The Dovetail™ Micro-C Kit uses micrococcal nuclease (MNase) for chromatin digestion prior to proximity ligation. The Kit provides all the reagents necessary for performing the proximity ligation steps on mammalian samples prior to NGS library generation. The kit is compatible with the Dovetail™ Library Module for Illumina (Cat # 25004) and 3rd party standard paired-end library preparation kits for Illumina sequencing.
Specifications
| Reactions | 8 |
|---|---|
| Validated Samples | Mammalian Cells |
| Technique | Hi-C |
| Labeling | Research Use Only |
| Application(s) | Chromatin conformation analysis |
Key Benefits
The Dovetail Micro-C Kit offers the following key benefits:
- Sequence-independent chromatin fragmentation enables even genome-wide detection of chromatin contacts (up to 20% of the genome lacks coverage using restriction enzyme based Hi-C approaches)
- Ultra-high nucleosome-level resolution of chromatin contacts
- Highest signal-to-noise data with both enrichment of long-range informative reads and nucleosome protected fragments
Library Enrichment
Dovetail Micro-C Libraries Are Enriched For Desirable Hi-C Properties. The MNase enzyme possesses both sequence-independent endonuclease and exonuclease activities so generated fragments are nucleosome length (146 bp). The proximity ligation portion of the protocol is optimized to maximize long-range interactions. The resulting highly uniform, short fragments enable nucleosome-level resolution of chromatin contacts, a theoretical resolution maximum.
Topology
Improved calling of topological features
The ability to detect higher-order features, such as chromatin loops, in proximity ligation data is dependent on enriching long-range informative reads to capture chromatin interaction frequency. The increased chromosome conformation informative reads combined with ultra-high-resolution improves loop calling compared to RE-based methods.
Nucleosome Positioning
Dovetail Micro-C uniquely captures nucleosome positioning
Chromatin digested with MNase reveals a genome-wide nucleosome map that is visible in the Dovetail™ Micro-C libraries. The map consists of sequence read peaks correlating to DNA that is protected by the nucleosome and troughs representing intervening DNA that is accessible to MNase digestion. This oscillation occurs at a frequency of ~146 bp (the length of DNA wrapped around a mono-nucleosome). This feature is unique to Micro-C data as it is absent from RE-based approaches. The combined genome-wide nucleosome positioning and ultra-resolution chromosome topology enabled by Dovetail™ Micro-C facilitates mapping from nucleosome-to-nucleosome chromatin contacts.
Documents
Manuals & Protocols
- Coming soon! Please email Dovetail Support for a pre-release version
Scientific Literature
- Resolving the 3D landscape of transcription-linked mammalian chromatin folding
- Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF
- Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
- Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence
Contents & Storage
Module 1 of 2 (Shipped with cold packs; store 2 to 8 degrees Celsius)
- TE Buffer pH 8.0
- Wash Buffer
- TWB Solution
- 2x NTB Solution
- LWB Solution
- NWB Solution
- Chromatin Capture Beads
- Crosslink Reversal Buffer
- Strepavidin Beads
- 10x RBC Lysis Buffer
- 20% SDS