Description

This track shows the interactions between DNA segments that are bound by SMC1 in murine embryonic stem cells detected by Chromatin Interaction Analysis with Paired-End Tag sequencing (ChIA-PET) (Dowen, Fan, Hnisz, Ren et al., 2014).  A chromatin interaction is defined as two genomic loci in the genome are far from each other on the linear genomic scale, but are spatially close to each other in the nucleus and have SMC1 present at both ends.

The PET interactions (merged_Smc1_unique_PETs.bb) track shows all intra-chromosomal paired-end tags (PETs) from Smc1 ChIA-PET. This file allows users to view all mapped PET data. 

The high-confidence interactions (merged_Smc1.interactions.N3FDR0.01_intrachromosomal_filteredInteractions.bb) track shows Intra-chromosomal high-confidence Smc1 ChIA-PET interactions between two genomic loci. This file allows users to view the published high-confidence data.

The enriched regions (merged_Smc1_unique_anchor_1e-9_nolambda_peaks.bb) track shows PET peaks that show local enrichment of PETs across the genome. This file allows users to view the regions that show local enrichment of ChIA-PET reads. 

The PET pileup signal (merged_Smc1_unique_PETanchor.bw) track shows a standard wig file that show signal density based on the aligned ChIA-PET reads. This file allows users to view the distribution of the align ChIA-PET reads across the genome. 

Display Conventions and Configuration

In the graphical display, the PET interactions are represented by two blocks one for each end. These blocks are connected by a horizontal line. Local enrichment in tags from PETs is used to identify anchors of interactions. The number of PETs spanning anchors reflects the strength of a chromatin interaction. The density graph of the tags shows the ChIP enrichment at different points of genome, and high peaks indicate binding sites.

Intra-chromosomal high-confidence ChIA-PET interactions (merged_Smc1.interactions.N3FDR0.01_intrachromosomal_filteredInteractions.bb): Two genomic loci in the genome are far from each other on the linear genomic scale, but are spatially close to each other in the nucleus and have SMC1 present at both ends. BED12 format is used to represent the interactions between genomic loci.

ChIA-PET Signal (merged_Smc1_unique_PETanchor.bw): Density graph (wiggle) of signal density based on the aligned individual ChIA-PET tags.

Methods

ChIA-PET was performed as previously described (Chepelev et al., 2012; Fullwood et al., 2009; Goh et al., 2012; Li et al., 2012) using SMC1 as the target antibody. In brief, murine ESCs (up to 1 X 10^8 cells) were treated with 1% formaldehyde at room temperature for 10 min and then neutralized using 0.2 M glycine. The crosslinked chromatin was fragmented by sonication to size lengths of 300–700 bp. The anti-SMC1 antibody (Bethyl, A300-055A) was used to enrich SMC1-bound chromatin fragments. A portion of ChIP DNA was eluted from antibody-coated beads for concentration quantification and for enrichment analysis using quantitative PCR. For ChIA-PET library construction, ChIP DNA fragments were end repaired using T4 DNA polymerase (NEB) and ligated to two different types of PET linkers. After linker ligation, the two samples were combined for proximity ligation in diluted conditions. Following proximity ligation, the paired-end tag (PET) constructs were extracted from the ligation products and the PET templates were subjected to 50 3 50 paired-end sequencing using Illumina HiSeq 2000. The reads from ChIA-PET datasets were processed as described in Dowen et al., 2014.

Genome

NCBI37/mm9

Credits

Whitehead Institute: Jill M. Dowen, Zi Peng Fan,Denes Hnisz, Brian J. Abraham, Lyndon N. Zhang, Abraham S. Weintraub, Jurian Schuijers, Tong Ihn Lee, and Richard A. Young.

NHLBI, National Institutes of Health: Gang Ren, Keji Zhao

Please direct all questions to young_computation ( young_computation@wi.mit.edu ).

Publications

Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang L, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. (2014). Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell, 2014; 159(2):374-87. 

References

Chepelev, I., Wei, G., Wangsa, D., Tang, Q., and Zhao, K. (2012). Characteriza- tion of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res. 22, 490–503.

Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang L, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. (2014). Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell, 2014; 159(2):374-87. 

Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., et al. (2009). An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58–64.

Goh, Y., Fullwood, M.J., Poh, H.M., Peh, S.Q., Ong, C.T., Zhang, J., Ruan, X., and Ruan, Y. (2012). Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) for mapping chromatin interactions and understand- ing transcription regulation. J. Vis. Exp.. http://dx.doi.org/10.3791/3770.

Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., Poh, H.M., Goh, Y., Lim, J., Zhang, J., et al. (2012). Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98.