Yael Nechemia-Arbely, PhD

Assistant Professor

2.32d Hillman Cancer Center
Pittsburgh, PA 15232
Phone: 412-623-3228
Fax: 412-623-7761

Education

B.Sc.Med (Basic Medical Sciences), The Hebrew University of Jerusalem, Israel, 2001
M.Sc.Med (Human Genetics), The Hebrew University of Jerusalem, Israel, 2003
Ph.D  (Biochemistry and Cell Biology), The Hebrew University of Jerusalem, Israel, 2010
 
Yael Nechemia-Arbely, PhD

Background

The centromere is a central genetic element responsible for accurate chromosome segregation during cell division. Paradoxically, centromeres are neither defined by DNA sequences nor conserved among species. Rather, functional centromeres are specified through the stable acquisition of a non-DNA sequence-dependent “epigenetic mark” (Cleveland et al., 2003). A prime candidate for such an epigenetic mark is CENP-A, a histone H3 variant found exclusively in nucleosomes at all active centromeres (Fachinetti et al., 2013). CENP-A-containing chromatin underlies the mitotic kinetochore, the proteinaceous complex that mediates the physical connection between each chromosome to spindle microtubules.

Failure of normal chromosome delivery have broad medical implications, including infertility and birth defects. Moreover, many human tumors have abnormal numbers of chromosomes, a condition known as aneuploidy, and several types of cancer acquired neocentromeres (epigenetic stable acquisition of a new centromere at a new chromosomal site). Therefore, identification of the initial events driving mammalian centromere assembly, as well as the mechanisms required for centromere maintenance and propagation, is of high biological relevance given its broad effects on infertility and tumor development.

Research

CENP-A containing chromatin is a an octameric nucleosome across the entire cell cycle

Fig. 1. CENP-A chromatin is an octameric nucleosome with transient DNA unwrapping. (A) Main proposals for CENP-A containing chromatin particles. (B) CENP-A-bound DNA sequences were analyzed for their nucleosomal DNA length across the cell cycle by microcapillary electrophoresis (Bioanalyzer). Adapted from Nechemia-Arbely et al., 2017.
Using a combination of biochemical, hydrodynamics and genome-wide approaches we recently defined the nature of centromeric chromatin, resolving a longstanding debate in centromere biology (Fig. 1A). We used new reference models for 23 human centromeres to show that the overwhelming majority of centromeric DNAs are assembled with histone H3.1-containing nucleosomes and that human CENP-A chromatin is an octameric nucleosome, with two molecules of CENP-A, across the entire cell cycle with no oscillation between hemisomes to octameric nucleosomes (Nechemia-Arbely et al., 2017) (as suggested by others (Bui et al., 2012)) but with unwinding of the nucleosomal DNA at entry/exit (Fig.1B). This evidence refutes models for hemisomes that may briefly transition to octameric nucleosomes (Bui et al., 2012).
DNA replication restricts CENP-A to centromeres and corrects errors in CENP-A deposition
Here, we tackled an unresolved question of high interest in genetics and cell biology: how are centromeres specified, maintained, and propagated across the cell cycle when CENP-A is diluted during DNA replication and replenished half a cell cycle later, at exit of mitosis? Using CENP-A ChIP-sequencing combined with Repli-seq (replication timing sequencing) and genome-wide mapping onto unique centromere reference models, we discovered that while CENP-A is loaded onto centromeres at mitotic exit (Jansen et al., 2007; Nechemia-Arbely et al., 2012), CENP-A is also ectopically loaded outside of the centromeres (Nechemia-Arbely et al., 2019). We identified a DNA replication-dependent error correction mechanism that acts in S-phase to remove ectopically loaded CENP-A while maintaining the positions of centromere-bound CENP-A with high precision throughout DNA replication (Nechemia-Arbely et al., 2019). We find that DNA replication serves as an error correction mechanism that restricts CENP-A to centromeres by removing it from the ectopic sites of deposition at the chromosome arms. Ectopic CENP-A peaks are removed as DNA replication progresses (Fig. 2).
 

Fig. 2. Ectopic CENP-A is removed contemporaneously with replication fork progression.
This error correction mechanism explains how centromere identity is epigenetically maintained and restricted to one position on the chromosome, a finding of high importance for our understanding of evolutionary time-scale of faithful chromosome inheritance (Fig. 3).
CENP-A retention at centromeres is mediated by CENP-C and the CCAN complex it nucleates, revealing a novel role for this centromeric complex in interphase. This error correction mechanism explains how centromere identity is epigenetically maintained and restricted to one position on the chromosome, a finding of high importance for our understanding of evolutionary time-scale of faithful chromosome inheritance (Fig. 3).

Correction of errors in CENP-A deposition coupled with retention of centromeric CENP-A results in the epigenetic maintenance of centromere identity

Fig. 3. Error correction of CENP-A deposition during DNA replication. CENP-A ChIP-seq shows precise retention of centromeric CENP-A during DNA replication, while ectopic CENP-A is removed from the chromosome arms during DNA replication (Nechemia-Arbely et al., 2019).

Current efforts are aimed towards understanding:

  1. the epigenomic landscape of centromeric chromatin
  2. consequences of ectopic CENP-A deposition in human cells
  3. is the error correction mechanism disrupted in cancer cells?
  4. regulation and maintenance of centromeric chromatin across the cell cycle in health and disease

Journal Articles

Barra V, Logsdon GA, Scelfo A, Hoffmann S, Hervé S, Aslanian A, Nechemia-Arbely Y, Cleveland DW, Black BE and Fachinetti D. Phosphorylation of CENP-A on serine 7 does not control centromere function. Nat Commun 10:175, 2019.
Nechemia-Arbely Y, Miga KH, Shoshani O, Aslanian A, McMahon MA, Lee AY, Fachinetti D, Yates III JR, Ren B and Cleveland DW. DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres. Nat Cell Biol, 2019.
Nechemia-Arbely Y, Fachinetti D, Miga KH, Sekulic N, Soni GV, Kim DH, Wong AK, Lee AY, Nguyen K, Dekker C, Ren B, Black BE and Cleveland DW. Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points. J Cell Biol 216:607-621, 2017.
Hoffmann S, Dumont M, Barra V, Ly P, Nechemia-Arbely Y, McMahon MA, Hervé S, Cleveland DW and Fachinetti D. CENP-A is  dispensable for mitotic centromere function after initial centromere/kinetochore assembly. Cell Rep 17:2394-2404, 2016.
Fachinetti D, Folco HD, Nechemia-Arbely Y, Valente LP, Nguyen K, Wong AJ, Zhu Q, Holland AJ, Desai A, Jansen LE adn Cleveland DW. A two-step mechanism for epigenetic specification of centromere identity and function. Nat Cell Biol 15:1056-1066, 2013.
Nechemia-Arbely Y, Fachinetti D and Cleveland DW. Replicating centromeric chromatin: spatial and temporal control of CENP-A assembly. Exp Cell Res 318:1353-1360, 2012.