Researchers from the Whitehead Institute for Biomedical Research and the Massachusetts Institute of Technology introduce a reporter method for scrutinizing DNA methylation patterns in individual cells. The team took advantage of methylation-sensitive promoters as well as the presence of cytosine and guanine-rich sequences that influence methylated cytosines nearby to develop a so-called reporter of genomic methylation — a green fluorescence protein-based reporter under the control of an imprinted gene promoter. For their proof-of-principle experiments, the study's authors demonstrated that this approach could be used to detect methylation changes at specific sites in the genome in differentiating mouse stem cells or somatic cells being reprogrammed to become induced pluripotent stem cells.
A team led by University of North Carolina at Chapel Hill investigators describes molecular features detected in hundreds of invasive breast tumors. Using exome sequencing, RNA sequencing, microRNA sequencing, and array-based methylation and SNP profiling, the researchers assessed tumor and matched normal samples from 127 invasive lobular carcinoma cases, 490 cases of invasive ductal carcinoma, and 88 mixed lobular/ductal cases. They also tested a subset of samples with reverse-phase protein array and/or transcriptome sequencing. Together, the data pointed to a preponderance of mutations in PTEN, TBX3, and FOX11 in the invasive lobular carcinomas, for example, while molecular features helped to classify apparent histologic hybrids into one subtype or the other. GenomeWeb has more on the study, here.
Broad Institute researchers led a team reporting on a new RNA-guided nuclease enzyme that they believe has promise as an alternative to Cas9 for those interested in CRISPR-based genome editing. In contrast to Cas9, the Cpf1 enzyme chops DNA using a staggered double-strand break, they found, and appears to offer some advantages when selecting a genome editing target site. The team tracked down the protein based on a candidate study of more than a dozen Cpf1-family proteins in Acidominococcus and Lachnospiraceae bacteria. GenomeWeb also covers this study, here.