The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

The DNA Damage Response: Making It Safe to Play with Knives

Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2-5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and with few byproducts, the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay-Sachs disease (requiring a deletion in HEXA); to install a protective transversion in PRNP; and to insert various tags and epitopes precisely into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, has complementary strengths and weaknesses compared to base editing, and induces much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.

/pdf/search-and-replace-genome-editing-without-double-strand-rik2u7n3yw.pdf

Search-and-replace genome editing without double-strand breaks or donor DNA

PARP inhibitors (PARPi), a cancer therapy targeting poly(ADP-ribose) polymerase, are the first clinically approved drugs designed to exploit synthetic lethality, a genetic concept proposed nearly a century ago. Tumors arising in patients who carry germline mutations in either BRCA1 or BRCA2 are sensitive to PARPi because they have a specific type of DNA repair defect. PARPi also show promising activity in more common cancers that share this repair defect. However, as with other targeted therapies, resistance to PARPi arises in advanced disease. In addition, determining the optimal use of PARPi within drug combination approaches has been challenging. Nevertheless, the preclinical discovery of PARPi synthetic lethality and the route to clinical approval provide interesting lessons for the development of other therapies. Here, we discuss current knowledge of PARP inhibitors and potential ways to maximize their clinical effectiveness.

/pdf/parp-inhibitors-synthetic-lethality-in-the-clinic-4hzn79vbnn.pdf

PARP inhibitors: Synthetic lethality in the clinic

The DNA Damage Response: Ten Years After

https://www.zora.uzh.ch/id/eprint/190449/1/Functional_Radiogenetic_Profiling_Implicates_ERCC6L2_in_Non-homologous_End_Joining__1-s2.0-S2211124720310536-main.pdf

Functional Radiogenetic Profiling Implicates ERCC6L2 in Non-homologous End Joining

Across mammals, PRDM9 binding localizes almost all meiotic recombination hotspots However, most PRDM9 motif sequence matches are not bound, and most PRDM9-bound loci do not become hotspots To explore factors that affect binding and subsequent recombination outcomes, we mapped human and chimp PRDM9 binding sites in a human cell line, and measured PRDM9-induced H3K4me3 and gene expression changes These data revealed varied DNA-binding modalities of PRDM9, and histone modifications that predict binding At sites where PRDM9 binds, specific cis sequence motifs associated with TRIM28 recruitment, and histone modifications, predict whether recombination subsequently occurs These results implicate the large family of KRAB-ZNF genes in consistent, localized meiotic recombination suppression PRDM9 affects gene expression for a small number of genes including CTCFL and VCX , by binding nearby Finally, we show that PRDM99s DNA-binding zinc finger domain strongly impacts the formation of multimers, with a pair of highly diverged alleles multimerizing less efficiently

http://www.biorxiv.org/content/biorxiv/early/2017/05/31/144295.full.pdf

Human PRDM9 Can Bind And Activate Promoters, And Other Zinc-Finger Proteins Associate With Reduced Recombination In cis

The tumor suppressor protein 53BP1 was first identified as a p53-interacting protein over two decades ago, however its direct contribution to p53-dependent cellular activities has remained enigmatic. Having reinvestigated the link between 53BP1 and p53, we now show 53BP1 plays an important role in directly stimulating genome-wide p53-dependent gene transactivation and repression events in response to ionizing radiation (IR) and synthetic p53 activation. We have also fine-mapped the domains in 53BP1 that modulate p53 activity and reveal it requires both auto-oligomerization and its tandem-BRCT domain-mediated bivalent interactions with p53 and the ubiquitin-specific protease USP28. Loss of 53BP1 or USP28 catalytic activities results in inefficient p53-dependent cell-cycle checkpoint and exit responses. Mechanistically, we show 53BP1-USP28 cooperation to be essential for stimulating normal p53-promoter element interactions and downstream gene transactivation-associated events, yet dispensable for 53BP1-dependent DSB repair regulation. Collectively, our data indicate a upstream role for 53BP1-USP28 complexes in priming p539s transcriptional potential, providing a mechanistic explanation for 53BP1-p53 cooperation in controlling anti-tumorigenic cell-fate decisions. Moreover, we reveal these activities to be distinct and separable from 53BP19s regulation of DNA double-strand break repair pathway choice, and establish the prime function for the 53BP1 BRCT domain and its interaction partner USP28. Our study therefore defines important and novel functions for 53BP1 in enforcing a vital tumor suppressor pathway that are likely to contribute to tumor suppression. In the meeting we will describe these findings and update on recent progress. This abstract is also being presented as Poster B04. Citation Format: Raquel Cuella-Martin, Catarina Oliveira, Helen E. Lockstone, Suzanne Snellenberg, Natalia Grolmusova, J Ross Chapman. A 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr PR20.

J. Ross Chapman

Papers

Functional Radiogenetic Profiling Implicates ERCC6L2 in Non-homologous End Joining

Human PRDM9 Can Bind And Activate Promoters, And Other Zinc-Finger Proteins Associate With Reduced Recombination In cis

Abstract PR20: A 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms

checkpoint signaling in Xenopus