Publications by authors named "Nina P Farrell"
Article Synopsis
- * A deep-learning model can predict allele-specific activity using only local nucleotide sequences, emphasizing key transcription-factor-binding motifs affected by genetic variants.
- * Combining EN-TEx with previous genome annotations shows significant connections between allele-specific loci and GWAS loci, and aids in transferring known eQTLs to challenging tissue types, improving personal functional genomics research.
The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq) to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III.
View Article and Find Full Text PDFATP-dependent chromatin remodellers allow access to DNA for transcription factors and the general transcription machinery, but whether mammalian chromatin remodellers target specific nucleosomes to regulate transcription is unclear. Here we present genome-wide remodeller-nucleosome interaction profiles for the chromatin remodellers Chd1, Chd2, Chd4, Chd6, Chd8, Chd9, Brg1 and Ep400 in mouse embryonic stem (ES) cells. These remodellers bind one or both full nucleosomes that flank micrococcal nuclease (MNase)-defined nucleosome-free promoter regions (NFRs), where they separate divergent transcription.
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