|
DNase-Seq
DNase-seq (DNase I hypersensitive sites sequencing) is a method in molecular biology used to identify the location of regulatory regions, based on the genome-wide sequencing of regions sensitive to cleavage by DNase I. FAIRE-Seq is a successor of DNase-seq for the genome-wide identification of accessible DNA regions in the genome. Both the protocols for identifying open chromatin regions have biases depending on underlying nucleosome structure. For example, FAIRE-seq provides higher tag counts at non-promoter regions. On the other hand, DNase-seq signal is higher at promoter regions, and DNase-seq has been shown to have better sensitivity than FAIRE-seq even at non-promoter regions. DNase-seq Footprinting DNase-seq requires some downstream bioinformatics analyses in order to provide genome-wide DNA footprints. The computational tools proposed can be categorized in two classes: segmentation-based and site-centric approaches. Segmentation-based methods are based on the application ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FAIRE-Seq
FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is a method in molecular biology used for determining the sequences of DNA regions in the genome associated with regulatory activity. The technique was developed in the laboratory of Jason D. Lieb at the University of North Carolina, Chapel Hill. In contrast to DNase-Seq, the FAIRE-Seq protocol doesn't require the permeabilization of cells or isolation of nuclei, and can analyse any cell type. In a study of seven diverse human cell types, DNase-seq and FAIRE-seq produced strong cross-validation, with each cell type having 1-2% of the human genome as open chromatin. Workflow The protocol is based on the fact that the formaldehyde cross-linking is more efficient in nucleosome-bound DNA than it is in nucleosome-depleted regions of the genome. This method then segregates the non cross-linked DNA that is usually found in open chromatin, which is then sequenced. The protocol consists of cross linking, phenol extraction a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNase I Hypersensitive Site
In genetics, DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the DNase I enzyme. In these specific regions of the genome, chromatin has lost its condensed structure, exposing the DNA and making it accessible. This raises the availability of DNA to degradation by enzymes, such as DNase I. These accessible chromatin zones are functionally related to transcriptional activity, since this remodeled state is necessary for the binding of proteins such as transcription factors. Since the discovery of DHSs 30 years ago, they have been used as markers of regulatory DNA regions. These regions have been shown to map many types of cis-regulatory elements including promoters, enhancers, insulators, silencers and locus control regions. A high-throughput measure of these regions is available through DNase-Seq. Massive analysis The ENCODE project proposes to map all of the DHSs in the human genome with the intention of cataloging human regulatory DN ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Footprinting
DNA footprinting is a method of investigating the sequence specificity of DNA-binding proteins in vitro. This technique can be used to study protein-DNA interactions both outside and within cells. The regulation of transcription has been studied extensively, and yet there is still much that is unknown. Transcription factors and associated proteins that bind promoters, enhancers, or silencers to drive or repress transcription are fundamental to understanding the unique regulation of individual genes within the genome. Techniques like DNA footprinting help elucidate which proteins bind to these associated regions of DNA and unravel the complexities of transcriptional control. History In 1978, David Galas and Albert Schmitz developed the DNA footprinting technique to study the binding specificity of the lac repressor protein. It was originally a modification of the Maxam-Gilbert chemical sequencing technique. Method The simplest application of this technique is to assess whethe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Biology
Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physical structure of biological macromolecules is known as molecular biology. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena - uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology. In 1945 the term molecular biology was used by physicist William Astbury. In 1953 Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by Ro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNase I
Deoxyribonuclease I (usually called DNase I), is an endonuclease of the DNase family coded by the human gene DNASE1. DNase I is a nuclease that cleaves DNA preferentially at phosphodiester linkages adjacent to a pyrimidine nucleotide, yielding 5'-phosphate-terminated polynucleotides with a free hydroxyl group on position 3', on average producing tetranucleotides. It acts on single-stranded DNA, double-stranded DNA, and chromatin. In addition to its role as a waste-management endonuclease, it has been suggested to be one of the deoxyribonucleases responsible for DNA fragmentation during apoptosis. DNase I binds to the cytoskeletal protein actin. It binds actin monomers with very high (sub-nanomolar) affinity and actin polymers with lower affinity. The function of this interaction is unclear. However, since actin-bound DNase I is enzymatically inactive, the DNase-actin complex might be a storage form of DNase I that prevents damage of the genetic information. This protein is stor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hidden Markov Model
A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process — call it X — with unobservable ("''hidden''") states. As part of the definition, HMM requires that there be an observable process Y whose outcomes are "influenced" by the outcomes of X in a known way. Since X cannot be observed directly, the goal is to learn about X by observing Y. HMM has an additional requirement that the outcome of Y at time t=t_0 must be "influenced" exclusively by the outcome of X at t=t_0 and that the outcomes of X and Y at t handwriting recognition, handwriting, gesture recognition, part-of-speech tagging, musical score following, partial discharges and bioinformatics. Definition Let X_n and Y_n be discrete-time stochastic processes and n\geq 1. The pair (X_n,Y_n) is a ''hidden Markov model'' if * X_n is a Markov process whose behavior is not directly observable ("hidden"); * \operatorname\bigl(Y_n \i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Position Weight Matrix
A position weight matrix (PWM), also known as a position-specific weight matrix (PSWM) or position-specific scoring matrix (PSSM), is a commonly used representation of motifs (patterns) in biological sequences. PWMs are often derived from a set of aligned sequences that are thought to be functionally related and have become an important part of many software tools for computational motif discovery. Background Creation Conversion of sequence to position probability matrix A PWM has one row for each symbol of the alphabet (4 rows for nucleotides in DNA sequences or 20 rows for amino acids in protein sequences) and one column for each position in the pattern. In the first step in constructing a PWM, a basic position frequency matrix (PFM) is created by counting the occurrences of each nucleotide at each position. From the PFM, a position probability matrix (PPM) can now be created by dividing that former nucleotide count at each position by the number of sequences, thereb ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
