006