Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Vast knowledge is available on transcription factor binding. Unfortunately, not much is known about the structure and function of complete DNA interactomes. Even less is known about organisms with larger genomes. Presently mouse, human, and other large genomes have been sequenced. Thus, it is feasible to quantify how transcription factors are carried along a whole genome for various cells in physiological conditions. If measurements are obtained, such provide an outline of function and makeup of DNA interactomes. The interactions occurring between the chromosome and transcription factors can be analyzed using chromatin immunoprecipitation (ChIP). The technique ChIP involves an immune …show more content…
All strong established NRSF (≥90% match to prior developed motif model) motifs across the human genome were detectable populated. The high detectable binding propose that no strong sites were missed and all sites are available for NRSF binding in some individual Jurkat cells part time. Other studies with ChIPSeq-positive signals in transfection analysis were similar to a wide range of ChIPSeq signals with all except one being positive in each ChIPSeq conducted experiment. These results and the sensitivity results, showed NRSF interactome measurements to be genome-comprising and have been studied thoroughly enough to include more sites known than any prior experiment. The level of genome-wholeness is deducible to Solexa/Illumina sequencing sampling and is greater than in previous studies of cAMP response element binding protein (CREB) interactomes measured by SACO and the p53 interactomes measured by ChIPPet. NRSF binding near promoters was concluded to be a repressor of transcription of Jurkat cells. This was found by seeking out high-confidence promoter predictions in 1KB of a ChIPSeq peak and hybridizing labeled RNA to Illumina RefSeq8 Sentrix arrays. A MEME search concluded only 2 candidate motifs when their experimental interactome peak domains were applied to the search. The two motifs from the MEME search were concluded to correspond to the left and right sides of the established motif and a distinctive design was found within 50 bp of multiple ChIPSeq peaks. Also, they observed a few binding positions that had multiple grouped occurrences of noncanonical motifs along the canonical one. This new finding could not be compared to structural data of NRSF because none is currently available. They found genes encoding 110 transcription factors, 22 microRNAs, and 5 slicing regulators all associated with NRSF. This proposes a possible negative autoregulatory feedback mechanism. For the first time, they
Vast knowledge is available on transcription factor binding. Unfortunately, not much is known about the structure and function of complete DNA interactomes. Even less is known about organisms with larger genomes. Presently mouse, human, and other large genomes have been sequenced. Thus, it is feasible to quantify how transcription factors are carried along a whole genome for various cells in physiological conditions. If measurements are obtained, such provide an outline of function and makeup of DNA interactomes. The interactions occurring between the chromosome and transcription factors can be analyzed using chromatin immunoprecipitation (ChIP). The technique ChIP involves an immune …show more content…
All strong established NRSF (≥90% match to prior developed motif model) motifs across the human genome were detectable populated. The high detectable binding propose that no strong sites were missed and all sites are available for NRSF binding in some individual Jurkat cells part time. Other studies with ChIPSeq-positive signals in transfection analysis were similar to a wide range of ChIPSeq signals with all except one being positive in each ChIPSeq conducted experiment. These results and the sensitivity results, showed NRSF interactome measurements to be genome-comprising and have been studied thoroughly enough to include more sites known than any prior experiment. The level of genome-wholeness is deducible to Solexa/Illumina sequencing sampling and is greater than in previous studies of cAMP response element binding protein (CREB) interactomes measured by SACO and the p53 interactomes measured by ChIPPet. NRSF binding near promoters was concluded to be a repressor of transcription of Jurkat cells. This was found by seeking out high-confidence promoter predictions in 1KB of a ChIPSeq peak and hybridizing labeled RNA to Illumina RefSeq8 Sentrix arrays. A MEME search concluded only 2 candidate motifs when their experimental interactome peak domains were applied to the search. The two motifs from the MEME search were concluded to correspond to the left and right sides of the established motif and a distinctive design was found within 50 bp of multiple ChIPSeq peaks. Also, they observed a few binding positions that had multiple grouped occurrences of noncanonical motifs along the canonical one. This new finding could not be compared to structural data of NRSF because none is currently available. They found genes encoding 110 transcription factors, 22 microRNAs, and 5 slicing regulators all associated with NRSF. This proposes a possible negative autoregulatory feedback mechanism. For the first time, they