In the early online edition of Genome Research, an international team led by investigators at Nanjing Agricultural University and BGI-Shenzhen presents a draft genome for pear, Pyrus bretschneideri. Using BAC-by-BAC Sanger sequencing and Illumina HiSeq 2000 high-throughput sequencing, the group generated enough reads to cover around 97 percent of the pear genome's estimated 512 million bases to an average depth of 194-fold. Roughly three-quarters of the sequence was anchored to the plant's chromosomes, the team note. Its analyses of the genome unearthed more than 42,800 predicted protein-coding genes and roughly 270 million bases of repeat sequence, while comparisons to sequences from apple, grape, and other plants provided clues to pear's evolutionary history and genetic capabilities.
The origins of DNA replication — and the timing of replication — are apparently influenced by transcription levels at these sites, another new study suggests. Italian researchers used chromatin immunoprecipitation combined with sequencing to look at genome-wide binding patterns for ORC1, a protein found at active replication origins. After verifying that the ORC1-bound sites were actively replicating in the HeLa cells, the researchers took a closer look at the relationships between replication and transcription at these sites, which overlap with transcription start sites. Their results suggest that DNA replication origins at the TSSs of more highly expressed coding genes go through a spurt of replication early in the DNA synthesis or "S" phase of the cell cycle, whereas origins of replication that coincide with the TSSs of non-coding sequences with lower expression remain active throughout S-phase.
Last but not least, the Harvard Medical School Center for Biomedical Informatics' Peter Park and his colleagues describe the analytical methods they applied to 8,227 human cancer genomes that had been subjected to array comparative genome hybridization-based copy-number profiling for more than 100 past studies. By scrutinizing this data anew, the team nailed down some recurrent chromosomal alterations that seem to span tumor types and others that tend to be specific to certain tumors or groups of developmentally related cancers. The work also pointed to copy-number patterns associated with rare, extensive genomic rearrangement events called chromothripsis. "Taken together," the study's authors say, "our comprehensive view of copy number alterations provides a framework for understanding the functional significance of various genomic alterations in cancer genomes."