Enhancer RNAs: Methods and Protocols (Methods in Molecular by Ulf Andersson Ørom

By Ulf Andersson Ørom

This quantity offers a entire review of the experimental and computational methodologies used to check the functionality of lengthy non-coding RNA (ncRNAs) expressed from enhancers. bankruptcy element either wet-lab and dry-lab suggestions and annotating lengthy ncRNAs and exploring transcription through assessing the place transcription starts off and customarily the way it occurs.Written within the hugely profitable Methods in Molecular Biology series structure, chapters contain introductions to their respective themes, lists of the mandatory fabrics and reagents, step by step, comfortably reproducible laboratory protocols, and tips about troubleshooting and heading off recognized pitfalls.

 

Authoritative and state of the art, Enhancer RNAs: equipment and Protocols goals to make sure winning leads to this swiftly constructing field.

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Enhancer RNAs: Methods and Protocols (Methods in Molecular Biology)

This quantity presents a finished assessment of the experimental and computational methodologies used to check the functionality of lengthy non-coding RNA (ncRNAs) expressed from enhancers. bankruptcy aspect either wet-lab and dry-lab ideas and annotating lengthy ncRNAs and exploring transcription through assessing the place transcription begins and usually the way it happens.

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Add appropriate amount of probe for both eRNA and proteincoding transcript to 50 μl hybridization buffer to make a final concentration of 1 ng/μl for each probe set. Probe stock should be concentrated enough to not considerably dilute the hybridization buffer. Mix by pipetting. 4. Equilibrate the cells by replacing the 70 % ethanol in the well containing the cover slip with wash buffer and incubate at room temperature for at least 2 min. 5. Place the entire volume of probe in hybridization buffer on the parafilm covering the glass plate to form a droplet.

Store at 4 °C overnight. 8. Add 10 μg of antibody/IP to the pre-cleared lysate and incubate on a rotating platform overnight at 4 °C. 9. The next day, wash protein A/G plus beads twice with cold PBS and once with diluted high-salt lysis buffer (300 mM NaCl final). Use 20 μL final bead volume per IP. 10. Add washed beads to the lysate–antibody mix and incubate for at least 2 h at 4 °C. 11. Spin down the beads in a microcentrifuge at 6000 rpm (3300 × g) for 1 min at 4 °C. 12. Remove the supernatant and wash as follows: 2× low-salt Wash Buffer, 2× high-salt Wash Buffer, 2× LiCl Wash Buffer, 1× TE.

1 Schematic representation of the TSA method. Biotinylated probes bind to target RNA, after which streptavidin–HRP conjugate is introduced to bind the biotin. The HRP then activates dye-labeled tyramide, resulting in the accumulation of multiple copies of dye per probe. B biotin, SA streptavidin, HRP horseradish peroxidase, T tyramide 22 Youtaro Shibayama et al. Fig. 2 Schematic representation of the TSA method multiplexed with smFISH. Enhancer transcript is targeted by a small number (~10) of biotinylated probes, while intronic RNA from a protein-coding gene is targeted by a larger number (~30–50) of dye-labeled probes.

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