Chromatin & Transcription

RNA Immunoprecipitation (RIP) is a widely used method for studying interactions between RNA molecules and RNA-binding proteins (RBPs). This technique enables researchers to investigate post-transcriptional regulation, RNA stability, splicing, localization, and translation, all of which are mediated by RBPs. RIP involves the immunoprecipitation of RNA-protein complexes from cell or tissue lysates using antibodies specific to the RBP of interest. The captured RNA can then be analyzed using qRT-PCR, microarrays, or next-generation sequencing (RIP-Seq) to identify and quantify the RNA species bound to the target protein. Over the years, RIP has become an indispensable tool for understanding the epitranscriptome and the dynamics of protein-RNA interactions.

Chromatin immunoprecipitation (ChIP) is a laboratory technique used to study the interaction between proteins and DNA in a specific region of the genome. It allows researchers to identify which proteins bind to specific DNA sequences and to determine the relative strength of these interactions. The basic principle of ChIP is to isolate chromatin (the complex of DNA and proteins that make up the chromosomes in cells) from cells or tissue, and then use an antibody specific to a particular protein of interest to pull down (precipitate) the DNA sequences that are bound to that protein. The precipitated DNA sequences can then be analyzed using techniques such as polymerase chain reaction (PCR) or DNA sequencing to identify the specific DNA sequences that are bound to the protein of interest. ChIP is a powerful tool for studying gene regulation and has been widely used to identify regulatory elements in the genome, including promoters, enhancers, and other regulatory elements that control gene expression. It has also been used to study the role of specific proteins in various biological processes, including development, differentiation, and disease. ChromaFlash High Sensitivity ChIP Kit

Chromatin Immunoprecipitation Sequencing (ChIP-seq) is a technique used to study protein-DNA interactions in the genome. It involves immunoprecipitation of a specific protein or protein complex that is bound to DNA, followed by high-throughput sequencing of the DNA to determine the location of the protein binding sites. ChIP-seq is widely used in the fields of epigenetics and transcriptional regulation to identify the binding sites of transcription factors, cofactors, and other r...

Chromatin immunoprecipitation (ChIP) is a popular tool for studying genome-wide protein/DNA interactions in cells, whereby target histone or transcription factor-complexed DNA is enriched, and the interaction regions are mapped, generally via next-generation sequencing. Due to the limitations of ChIP, mainly, 1) its requirement for large amounts of starting material, 2) long processing times, and 3) low resolution, Cleavage Under Target and Release Using Nuclease (CUT&RUN) emerged to address these issues. The technique, which is performed in situ on intact cells or nuclei without fixation, entails cleavage of chromatin at specific antibody-occupied sites by a pAG-MNase fusion protein and the subsequent release of protein/DNA complexes. CUT&RUN has several advantages over ChIP, including less starting material and higher resolution. However, the pAG-MNase fusion protein used in the procedure can generate non-specific cleavage by antibody un-coupled pAG-MNase, significantly limiting the specificity of CUT&RUN use for most transcription factors in different species and cell/tissue types and causing the target protein-interacted DNA region profiles to be seriously affected. In addition, CUT&RUN is still time-consuming. CUT&RUN-Fast and CUT&LUNCH An improved CUT&RUN technique, CUT&RUN-Fast, was developed by EpigenTek that employs a novel and unique nucleic acid cleavage enzyme mix, which has low sequence bias, to simultaneously fragment chromatin and cleave/remove any DNA sequences in both ends of the target protein/DNA complex without affecting DNA occupied by the target protein, thereby increasing specificity and resolution. This also greatly speeds up the process and avoids overnight incubation. Recently, EpigenTek has further refined the CUT&RUN-Fast method with the new Cleavage Under Target and Liberate Unique Nucleic Complex Homogenously (CUT&LUNCH), which features an extremely fast protocol, further enhanced specificity, and minimized background. Performing a CUT&LUNCH Experiment The CUT&LUNCH assay’s streamlined procedure allows you to selectively enrich target protein/DNA complexes very quickly. The rapid 3-step protocol can be completed in just under 2 hours, minimizing nuclear damage and chromatin loss while preserving native chromatin structure: Step 1: Antibody Binding to Target (30 minutes) Step 2: Enzyme Cleavage (10 minutes) Step 3: Selective Recovery and Purification (60 minutes) Advantages of CUT&LUNCH vs Traditional CUT&RUN and ChIP CUT&LUNCH Traditional CUT&RUN ChIP Workflow convenience Convenient

Measurement of direct interactions between protein and DNA in vitro has an advantage in analyzing the binding of different transcription factors to specific DNA consensus sequences located in the gene promoters. By investigating protein-DNA interaction in vitro, it is possible to identify the genetic targets of DNA, which leads to a better understanding of cellular processes.

Chromatin is the complex of DNA and proteins that make up the chromosomes in a cell's nucleus. Chromatin can be more or less accessible, depending on the presence of specific proteins and chemical modifications. When chromatin is highly accessible, it is more likely to be transcribed into RNA. When it is less accessible, transcription is less likely to occur. Measuring chromatin accessibility can be important for a variety of reasons: First, chromatin accessibility ...