Bassem Al-Sady, PhD

Associate Professor
Department of Microbiology and Immunology
+1 415 502-8655
Research Overview: 

Heterochromatin is a specialized protein-nucleic acid composite that silences the activity of genes over large contiguous chromosomal regions, and that has been visualized as a distinct nuclear ultra-structure for almost a century. Remarkably, the mechanisms guiding heterochromatin spreading along the chromosome and precise re-assembly every cell cycle remain obscure, although they critically relate to the potential of heterochromatin to epigenetically regulate genomic loci.

Excitingly, it is now appreciated that heterochromatin spreading plays a key role in the genome partitioning process that shapes cell fate. Heterochromatin exists in small regions, presumably around nucleation sites in embryonic stem cells that expand differentially depending on the lineage track. The same pattern is recapitulated in hematopoiesis, where heterochromatin regions expand as progenitors differentiate. Once the spreading reaction has completed, the new pattern is stably adopted. How heterochromatin spreading from small nucleation sites in stem cells and progenitors is developmentally regulated to drive lineage fates, or how lineages decisions direct differential spreading is completely unknown.

The lab aims to elucidate critical mechanisms that underlie the formation of epigenetic states and their stable inheritance and developmental regulation. To address these mechanisms, we are using two broad approaches, biochemical reconstitution of heterochromatin assembly and single cell analysis of the spreading reaction in yeast and mammalian live cells.

Our local collaborators at UCSF on these questions include the Spitzer, Buchwalter, Ramani, Panning, and McManus labs.

Primary Thematic Area: 
Developmental & Stem Cell Biology
Secondary Thematic Area: 
Cancer Biology & Cell Signaling
Research Summary: 
Mechanisms of formation and maintenance of epigenetic elements
Mentorship Development: 

3/2019 - Promoting Student Mental Health
4/2019 - Sharpening your Mentoring Skills (SyMS)
6/2019 - Implicit Bias Workshop
Initiated the faculty peer-to-peer training effort of the Graduate Mentor Development Program
9/2020 - DEI Champions Training
2/2021 - Three Truths and Three Tries: Facing and Overcoming Critical Social Justice Challenges at the Micro, Mezzo, and Macro Levels
11/2021 - Defining Distance Traveled: A Working Session
1/2022 Equity Based Interview Practices
5/2022 Effective Strategies for IDPs



A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation.

bioRxiv : the preprint server for biology

Muhammad A, Sarkadi Z, van Emden T, Mazumder A, Capella M, Fekete G, Sreechakram VNS, Al-Sady B, Papp B, Barrales RR, Braun S

A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading.


Challal D, Menant A, Goksal C, Leroy E, Al-Sady B, Rougemaille M

Proteome effects of genome-wide single gene perturbations.

Nature communications

?zt?rk M, Freiwald A, Cartano J, Schmitt R, Dejung M, Luck K, Al-Sady B, Braun S, Levin M, Butter F

Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction.

PLoS genetics

Greenstein RA, Ng H, Barrales RR, Tan C, Braun S, Al-Sady B