SMARCAL1 maintains telomere integrity during DNA replication

Abstract

The SMARCAL1 (SWI/SNF related, matrix-associated, actin-dependent, regulator of chromatin, subfamily A-like 1) DNA translocase is one of several related enzymes, including ZRANB3 (zinc finger, RAN-binding domain containing 3) and HLTF (helicase-like transcription factor), that are recruited to stalled replication forks to promote repair and restart replication. These enzymes can perform similar biochemical reactions such as fork reversal; however, genetic studies indicate they must have unique cellular activities. Here, we present data showing that SMARCAL1 has an important function at telomeres, which present an endogenous source of replication stress. SMARCAL1-deficient cells accumulate telomere-associated DNA damage and have greatly elevated levels of extrachromosomal telomere DNA (C-circles). Although these telomere phenotypes are often found in tumor cells using the alternative lengthening of telomeres (ALT) pathway for telomere elongation, SMARCAL1 deficiency does not yield other ALT phenotypes such as elevated telomere recombination. The activity of SMARCAL1 at telomeres can be separated from its genome-maintenance activity in bulk chromosomal replication because it does not require interaction with replication protein A. Finally, this telomere-maintenance function is not shared by ZRANB3 or HLTF. Our results provide the first identification, to our knowledge, of an endogenous source of replication stress that requires SMARCAL1 for resolution and define differences between members of this class of replication fork-repair enzymes.SMARCAL1 | telomere | replication stress | c-circle T he complete and accurate duplication of the genome in each cell-division cycle is challenged by many sources of replication stress including DNA template damage, collisions between replication and transcriptional machineries, and difficult-to-replicate DNA sequences. To overcome these challenges, cells use a multifaceted replication stress response that includes specialized enzymes that stabilize, repair, and restart stalled replication forks.Among these enzymes are members of the SNF2 family of DNA-dependent ATPases that include SMARCAL1 (SWI/SNF related, matrix-associated, actin-dependent, regulator of chromatin, subfamily A-like 1), ZRANB3 (zinc finger, RAN-binding domain containing 3), and HLTF (helicase-like transcription factor) (1). These DNA translocases bind replication fork structures, hydrolyze ATP, and perform branch migration reactions (2-11). Each of these enzymes can catalyze fork regression in vitro, although it is still unclear whether they perform this reaction in vivo (3, 4, 6-8, 11, 12). SMARCAL1 and ZRANB3 also can catalyze DNA strand annealing, disrupt displacement loop structures, and catalyze fork restoration reactions to return a regressed fork back into a normal fork structure (3,4,13).Given the overlapping biochemical activities among these translocases, it is unclear why the cell employs so many different enzymes at stalled forks. Genetic studies indicate these proteins have distinct functions. HLTF ...

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

“…Yeast SWI/SNF is required for telomeric silencing (Dror and Winston 2004), and telomeric expansion (Tomar et al 2008). Mammalian cells lacking SMARCAL1, which is a SNF2 family ATPase but is not a subunit of the mammalian SWI/SNF complex, accumulate elevated levels of telomere-associated DNA damage (Poole et al 2015). Moreover, knockdown of the mammalian SWI/SNF enzyme subunit, ARID1A, reduces telomeric repeatcontaining RNA (TERRA) levels by at least twofold (Scheibe et al 2013).…”

SMARCAL1 and telomeres: Replicating the troublesome ends

“…We have shown that SMARCAL1 depletion in 2 telomerase-positive cells lines, HeLa cells and MEFs, results in an increase in telomere damage. 25 Taken together, our data indicate SMAR-CAL1 function during telomere replication is a more universal requirement during telomere replication rather than an ALT-specific telomere repair pathway. …”

“…29 However, we were unable to detect any of these phenotypes in SMARCAL1-deficient cells. 25 This is the first case, to our knowledge, of persistent C-circles without the presence of other ALT phenotypes. Thus, Ccircles may not always indicate cells are using the ALT mechanism of telomere elongation.…”

“…Importantly, we did not observe an accumulation of C-circles in HLTF-or ZRANB3-deficient cells. 25 Nor did we observe C-circle accumulation in cells depleted of the RecQ helicases WRN or BLM.…”

“…25 Furthermore, this telomere replication function of SMARCAL1 is not shared by ZRANB3 or HLTF, providing the first evidence for the diverging functions of these SNF2 family enzymes in the resolution of endogenous sources of replication stress.…”