Significance: Identifying proteins selectively associated with a genomic locus provides an important entry point toward understanding how a specific gene is regulated. Over the years, there have been several reports describing targeted chromatin-purification methods. However, none has been widely adopted due to the complexity and investment required for such protocols. Here, we present an adaptable chromatin purification system, CLASP, that capitalizes on the versatility of purified dCas9 RNA/protein complexes. We deployed CLASP to purify and identify proteins associated with telomere sequences in human cells as a proof of concept. Next, we targeted a different genomic locus, theDrosophila melanogasterhistone cluster, and identified several regulators of the essential histone locus and validated their functional association with genes within the locus.

The extracellular matrix (ECM) is a three-dimensional network of macromolecules that provides a microenvironment capable of supporting and regulating cell functions. However, only a few research organisms are available for the systematic dissection of the composition and functions of the ECM, particularly during regeneration. We utilized the free-living flatworm Schmidtea mediterranea to develop an integrative approach consisting of decellularization, proteomics, and RNAi to characterize and investigate ECM functions during tissue homeostasis and regeneration. ECM-enriched samples were isolated from planarians, and their proteomes were characterized by LC-MS/MS. The functions of identified ECM components were interrogated using RNA interference. Using this approach, we found that heparan sulfate proteoglycan is essential for tissue regeneration. Our strategy provides an experimental approach for identifying both known and novel ECM components involved in regeneration.