Sharon L. Squazzo

TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.

TL;DR: The transcriptional landscape of the four human HOX loci is characterized at five base pair resolution in 11 anatomic sites and 231 HOX ncRNAs are identified that extend known transcribed regions by more than 30 kilobases, suggesting transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance.

TL;DR: Surprisingly, the PRC complexes can be localized to discrete binding sites or spread through large regions of the mouse and human genomes, and it is suggested that OCT4 maintains stem cell self-renewal, in part, by recruitingPRC complexes to certain genes that promote differentiation.

TL;DR: A genome-scale chromatin immunoprecipitation comparison of two modifications of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors.

TL;DR: A computational genomics approach (termed ChIPModules), which begins with experimentally determined binding sites and integrates positional weight matrices constructed from transcription factor binding sites, to identify transcriptional regulatory modules for E2F1, demonstrating the strength of the sequence-based, unbiased, and universal protocol.