The goal of this analysis was to check for chromatin rearrangements in response to DMSO treatment by identifying presence of CTCF motifs at the boundaries of known chromatin loops. The steps performed were:
Scan the full set of ATAC-seq peaks from DMSO dataset for CTCF consensus motif with MOODS motif scanner. Also scan the set of differential peaks between DMSO & Control at earlyG1, lateG1, SG2M. The positive and negative strands were scanned for all all peaks to identify the direction that motifs are facing.
consensus CTCF motif from Kim et al, 2007, Cell: GTGGCCACCAGGGGGCGCCC
Obtained known chromatin loops in multiple cell types from Oana:
/srv/scratch/oursu/3Dgenome/data/HiC/loops
Look at peaks where MOODS reports a high-confidence CTCF consensus motif hit. Identify the subset of such peaks that fall within known CTCF loops.
Filter the set of results from (3) to just those loops where we observe a CTCF motif on + strand on one end of the loop, and a CTCF motif on - strand on other end of the loop (i.e. the CTCF motifs are facing each other).
The hits from (4) are included in the Excel file that is attached to this post.
The "green" columns are metadata from Oana's loop lists across different cell types. The orange columns indicate CTCF motifs in the DMSO dataset that are contained on the positive strand within the first end of the loop. The purple columns indicate CTCF motifs in the DMSO dataset that are contained on the negative strand in the second end of the loop.
One interesting thing to note: I am not seeing any CTCF hits contained within loops when examining the differential peaks, hits only appear for peaks that are stable in both DMSO & Control conditions.
Anshul, what should the next steps be for this analysis? Do you have some time to meet and discuss?
CTCF_in_chromatin_loops.xlsx
The goal of this analysis was to check for chromatin rearrangements in response to DMSO treatment by identifying presence of CTCF motifs at the boundaries of known chromatin loops. The steps performed were:
Scan the full set of ATAC-seq peaks from DMSO dataset for CTCF consensus motif with MOODS motif scanner. Also scan the set of differential peaks between DMSO & Control at earlyG1, lateG1, SG2M. The positive and negative strands were scanned for all all peaks to identify the direction that motifs are facing. consensus CTCF motif from Kim et al, 2007, Cell: GTGGCCACCAGGGGGCGCCC
Obtained known chromatin loops in multiple cell types from Oana: /srv/scratch/oursu/3Dgenome/data/HiC/loops
Look at peaks where MOODS reports a high-confidence CTCF consensus motif hit. Identify the subset of such peaks that fall within known CTCF loops.
Filter the set of results from (3) to just those loops where we observe a CTCF motif on + strand on one end of the loop, and a CTCF motif on - strand on other end of the loop (i.e. the CTCF motifs are facing each other).
The hits from (4) are included in the Excel file that is attached to this post. The "green" columns are metadata from Oana's loop lists across different cell types. The orange columns indicate CTCF motifs in the DMSO dataset that are contained on the positive strand within the first end of the loop. The purple columns indicate CTCF motifs in the DMSO dataset that are contained on the negative strand in the second end of the loop.
One interesting thing to note: I am not seeing any CTCF hits contained within loops when examining the differential peaks, hits only appear for peaks that are stable in both DMSO & Control conditions.
Anshul, what should the next steps be for this analysis? Do you have some time to meet and discuss?