MNase-Seq/MAINE-Sequcleo-Sequc-seq

Micrococcal Nuclease Sequencing / Micrococcal Nuclease_Assisted Isolation of Nucleosomes / Isolated Nucleosome Sequencing / Isolated Nucleosome Sequencing

Micrococcal nuclease (MNase) is derived from Staphylococcus aureus, and its first use to determine chromatin structure dates back to 1975, when the method was called, variously, staphylococcal nuclease or micrococcal nuclease digestion of nuclei or chromatin (Sollner-Webb et al., 1975) (Axel et al., 1975). With the advent of NGS, MNase digestion (Schones et al., 2008) became more popular and the term MNase-Seq was coined finally (Kuan et al., 2009). The terms MNase-assisted isolation of nucleosomes sequencing (MAINE-seq) (Cusick et al., 1981) (Ponts et al., 2010), Nucleo-Seq (Valouev et al., 2011), and Nuc-seq (Chodavarapu et al., 2010) are not commonly used. MNase, fused to the protein of interest, has been also been used for calcium-dependent cleavage to study specific genomic loci in vivo (ChEC-seq) (Zentner et al., 2015).

In MNase-Seq, gDNA is treated with MNase. Sequences bound by chromatin proteins are protected from MNase digestion. Next, the DNA from the DNA-protein complexes is extracted and used to prepare a sequencing library. Deep sequencing provides accurate representation of the location of regulatory DNA-binding proteins in the genome (Schones et al., 2008)

Advantages:

• Can map nucleosomes and other DNA-binding proteins (Zentner et al., 2012)
• Can footprint subnucleosomal particles protecting as little as ~25 bp (Henikoff et al., 2011)
• Identifies location of various regulatory proteins in the genome
• Covers a broad range of regulatory sites

Disadvantages:

• MNase sites might not account for the entire genome
• AT-dependent sequence bias (Kensche et al., 2016)
• Integration of MNase with ChIP data is necessary to identify and differentiate similar protein-binding sites

Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109



References:

Lavender C. A., Cannady K. R., Hoffman J. A., et al. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PLoS Genet. 2016;12:e1006224

Rube H. T., Lee W., Hejna M., et al. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun. 2016;7:11025

de Dieuleveult M., Yen K., Hmitou I., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116

Cole H. A., Cui F., Ocampo J., et al. Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acids Res. 2016;44:573-581

Deniz O., Flores O., Aldea M., Soler-Lopez M. and Orozco M. Nucleosome architecture throughout the cell cycle. Sci Rep. 2016;6:19729

Devaiah B. N., Case-Borden C., Gegonne A., et al. BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat Struct Mol Biol. 2016;23:540-548

Johnson G. D., Jodar M., Pique-Regi R. and Krawetz S. A. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. Sci Rep. 2016;6:25864

Kensche P. R., Hoeijmakers W. A., Toenhake C. G., et al. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences. Nucleic Acids Res. 2016;44:2110-2124

Lombrana R., Alvarez A., Fernandez-Justel J. M., et al. Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major. Cell Rep. 2016;16:1774-1786

Maehara K. and Ohkawa Y. Exploration of nucleosome positioning patterns in transcription factor function. Sci Rep. 2016;6:19620

Matveeva E., Maiorano J., Zhang Q., et al. Involvement of PARP1 in the regulation of alternative splicing. Cell Discov. 2016;2:15046

Mieczkowski J., Cook A., Bowman S. K., et al. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun. 2016;7:11485

Ramakrishnan S., Pokhrel S., Palani S., et al. Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription. Nat Commun. 2016;7:11949

Wang M., Wang P., Tu L., et al. Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res. 2016;44:4067-4079

Edit: MNase-Seq/MAINE-Sequcleo-Sequc-seq

You must be logged in to edit this entry.

History: MNase-Seq/MAINE-Sequcleo-Sequc-seq

Revision by sbrumpton on 2017-06-21 09:36:17 - Show/Hide