Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

We present Micro-C XL, an improved method for analysis of chromosome folding at mononucleosome resolution. Using long crosslinkers and isolation of insoluble chromatin, Micro-C XL increases signal-to-noise ratio. Micro-C XL maps of budding and fission yeast genomes capture both short-range chromosome fiber features such as chromosomally interacting domains and higher order features such as centromere clustering. Micro-C XL provides a single assay to interrogate chromosome folding at length scales from the nucleosome to the full genome.

[1]  Wouter de Laat,et al.  The second decade of 3C technologies: detailed insights into nuclear organization , 2016, Genes & development.

[2]  Craig L. Peterson,et al.  Chromatin Higher Order Folding--Wrapping up Transcription , 2002, Science.

[3]  Aviv Regev,et al.  The Role of Nucleosome Positioning in the Evolution of Gene Regulation , 2010, PLoS biology.

[4]  L. Mirny,et al.  Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data , 2013, Nature Reviews Genetics.

[5]  A. Raj,et al.  Dynamic enhancer–gene body contacts during transcription elongation , 2015, Genes & development.

[6]  Nir Friedman,et al.  Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C , 2015, Cell.

[7]  P. Fraser,et al.  Comparison of Hi-C results using in-solution versus in-nucleus ligation , 2015, Genome Biology.

[8]  Geoffrey Fudenberg,et al.  Modeling chromosomes: Beyond pretty pictures , 2015, FEBS letters.

[9]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[10]  L. Mirny,et al.  Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization , 2012, Nature Methods.

[11]  T. Misteli,et al.  Long-Range Chromatin Interactions. , 2015, Cold Spring Harbor perspectives in biology.

[12]  Michael Hampsey,et al.  A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. , 2005, Genes & development.

[13]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[14]  S. Henikoff,et al.  Genome-wide profiling of salt fractions maps physical properties of chromatin. , 2009, Genome research.

[15]  Antonin Morillon,et al.  Gene loops juxtapose promoters and terminators in yeast , 2004, Nature Genetics.

[16]  Sergey V. Razin,et al.  Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub , 2013, Nucleic acids research.

[17]  Noam Kaplan,et al.  The Hitchhiker's guide to Hi-C analysis: practical guidelines. , 2015, Methods.

[18]  William Stafford Noble,et al.  A Three-Dimensional Model of the Yeast Genome , 2010, Nature.

[19]  Job Dekker,et al.  Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe , 2014, Nature.

[20]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[21]  Romain Koszul,et al.  Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms , 2014, eLife.

[22]  Nir Friedman,et al.  Epigenomics and the structure of the living genome , 2015, Genome research.

[23]  P. Gerhardt,et al.  Porosity of the Yeast Cell Wall and Membrane , 1974, Journal of bacteriology.

[24]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[25]  Job Dekker,et al.  Organization of the Mitotic Chromosome , 2013, Science.