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This Week in Genome Research: Mar 4, 2015

University of Washington researchers introduce a strategy called MIPSTR for simultaneously seeing germline or somatic short tandem repeats in samples from multiple individuals. The method involves mapping of mid-size sequencing reads representing short tandem repeats generated with the help of sing-molecule molecular inversion probes, the study authors say. When they applied MIPSTR to Arabidopsis thaliana plant populations, for example, the investigators successfully determined short tandem repeat genotypes at 102 different loci. They also applied it to mutation prone cells, demonstrating that it can detect somatic versions of the repeats.

Researchers from the US and Canada considered chromatin state in the context of chromatin conformation and vice versa using a newly developed computational approach for annotating and detecting relationships between different chromatin domains. With this approach, known as graph-based regularization, or GBR, the team characterized chromatin patterns in eight different cell types, tracking down small sets of so-called specific expression domains that appear to be regulated in a subset of the cell types tested.

Using an approach for profiling transcription factor recruitment sequences, called ChIP-exo, and a newly developed computational pipeline known as ExoProfiler, a team from Germany and France look at the DNA binding motifs associated with the binding of glucocorticoid receptors and related transcription factors in the genome. From the ChIP-exo patterns detected in their own experiments and existing datasets, the researchers found clues for interpreting direct and indirect regulatory binding from such experiments, In the case of the glucocorticoid receptor, for instance, they found binding can occur even without classical recognition sequences with the help of direct or indirect interactions involving several transcription factors.