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Nature Papers on New Approach to Study Chromatin Architecture, Analysis of Elite HIV Controllers

A new strategy for studying chromatin architecture that overcomes key limitations of current crosslinking-based chromosome conformation capture techniques is reported in Nature Biotechnology this week. Most methods used to investigate chromatin organization depend on extensive in situ crosslinking of protein with genomic DNA, which allows probing of the proximity between genomic loci mediated through the interacting proteins bound at each locus. These proteins, however, reduce resolution and increase background noise. To address this, a team led by scientists from the University of Chicago developed CAP-C — short for chemical-crosslinking assisted proximity capture — which uses multifunctional chemical crosslinkers that substitute the DNA-bound proteins to crosslink proximal genomic DNA loci directly. The varied sizes of the probes allow them to access both open and closed compartments, and DNA-bound proteins can be removed so that DNA can be homogeneously fragmented to around 50 to 200 base pairs in length, the researchers write. "This more uniform fragmentation reduces background noise on the 3D genomic maps by reducing false or heterogeneous ligation," while short-range chromatin interactions are enriched, increasing resolution and sensitivity.

By analyzing HIV-1 genomes and their corresponding chromosomal integration sites in infected individuals who control HIV replication without treatment, a group of investigators from Harvard University's Ragon Institute has uncovered new details about how these so-called elite controllers keep the virus at bay. Elite controllers, who account for less than 1 percent of HIV patients, are able to naturally suppress viral replication despite the presence of a replication-competent viral reservoir, but how this happens is unclear. To better understand this, the investigators used full-length individual provirus sequencing to profile the proviral reservoir landscape at single-genome resolution for 64 elite controllers, as well as 41 patients receiving antiretroviral therapy. As reported in Nature this week, they found the proviral reservoirs of elite controllers frequently consist of oligoclonal to near-monoclonal clusters of intact proviral sequences. Additionally, intact proviral sequences from elite controllers were integrated at highly distinct sites in the human genome and were preferentially located in centromeric satellite DNA or in KRAB-ZNF genes on chromosome 19, both of which are associated with heterochromatin features. The integration sites of intact proviral sequences from elite controllers showed an increased distance to transcriptional start sites and accessible chromatin of the host genome and were enriched in repressive chromatin marks. "As such, elite controllers seem to exemplify attributes of a 'block and lock' mechanism of viral control, which is defined by silencing of proviral gene expression through chromosomal integration into repressive chromatin locations," the study's authors write. They add that in one elite controller, they were unable to detect intact proviral sequences despite analyzing more than 1.5 billion peripheral blood mononuclear cells, pointing to the possibility of a sterilizing cure that has previously only been observed following allogeneic hematopoietic stem cell transplantation.