Transcription factors organize into functional groups on the linear genome and in 3D chromatin.

Transcription factors (TFs) and their binding sites have evolved to interact cooperatively or competitively with each other. Here we examine in detail, across multiple cell lines, such cooperation or competition among TFs both in sequential and spatial proximity (using chromatin conformation capture assays), considering in vivo binding data as well as TF binding motifs in DNA. We ascertain significantly co-occurring ("attractive") or avoiding ("repulsive") TF pairs using robust randomized models that retain the essential characteristics of the experimental data.

Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in and a Chromosome Number Change in Related Species.

The thermotolerant multidrug-resistant ascomycete rapidly emerged since 2009 causing systemic infections worldwide and simultaneously evolved in different geographical zones. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses.

Loss of centromere function drives karyotype evolution in closely related species.

Genomic rearrangements associated with speciation often result in variation in chromosome number among closely related species. species show variable karyotypes ranging between six and nine chromosomes. Here, we experimentally identified all eight centromeres in as 3-5-kb long kinetochore-bound regions that span an AT-rich core and are depleted of the canonical histone H3.