Dovetail™ Micro-C Kit

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

Reactions8
Validated SamplesMammalian Cells
TechniqueHi-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

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

Module 2 of 2 (Shipped with cold packs; store -30 to -10 degrees Celsius)

  • MNase Enzyme Mix
  • 10x Nuclease Digest Buffer
  • 100 mM MgCl2
  • 0.5M EGTA
  • End Polishing Enzyme Buffer
  • End Polishing Enzyme Mix
  • Intra-Aggregate Ligation Buffer
  • Intra-Aggregate Ligation Enzyme Mix
  • Bridge
  • 5x Bridge Ligation Buffer
  • 5x Bridge Ligation (T4 DNA Ligase)
  • Proteinase K
  • 250 mM DTT
  • HotStart PCR Ready Mix