In Genome Biology this week, scientists led by Claes Wadelius at Uppsala University have used ChIP-seq to study the genome-wide DNA binding sites of FOXA1 and FOXA3 in HepG2 cells. Comparing their data to previous results for FOXA2, they found that these forkhead box/winged helix family member transcription factors often bind close to each other and that FOXA2 interacts with both FOXA1 and FOXA3 in vivo, while FOXA1 and FOXA3 do not appear to interact. Additionally, they write, "we detected diverse patterns of trimethylation of lysine 4 on histone H3 (H3K4me3) at transcriptional start sites and directionality of this modification at FOXA binding sites."
Two recent papers present methods to help utilize information from genomic studies. In one, researchers from the Genomics Institute of the Novartis Research Foundation in San Diego, California, present BioGPS, "a centralized gene portal for aggregating distributed gene annotation resources." In a second, Curie Institute scientists have developed a tool to mine copy number and genotype information from tumor genomes. Called Genome Alteration Print, the method is "based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles," and does well even on low quality data, low tumor content, and highly rearranged tumor genomes, they say.
To identify the important adaptive genes in coral reefs, which continue to decline, scientists at the University of Texas, Austin, have constructed a high-resolution genetic linkage map for the reef-building coral Acropora millepora, "the first genetic map reported for any coral, or any non-Bilaterian animal," they say. The map contains 393 SNPs and 36 microsatellites across 14 linkage groups. When they compared it to other metazoan genomes — including human, nematode, fly, anemone, and placozoan — they found synteny regions.
Ana Marques and Chris Ponting at the University of Oxford have compared two mouse long noncoding RNA libraries to better understand their evolutionary history. Looking at a macroRNA catalog, which contained over 3,000 ncRNAs, and a lincRNA catalog, with 1,600 ncRNAs, they saw that "both have same relatively low degree of sequence constraint" and that there remains to be discovered a much larger pool of noncoding RNA in the mouse genome.