In a paper published online in advance in Genome Biology, researchers at the UK's University of Birmingham report their use of immunostaining and immunefluorescence microscopy techniques to characterize the "distribution of selected histone modifications across metaphase chromosomes from normal human lymphoblastoid cells." The team writes that bands of histone modifications "co-localize with regions relatively rich in genes and CpG islands" and that metaphase bands, when compared with data for "histone modification levels across the interphase genome" obtained from ENCODE and ChIP-seq experiments, "only occasionally overlap with gene-rich regions." Overall, the team suggests that their data reveal "extensive remodeling of the epigenome at mitosis."
Researchers at Australia's Curtin University, North Dakota State University, and their collaborators report a "first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres," which causes net form of net blotch — an important disease in barley. The team assembled this preliminary genome sequence using only short Solexa sequencing reads of isolate 0-1 and compared it against "BAC sequences, ESTs, orthologous genes and by PCR, and complemented by cytogenetic karyotyping and the first genome-wide genetic map for P. teres f. teres" for validation.
Meanwhile, investigators at the US Department of Agriculture and their collaborators present the Bovine Genome Atlas, which they say shows "novel distinctive tissue characteristics and evidence for improving genome annotation." The Bovine Gene Atlas — which contains RNA abundance data for 92 adult, juvenile, and fetal cattle tissues as well as three cattle cell lines that comprise 300.2 million total raw tag sequences — represents "the deepest and broadest transcriptome survey of any livestock genome to date," the team writes, adding that the study has identified the first "tissue-specific variation in the proportion of mitochondrial transcriptional tag abundance" in cattle.
Investigators at the National Center for Biotechnology Information and the National Institute of Diabetes and Digestive and Kidney Diseases describe LDsplit, a computational approach to interrogate recombination hotspots with genetic polymorphisms. The researchers report that with LDsplit, they found that for a "significant fraction of hotspots" on human chromosome 6, "there is an association between variations in intensity of historical recombination and sequence polymorphisms." In addition, the team also identified a conserved 11-mer motif "whose complement partially matches ... a critical motif for the regulation of recombination hotspots."