2.6 Identification of TADs and TAD boundaries
The normalized contact matrix was used as input to perform TAD
identification as reported in mammalian (Dixon et al., 2012).
Directionality index (DI) was calculated from upstream 2 Mb to
downstream 2 Mb along the center of each bin at 40 kb resolution and
Hidden Markov model (matlab 2013, HMM_calls.m) was then used to predict
the states of DI for final TAD generation. We used the same criteria 400
kb (distance between the two adjacent TADs) to distinguish unorganized
chromatin with topological boundaries, that was the topological
boundaries to be less than 400 kb and unorganized chromatin to be
greater than 400 kb. Transcription start sites (TSSs) were calculated
based on the number of annotated
genes. Firstly, the position of TAD Boundary center was obtained, and
then the number of TSS in each 10 Kb window of the upstream and
downstream of TAD Boundary Center with the distance delimiting size of
10 Kb was calculated.