Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler

Abstract

Posttranslational modifications play a key role in recruiting chromatin remodeling and modifying enzymes to specific regions of chromosomes to modulate chromatin structure. Alc1 (amplified in liver cancer 1), a member of the SNF2 ATPase superfamily with a carboxy-terminal macrodomain, is encoded by an oncogene implicated in the pathogenesis of hepatocellular carcinoma. Here we show that Alc1 interacts transiently with chromatin-associated proteins, including histones and the poly(ADP-ribose) polymerase Parp1. Alc1 ATPase and chromatin remodeling activities are strongly activated by Parp1 and its substrate NAD and require an intact macrodomain capable of binding poly(ADP-ribose). Alc1 is rapidly recruited to nucleosomes in vitro and to chromatin in cells when Parp1 catalyzes PAR synthesis. We propose that poly(ADPribosyl)ation of chromatin-associated Parp1 serves as a mechanism for targeting a SNF2 family remodeler to chromatin.Alc1 ͉ chromatin remodeling enzyme ͉ macrodomain ͉ poly-(ADP-ribose) polymerase ͉ Snf2-like ATPase I n eukaryotic cells, chromosomal DNA is packaged into nucleosomes, which are in turn folded into higher order nucleosome arrays in chromatin fibers. This packaging allows the Ϸ2 m of DNA that make up the human genome to fit into nuclei with diameters on the order of 2-6 m; however, it also blocks access to DNA of the machinery responsible for transcription, replication, and DNA repair. Eukaryotic organisms have evolved a set of chromatin modifying and remodeling enzymes that alter the structure of chromatin to control accessibility to the machineries responsible for DNA replication and repair and for transcription. These enzymes have been shown to be targeted to regions of modified chromatin by such domains as bromodomains, which can bind acetylated histones, or chromodomains, tudor domains, or MBT domains, which can interact with methylated histones (1-4).ALC1 (amplified in liver cancer 1), alternatively known as CHD1L, is a member of the SNF2 superfamily of ATPases, some of which function as chromatin remodeling enzymes (5-7). Sequence alignments suggest that Alc1 is similar to chromatin remodeling ATPases Snf2, Iswi, and Chd1, which have been implicated in transcription, DNA repair, and replication (7). Alc1 lacks identifiable chromo-, bromo-, tudor-, MBT, or other domains known to have chromatin targeting functions. Instead, it contains a carboxy-terminal macrodomain. Macrodomains have been shown through biochemical and structural analyses to bind ADP-ribose (8).Over 50% of human hepatocellular carcinoma (HCC) patients contain a chromosomal amplification at 1q21, which includes the ALC1 gene (9-11). Alc1-overexpressing cells exhibit increased colony formation in soft agar and increased tumorigenicity in nude mice (11), suggesting that ALC1 functions as an oncogene.While mounting evidence points to a potential role for Alc1 in oncogenesis, the molecular function of the Alc1 ATPase has not been studied. Here, we show that Alc1 is a chromatin remodeling enzyme that is recruited to nucleosom...

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.…”

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.…”

“…The first catalytic target is the auto-modification domain of PARP1 itself, followed by PARylation of histones and other proteins at DNA damage sites [19,20]. PARP1 promotes chromatin relaxation at DNA damage sites by PARylating and displacing histone H1 [21,22] and recruiting chromatin remodelers such as ALC1 [15,16,23], SMARCA5 [24] and CHD2 [25]. Chromatin relaxation allows access to DNA repair factors, some of which are recruited through binding PAR.…”