Molecular functions and cellular roles of the ChlR1 (DDX11) helicase defective in the rare cohesinopathy Warsaw breakage syndrome

Abstract

In 2010, a new recessive cohesinopathy disorder, designated Warsaw breakage syndrome (WABS), was described. The individual with WABS displayed microcephaly, pre- and postnatal growth retardation, and abnormal skin pigmentation. Cytogenetic analysis revealed mitomycin C (MMC)-induced chromosomal breakage; however, an additional sister chromatid cohesion defect was also observed. WABS is genetically linked to bi-allelic mutations in the ChlR1/DDX11 gene which encodes a protein of the conserved family of Iron-Sulfur (Fe-S) cluster DNA helicases. Mutations in the budding yeast ortholog of ChlR1, known as Chl1, were known to cause sister chromatid cohesion defects, indicating a conserved function of the gene. In 2012, three affected siblings were identified with similar symptoms to the original WABS case, and found to have a homozygous mutation in the conserved Fe-S domain of ChlR1, confirming the genetic linkage. Significantly, the clinically relevant mutations perturbed ChlR1 DNA unwinding activity. In addition to its genetic importance in human disease, ChlR1 is implicated in papillomavirus genome maintenance and cancer. Although its precise functions in genome homeostasis are still not well understood, ongoing molecular studies of ChlR1 suggest the helicase plays a critically important role in cellular replication and/or DNA repair.

Fig. 1

ChlR1 belongs to a family of sequence-related Iron–Sulfur (Fe–S) cluster DNA helicases. ChlR1 contains a conserved ATPase/helicase core domain characterized by the eight conserved helicase motifs (purple) and Fe–S cluster domain (yellow). ChlR1 belongs to a family of human DNA helicases (XPD, FANCJ, RTEL1) that are implicated in genetic diseases and cancer. The positions of the mutations genetically linked to WABS are shown above the Homo sapiens (Hs) ChlR1 depiction. Below the human Fe–S helicases are ChlR1 homologs from Saccharomyces pombe (Sp), Saccharomyces cerevisiae (Sc), Caenorhabditis elegans (Ce), and Mus musculus (Mmus), followed by the sequence-related Fe–S helicases MmusRTEL1 and CeDOG-1. The sequence length and percent similarity and identity with the ChlR1 ATPase/helicase domain for each of the Fe–S helicases is shown on the right. The BRCA1 and MLH1 interaction sites, as well as the BLM interaction domain are shown in FANCJ. The PCNA interaction motif (PIP) in ScChl1 and RTEL1, as well as RING finger domain (RING) in RTEL1 is shown

Fig. 2

Model depicting the role of ChlR1 in processing of DNA structures during cellular DNA replication that would affect sister chromatid cohesion. a Efficient maturation of Okazaki fragments is believed to be important for sister chromatid cohesion. 5′ flaps created by strand displacement synthesis can form hairpins that are refractory to cleavage by FEN-1. ChlR1 5′ to 3′ helicase activity may unwind the hairpin structure, enabling FEN-1 to track along the single-strand and perform cleavage at the junction. ChlR1 interacts with FEN-1 and stimulates it 5′ flap cleavage, resulting in a ligatable nick that can be sealed by ligase. b, c ChlR1 resolution of a G-quadruplex structure that arises during replication of parental DNA (b) or recombination between sister chromatids (c) may suppress chromosomal instability. ChlR1 efficiently unwinds a specialized form of G-quadruplex DNA in which anti-parallel strands form a G-tetrad stack (G2′). The ability of ChlR1 to resolve G2′ quadruplexes may help replication to proceed (b) or untangle sister chromatids to allow appropriate HR repair (c)