Bioinformatic experimental methods in DNA expression

Complexity of poly(A+) and poly(A-) polysomal RNA in mouse liver and cultured mouse fibroblasts
- polyadenylated mRNA (poly(A+)) 
- 30-50% of HeLa cells mRNA is not polyadenylated (poly(A-))
- poly(A+) and poly(A-) show little or no overlap in sequence

RNA-seq, - poly-A tail binds to poly-T beads
RNA-Seq, also called "Whole Transcriptome Shotgun Sequencing" [1] ("WTSS") and dubbed "a revolutionary tool for transcriptomics" [2], refers to the use of High-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content, a technique that is quickly becoming invaluable in the study of diseases like cancer [3]. Thanks to the deep coverage and base level resolution provided by next-generation sequencing instruments, RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions [3].

Cistrome This term http://cistrome.pbwiki.com was coined by investigators at the Dana-Farber Cancer Institute and Harvard Medical School to define the set of cis-acting targets (DNA binding sites) of a trans-acting factor (transcription factor, pioneer factor, restriction enzyme, etc) on a genome scale.

ChIP-chip - ChIP-on-chip - chromatin immunoprecipitation coupled with microarray
Horak, C. E. et al. GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp–chip analysis. Proc. Natl Acad. Sci. USA 99, 2924–2929 (2002).
The goal of ChIP-on-chip is to localize protein binding sites that may help identify functional elements in the genome. For example, in the case of a transcription factor as a protein of interest, one can determine its transcription factor binding sites throughout the genome. Other proteins allow the identification of promoter regions, enhancers, repressors and silencing elements, insulators, boundary elements, and sequences that control DNA replication[2].

ChIP-seq
Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods 4, 651–657 (2007).
Refs 115 and 116 are the first uses of chromatin immunoprecipitation and ultra-high-throughput sequencing to determine genome-wide binding sites of mammalian TFs
Chip-Sequencing is a recently developed technology that still uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points.
Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states. This epigenetic information is complementary to genotype and expression analysis. ChIP-Seq technology is currently seen primarily as an alternative to ChIP-chip which requires a hybridization array. This necessarily introduces some bias, as an array is restricted to a fixed number of probes. Sequencing, by contrast, is thought to have less bias, although the sequencing bias of different sequencing technologies is not yet fully understood.

SELEX
A procedure to identify protein ligands. For DNA-binding proteins, the protein is mixed with a pool of double-stranded oligonucleotides that contain a random core of nucleotides flanked by specific sequences. The protein–DNA complex is recovered, the oligonucleotides amplified by PCR and sequenced to reveal the binding specificity of the protein.

Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47–59 (2006).
A study combining SELEX and motif-finding methods to identify the DNA-binding specificities and target regions for five mammalian TFs.

In situ hybridization (ISH)
- is a type of hybridization that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough (e.g. plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH). This is distinct from immunohistochemistry, which localizes proteins in tissue sections. DNA ISH can be used to determine the structure of chromosomes. Fluorescent DNA ISH (FISH) can, for example, be used in medical diagnostics to assess chromosomal integrity. RNA ISH (hybridization histochemistry) is used to measure and localize mRNAs and other transcripts within tissue sections or whole mounts.

-- from wikipedia