MAINE-Seq/Mnase-Seq/Nucleo-Seq

MAINE-Seq/Mnase-Seq

Micrococcal nuclease (MNase)-assisted isolation of nucleosomes sequencing (MAINE-Seq), is a variation on the well-established use of MNase digestion to map nucleosome positions (MNase-Seq). It is estimated that almost half the genome contains regularly spaced arrays of nucleosomes, which are enriched in active chromatin domains . In MAINE-Seq, genomic DNA is treated with MNase. The DNA from the DNA-protein complexes is then extracted and sequenced. Sequences bound by regulatory proteins are protected from MNase digestion. Deep sequencing provides accurate representation of the location of regulatory proteins in the genome.

Pros:

• Can map nucleosomes and other DNA-binding proteins
• Identifies location of various regulatory proteins in the genome
• Covers broad range of regulatory sites

Cons:

• MNase sites might not account for the entire genome
• Does not provide much information about the kind of regulatory elements
• Integration of MNase with ChIP data is necessary to identify and differentiate similar protein-binding sites

• MAINE-Seq: Cusick M. E., Herman T. M., DePamphilis M. L. and Wassarman P. M. (1981) Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease. Biochemistry 20: 6648-6658
• MAINE-Seq: Ponts N., Harris E. Y., Prudhomme J., Wick I., Eckhardt-Ludka C., et al. (2010) Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res 20: 228-238
• MNase-Seq: Schlesinger F., Smith A. D., Gingeras T. R., Hannon G. J. and Hodges E. (2013) De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome Res 23: 1601-1614

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2. Comoglio F., Schlumpf T., Schmid V., Rohs R., Beisel C., et al. (2015) High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep 11: 821-834
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9. Yazdi P. G., Pedersen B. A., Taylor J. F., Khattab O. S., Chen Y. H., et al. (2015) Nucleosome Organization in Human Embryonic Stem Cells. PLoS One 10: e0136314
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