Human Centromeres - Epigenetics, Genome Stability and Cancer

Yael Nechemia-Arbely Lab

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Now recruiting!!

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OUR RESEARCH

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. 

 

The centromere is a central genetic element responsible for accurate chromosome segregation during cell division. 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.

Paradoxically, centromeres are neither defined by DNA sequences nor conserved among species. Rather, functional centromeres are specified through the stable acquisition of an epigenetic mark, named CENP-A, a histone H3 variant found exclusively in nucleosomes at all active centromeres. CENP-A-containing chromatin underlies the mitotic kinetochore, the proteinaceous complex that mediates the physical connection between each chromosome to spindle microtubules.

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The nature and composition of centromeric chromatin across the cell cycle

Using a combination of approaches we defined the nature of centromeric chromatin, resolving a longstanding debate in centromere biology. Using new reference models for 23 human centromeres we directly demonstrated 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 (as suggested by others) but with unwinding of the nucleosomal DNA at entry/exit. This evidence refutes models for hemisomes that may briefly transition to octameric nucleosomes.

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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.

Centromere-bound CENP-A is maintained with high precision throughout DNA replication

The 3-4% of α-satellite centromeric chromatin that contain CENP-A is precisely recycled to daughter centromeres during DNA replication. This maintenance of centromere-bound CENP-A through DNA replication requires CENP-C and the CCAN complex it nucleates. Thus, centromeric CENP-A is retained at the same centromeric sites with precision through DNA replication, leading to epigenetic maintenance of human centromeres. 

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CENP-A ChIP-seq identifies CENP-A binding at reference centromeres of 23 human chromosomes. (A) CENP-A ChIP-seq shows CENP-A binding peaks at the centromere of chromosome 8 for before and after DNA replication. CENP-A is precisely maintained at human centromeres during DNA replication. (B) High-resolution view of read mapping to a site that is single copy in the centromere reference model of chromosome 2, after filtering out multimapping reads.

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We are interested in understanding:

  • The relationship between CENP-A, CENP-C and CENP-T DNA binding at human centromeres across the cell cycle, to create an epigenomic landscape of centromeric chromatin across the cell cycle. 

  • The positional stability of human centromeres throughout cellular proliferation. Is CENP-A capable of precisely and stably specifying centromere position across a single cell cycle or throughout cellular proliferation?

DNA replication restricts CENP-A to centromeres and corrects errors in CENP-A deposition

CENP-A is diluted every S-phase and is replenished only half a cell cycle after at exit of mitosis. this raises the question of how centromeres are specified, maintained, and propagated across the cell cycle. 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, CENP-A is also ectopically loaded outside of the centromeres. We identified a DNA replication-dependent error correction mechanism that acts in S-phase to remove ectopically loaded CENP-A.

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In parallel to removal of CENP-A from ectopic sites, positions of centromere-bound CENP-A are maintained with high precision throughout DNA replication, in a mechanism that requires CENP-C and the CCAN complex it nucleates.

Thus, DNA replication serves as an error correction mechanism that restricts CENP-A to centromeres by removing it from ectopic sites of deposition at the chromosome arms. This error correction mechanism explains how centromere identity is epigenetically maintained and restricted to one position on the chromosome.

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We now seek to determine the consequences of ectopic CENP-A deposition in human cells, particularly in cancer cells, and whether the error correction mechanism of ectopic CENP-A is disrupted in cancer cells.

We thank the NIGMS and Pitt Office of Research for funding our research! 

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PUBLICATIONS

Chromothripsis drives the evolution of gene amplification in cancer

Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW

Nature. Dec 23 (2020)

Guarding the Genome: CENP-A-Chromatin in Health and Cancer

Mahlke MA, Nechemia-Arbely Y

Genes (Basel). Jul 16;11(7):810 (2020)

 

DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres

Nechemia-Arbely Y, Miga KH, Shoshani O, Aslanian A, McMahon MA, Lee AY, Fachinetti D, Yates III JR, Ren B and Cleveland DW

Nature Cell Biology 21(6):743-754 (2019)

  • Nature Cell Biology News and Views: Centromere maintenance during DNA replication

 

Phosphorylation of CENP-A on serine 7 does not control centromere function

Barra V, Logsdon GA, Scelfo A, Hoffmann S, Hervé S, Aslanian A, Nechemia-Arbely Y, Cleveland DW, Black BE, Fachinetti D

Nature Communication 11;10(1):175 (2019)

 

Human centromeric CENP-A-containing chromatin is a homotypic, octameric nucleosome at all cell cycle points

Nechemia-Arbely Y, Fachinetti D, Miga KH, Sekulic N, Soni GV, Wong AK, Lee AY, Nguyen K, Dekker C, Ren B, Black BE, Cleveland DW

Journal of Cell Biology 6;216(3):607-621 (2017)

  • Journal of Cell Biology Special Focus: Genome Stability, Special Collection: Nuclear Organization and Function

 

Interleukin 6-dependent genomic instability heralds accelerated carcinogenesis following liver regeneration on a background of chronic hepatitis

Lanton T, Shriki A, Nechemia-Arbely Y, Abramovitch R, Levkovitch O, Adar R, Paldor M, Goldenberg D, Sonnenblick A, Peled A, Rose-John S, Galun E, Axelrod HJ

Hepatology 65(5):1600-1611 (2017)

 

CENP-A Is Dispensable for Mitotic Centromere Function after Initial Centromere/Kinetochore Assembly

Hoffmann S, Dumont M, Ly P, Nechemia-Arbely Y, McMahon MA, Cleveland DW, Fachinetti D

Cell Reports 22;17(9):2394-2404 (2016)

 

A two-step mechanism for epigenetic specification of centromere identity and function

Fachinetti D, Folco D, Nechemia-Arbely Y, Valente L, Nguyen K, Zou Q, Holland AJ, Verma IM, Desai A, Jansen LET, Cleveland DW

Nature Cell Biology 15(9):1056-66 (2013)

  • Nature Cell Biology News and Views: Swapping CENP-A at the centromere

 

Replicating centromeric chromatin: spatial and temporal control of CENP-A assembly

Nechemia-Arbely Y, Fachinetti D, Cleveland DW

Experimental Cell Research 15;318(12):1353-60 (2012)

 

GROUP MEMBERS

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Yael Nechemia-Arbely Ph.D.

Principal Investigator

Assistant Professor of Pharmacology and Chemical Biology

Email | Faculty Profile 

Yael earned her doctorate in Biochemistry and Cell Biology from the Hebrew University of Jerusalem, Israel. She worked with Jonathan Axelrod and Eithan Galun to investigate the role of IL-6 in regeneration of the kidney and liver following injury. During her PhD she became interested in one of the most universal and fascinating processes in cell biology - Mitosis. This led her to pursue postdoctoral training in the US with Don Cleveland at the Ludwig Institute for Cancer Research and UCSD School of Medicine, where she investigated human centromeres – a chromosomal region that is essential for mitosis. After enjoying sunny San Diego, Yael moved to University of Pittsburgh at the end of 2018 to open her independent group at the UPMC Hillman Cancer Center and the Department of Pharmacology and Chemical Biology. Beyond science, she loves arts and crafts and exploring the nature while hiking with her family.

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Lior Lumerman M.Sc.

Lab Manager and Research Specialist

lumermanl@upmc.edu

Lior received her M.Sc. in Molecular Biology from the Hebrew University of Jerusalem, Israel. She moved to University of Pittsburgh and joined the lab at the end of 2019 as a research specialist and lab manager. She is helping the lab in all things centromeres related! She loves good coffee and traveling around the world. 

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Kylie Zaffina
Undergrad
kfz6@pitt.edu
Kylie is a fourth-year undergraduate student pursuing her B.S. in biological sciences at the University of Pittsburgh. Kylie joined our lab in 2021 to assist us in all of our CENP- A/B/C questions. She enjoys exploring new coffee shops, cooking, and crafting.

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Megan Mahlke Ph.D.

Postdoctoral Associate

mahlkem@upmc.edu

Megan received her Ph.D. in Cellular and Molecular Biology from University of Texas at San Antonio, where she studied the epigenetics of human and non-human primate stem cells. Megan joined the lab in 2019 with a desire to apply her knowledge of epigenetics and bioinformatics to understanding regulation of centromere function, and in particular, the role of the histone H3 centromere variant CENP-A. She enjoys watching and collecting horror movies, live music, and going on adventures outdoors with her family. 

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Poulomi Nath Ph.D.

Postdoctoral Associate

nathp3@upmc.edu

Poulomi received her Ph.D. in molecular endocrinology and reproduction from Visva-Bharati University, India. During her Ph.D. she worked on signaling mechanisms in regulation of meiotic cell-cycle progression in oocyte models. Poulomi joined the lab in 2020 with an interest in understanding the human centromere function during cell-cycle progression and in cancer. She is always happy to help, enjoys watching movies, cooking new foods with Indian touch, traveling and occasionally singing.

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Shaoyang Yan
Visiting scholar
shaoyang@pitt.edu

Shaoyang is a fourth-year undergraduate student in Tsinghua University, aiming at an M.D./Ph.D. degree in clinical medicine. He joined our lab in 2022, as a visiting scholar to have a comprehensive training in biomedical science. He loves to listen to music from different cultures and play sports with his best friends.

Past Lab Members

 

Marlene Taja-Moreno M.Sc

Lab Technician

Rebecca Raphael M.Sc

Lab Technician

NEWS

October 2021

Sooo excited to receive the UPMC Hillman Cancer Center 2021 Junior Scholar award for Basic Cancer Research

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July 2021

Extremely happy and proud to share that we are getting funded by the NIGMS R35 ESI MIRA award!

Celebrating with some sushi (over TSDC seminar) and Champagne:

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                                            We are looking for postdocs, please apply!

June 2021

Wonderful presentation of Megan at the GSP Virtual Mini-symposium!

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June 2021

Happy Birthday Poulomi! 

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June 2021

Watching together the TSDC seminar series

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June 2021

Celebrating with the lab, as Yael receives the Pitt CMRF pilot award!

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May 2021

Happy birthday Megan!

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April 2021

We've been missing our in person meetings!! So good to be back!

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February 2021

Welcome back Megan and congrats on your baby!!

 

November 2020

Poulomi Nath joins our lab as a postdoc. Welcome Poulomi!

August 2020

Saying goodbye to Marlene who is leaving us to start her PhD in Mexico. Good luck Marlene!

 

July 2020

Yael is chairing a session of The Socially Distant Centromere, an online seminar series organized by GRC Centromere Biology Conference chairs

 

June 2020

Megan’s review linking CENP-A to cancer is published in Genes!

 

March – June 2020

Very sad to see our lab is shut down due to Covid-19.

 

January 2020

Megan Mahlke joins the lab as a postdoctoral fellow. Welcome Megan!

 

December 2019

Yael presents at the UPMC Hillman Genome Stability Chromatin Club mini symposium

 

December 2019

Marlene Taja-Moreno joins the lab as a research technician. Welcome Marlene!

 

November 2019

Lior Lumerman joins the lab as the lab manager. Welcome Lior!

August 2019

Yael visits at the Hospital of Sick Kids Research Institute, Toronto, and present at their Cell Biology seminar series

 

July 2019

Yael visits Israel and presents at Tel Aviv University and at The Hebrew University of Jerusalem

 

June 2019

Our paper revealing an error correction mechanism that restricts CENP-A to centromeres is published in Nature Cell Biology!

 

June 2019

Yael is awarded 2019 Hillman Early-Career Fellow for Innovative Cancer Research

 

May 2019

Becky joins the lab as a lab technician. Welcome Becky!

 

December 2018

The lab has officially opened at UPMC Hillman Cancer Center! 

JOIN OUR TEAM

Postdoctoral Fellows

We are always looking for great scientists to join our group. Individuals with a strong background in cell and molecular biology, biochemistry, microscopy, and/or computational genomics are encouraged to apply. Candidates are invited to submit a CV, contact information for 3 references and a cover letter describing research interests and career goals. Applicants must hold a doctoral degree in a relevant scientific area before starting the position and show significant promise for leading an independent research project, including outstanding publications in peer-reviewed journals and/or pre-prints.

Graduate Students

We are part of the Molecular Pharmacology Graduate Program (MPGP) Ph.D. training program within the University of Pittsburgh School of Medicine Interdisciplinary Biomedical Graduate Program. Currently enrolled students who are interested in pursuing a rotation in our lab should contact Yael. ​

Please direct all applications and inquiries via email to Dr. Yael Nechemia-Arbely at arbelyy@upmc.edu

 
 

GET IN TOUCH

Dr. Yael Nechemia-Arbely

Assistant Professor

 

University of Pittsburgh

School of Medicine

 

Department of Pharmacology & Chemical Biology

Phone: 412-623-3228
Email: arbelyy@upmc.edu

Social media:

5117 Centre Avenue

Pittsburgh,

PA 15213

Office: 2.32d

Lab: 2.6

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