Poly(ADP-ribose)–Dependent Regulation of DNA Repair by the Chromatin Remodeling Enzyme ALC1

Abstract

SummaryALC1, a novel PARP1-stimulated chromatin-remodelling enzyme promotes DNA repair.Post-translational modifications play key roles in orchestrating chromatin plasticity. Although various chromatin-remodelling enzymes have been described that respond to specific histone modifications, little is known about the role of poly(ADP-ribose) in chromatin remodelling. Here, we identify a novel chromatin-remodelling enzyme, ALC1 (Amplified in Liver Cancer 1), that is specifically regulated by poly(ADP-ribosyl) ation. ALC1 binds poly(ADP-ribose) via a C-terminal Macro domain and catalyzes PARP1-stimulated nucleosome sliding, conferred by an N-terminal ISWI-related helicase core. Our results define ALC1 as a novel DNA damage-response protein, whose role in this process is sustained by its association with known DNA repair factors and its rapid poly(ADP-ribose)-dependent recruitment to DNA damage sites. Furthermore, we show that depletion or overexpression of ALC1 results in sensitivity to DNA-damaging agents. Collectively, these results provide new insights into the mechanisms by which poly(ADP-ribose) regulates DNA repair.The restricted accessibility of DNA within chromatin presents a barrier to DNA manipulations that require direct protein-DNA interactions (1-3). Processes such as transcription, repair and replication that require efficient DNA recognition are therefore dependent on the appropriate modulation of chromatin structure. Chromatin relaxation is a critical event that occurs during DNA repair and is associated with post-translational poly(ADP-ribose) (PAR) modification (4). PAR is synthesized in a reaction that utilizes NAD+ as a substrate by the PARP family of enzymes, of which PARP1 (and to a lesser extent PARP2) respond to DNA strand breaks (5-7). As a consequence of poly(ADP-

CHD1L Regulated PARP1-Driven Pluripotency and Chromatin Remodeling During the Early-Stage Cell Reprogramming

“…3D). Comparing the results of the two CHD1L mutants, the mutation of the CHD1L macro‐domain led to a more prominent reduction in the PARP1/CHD1L interaction, indicating that the macro‐domain of CHD1L is the major PAR binding motif, as described by previous biochemical studies 22, 23. Collectively, these data indicate that PAR affinity for CHD1L is crucial for the interaction between PARP1 and CHD1L, especially at the functional macro‐domain, during early reprogramming.…”

“…3A, right). It has been shown that the macro‐domain of CHD1L serves an essential role for PAR binding and PARP1‐dependent recruitment of CHD1L to DNA damage sites 22, 23. To determine whether the macro‐domain of CHD1L is involved in the PARP1/CHD1L interaction during cell reprogramming, CHD1L wild‐type (CHD1L‐WT) and two mutant types—a helicase‐domain mutant (CHD1L‐K77R) and macro‐domain mutant (hCHD1L‐D723A)—were ectopically expressed in MEFs with OSKM transfection for 6 days.…”

“…CHD binding protein 1‐like (CHD1L) is a member of the Snf2 family of ATP‐dependent chromatin‐remodelers 22, 23. It has been suggested that in embryo implantation, CHD1L is essential for maintaining the embryonic state of the preimplantation embryo 24.…”

“…The macro‐domains of CHD1L have been shown to function as binding modules for metabolites of NAD + , including PAR 26. Previous studies have shown that CHD1L is a target protein for Parp1‐regulated PARylation and recruits DNA damage sites with Parp1 through its macro‐domain 22, 23. Proteomic analysis of PAR‐associated proteins in a previous study showed that CHD1L is significantly increased in pluripotent cells but decreased during the differentiation process 27.…”

Simultaneous dual-channel imaging to quantify interdependent protein recruitment to laser-induced DNA damage sites

“…PCNA is a ring-shaped clamp around DNA that serves as a loading platform for proteins involved in DNA replication and repair [14]. ALC1 is an SNF2-type chromatin remodeling ATPase, which is activated upon PAR binding to its macro domain at DNA damage sites [15,16]. PARP1, PARG, PCNA and ALC1 are all recruited to laser-induced DNA damage sites albeit with distinct recruitment kinetics.…”