The internet is full of lectures and interviews featuring scientists who made groundbreaking discoveries. Below, I have listed key topics in chromatin and gene regulation.
Please note that this is not intended to be a comprehensive review. Many important scientists and their groundbreaking work are not readily available in talk or interview formats online.

[SPECIFICITY]

• Francois Jacob (The Central Dogma, Gene Regulation)   YouTube
  

  - How do bacteria respond to different sugar sources? How does a dormant virus begin replicating and exit its host? These fundamental questions in gene regulation led François Jacob to realize that, at their core, they represent the same regulatory principles. While I will focus on eukaryotic gene regulation through chromatin modification, I had to begin with Jacob and Monod, whose work laid the foundation for the field.
  To fully appreciate this interview, a background in early molecular biology experiments is helpful. However, it is rare to find discussions that cover the operon model, the PaJaMa experiment, and the discovery of mRNA by himself.

• Mark Ptashne: Genetic Switches   YouTube
  

  - Jacob and Monod provided genetic evidence for the existence of a repressor in gene regulation. It was Mark Ptashne and Walter Gilbert who later isolated the repressor and demonstrated its sequence-specific DNA-binding properties. At the time, scientists debated which biomolecule could provide such specificity - RNA seemed more likely than protein, as it could base-pair with target DNA. Ptashne and Gilbert’s experiments shifted this perspective, establishing the concept of sequence-specific DNA-binding proteins and their role in gene regulation. While this lecture does not focus on their early experiments, it is still well worth watching.

• Robert Tjian: 1) Introduction to Transcription   YouTube / 2) Gene regulation: Why so complex?   YouTube
  

  - Now, moving to eukaryotes - Bob Tjian discusses the purification of Sp1, the first human transcription factor identified as a sequence-specific 'eukaryotic' DNA-binding protein. In the following lecture, he explores chromatin and general transcription factors, laying the groundwork for understanding eukaryotic gene regulation. This marks the beginning of a more complex exploration into how gene expression is controlled in eukaryotic systems.

To be updated. (Feb 16, 2025)

Below, I listed relevant background reading material for our lab's work on canonical PRC1 in spermatogenesis (last updated 2024).

• Nucleosome compaction as a regulatory mechanism during development, Bob Kingston, CSHL Keynote (2016)   YouTube
  

  - Bob is my postdoctoral advisor. His talk was a while ago, but it still provides a relevant background for our lab's current thinking on the PRC1 function.

• The molecular principles of gene regulation by Polycomb repressive complexes, Blackledge and Klose (2021) Nat Rev Mol Cell Biol.

  - This is my favorite recent review on the molecular mechanism of the Polycomb function.

• Context-specific Polycomb mechanisms in development, Kim and Kingston (2022) Nat Rev Genet.

  - Bob and I tried to illustrate how the core Polycomb mechanisms are modified by changing its subunits and how those different complexes are utilized and repurposed in diverse biological contexts.

• Cell type-specific role of CBX2 and its disordered region in spermatogenesis, Kim, ..., Kingston (2023) Genes Dev.

  - This is my postdoctoral work, characterizing CBX2, a component of cPRC1, function in spermatogenesis. It will be directly relevant to the lab's project in CBX7 in spermatogenesis.

• Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge, Grau, ..., Kingston (2011) Genes Dev.

  - This paper showed the chromatin compaction activity of CBX components of cPRC1. It also identified basic residues (Lysine, Arginine), and their positive charge are critical for the compaction activity.

• Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells, Morey, ..., Di Croce (2012) Cell Stem Cell.

  - This is one of the first papers showing CBX paralog switching during cellular differentiation (mouse embryonic stem cell differentiation).

• SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing, Isono, ..., Koseki (2013) Dev Cell.

  - This paper demonstrates the cellular and organismal function of the 'structural' activity of cPRC1 driven by the polymerization activity of the PHC subunit. One of my favorite Polycomb papers.

• List of landmark discoveries in the Polycomb and Trithorax field, Giacomo Cavalli Cavalli Lab Webpage

  - For further reading - Giacomo Cavalli has an excellent list of landmark papers. Knowing the history of the field is as important as being up to date on the recent discoveries.

• Spermatogenesis: The Commitment to Meiosis, Michael Griswold, (2016) Physiol Rev.

  - This review covers spermatogonial stem cells entering meiosis with the retinoic acid signal.

• Deciphering the mitotic and meiotic phases of spermatogenesis in the mouse, Katherine Romer, (2016) Doctoral thesis, MIT

  - Chapter 1, Introduction: The first two parts, "Germ cell specification and differentiation of male and female gametes" and "Spermatogenesis," give a good overview of primordial germ cells to sperm differentiation.

• Gene regulation during meiosis, Gao, Qin, and Schimenti, (2024) Trends Genet.

  - A timely review of gene regulation focused on mammalian male meiosis.

• Staging of Mouse Seminiferous Tubule Cross-Sections, Ahmed and de Rooij, (2009) Methods Mol Biol.
  Assessment of Spermatogenesis Through Staging of Seminiferous Tubules, Meistrich and Hess, (2013) Methods Mol Biol.

  - It is critical to understand the cellular composition of the seminiferous tubules in different stages to evaluate the differentiation process in mice.

• Guidebook: Laboratory Mouse and Rat Colony Management, Pritchett-Corning, ..., Elder (2015) Charles River Laboratories

  - This is a helpful guidebook for anyone who begins to work with mice.

Below, I listed relevant background reading material for our lab's work on Kumgang-CHD4 in fly spermatogenesis (last updated, 2024).

• Blocking promiscuous activation at cryptic promoters directs cell type-specific gene expression, Kim, ..., Fuller (2017) Science

  - Discovery of Kumgang and its role in cryptic promoter silencing together with CHD4.

• Alternative promoter usage at the Notch1 locus supports ligand-independent signaling in T cell development and leukemogenesis, Gómez-del Arco, ..., Georgopoulos (2010) Immunity

  - IKAROS is a Kumgang-like ZFP that interacts with CHD4. This paper shows that the loss of IKAROS results in the expression of overactive Notch1 protein from an alternative promoter, driving leukemogenesis. I like this paper as I see parallels to Kumgang-mediated cryptic promoter suppression.

• The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression, Bornelöv, ..., Hendrich (2018) Mol Cell
  The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment, Burgold, ..., Hendrich (2019) EMBO J

  - The experiments in these papers are very nicely done. However, it is still difficult to clearly explain what the CHD4-containing complex does, which may indicate the main function is suppression of 'noise.' A lot to think about in comparison to the kumgang loss transcriptional phenotype.

• Lifestyle choices: Self-renewal, proliferation, and differentiation in an adult stem cell lineage, Minx Fuller, GSA Medal lecture (2022)   YouTube
  

  - Minx is my PhD advisor. She gave a nice overview of some of her scientific discoveries using fly spermatogenesis as an adult stem cell model.

• Functional analysis of the promoter regions of de novo genes_090 & 074 in Drosophila melanogaster and in vitro Topi C-terminal DNA interaction by SELEX, Shrinivas Dighe (2020) Doctoral thesis, Cardiff University

  - Chapter 1.1 to chapter 1.4 nicely describes fly spermatogenesis and gene regulation in post-mitotic male germ cells.

• Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements, Lu, ..., Fuller (2020) Genes Dev.

  - It has been known that fly testis-specific gene expression was regulated by short (>300bp) sequences close to their promoters. By performing ATAC-seq and CAGE-seq, Dan performed beautiful analyses of characterizing the promoter-proximal elements.

• Genetics on the Fly: A Primer on the Drosophila Model System, Hales, ..., Roberts (2015) Genetics

  - A good overview of Drosophila as an experimental model system.