Biology subjects

Getzler, A. J.

Publications and source records attributed to Getzler, A. J..

3 recordsLinked to original sources

bioRxiv2023

Mixed Lineage Leukemia (Mll1) establishes global histone H3K4 trimethylation and stem like memory Cd8 T cell formation

CD8+ T cells with stem cell-like properties (TSCM) sustain adaptive immunity to intracellular pathogens and tumors. However, the developmental origins and chromatin regulatory factors (CRFs) that establish their differentiation are unclear. Using an RNA interference screen of all CRFs we discovered the histone methylase Mll1 was required during T cell receptor (TCR) stimulation for development of a TSCM precursor state and mature memory (TMEM) cells, but not short-lived or transitory effector cell-like states, in response to viral infections and tumors. Mll1 was essential for widespread de novo deposition of histone H3 lysine 4 trimethylation (H3K4me3) upon TCR stimulation, which accounted for 70% of all activation-induced sites in mature TMEM cells. Mll1 promoted both H3K4me3 deposition and reduced TCR-induced Pol II pausing at genes whose single-cell transcriptional dynamics explained trajectories into nascent TSCM precursor states during viral infection. Our results suggest Mll1-dependent control of Pol II elongation and H3K4me3 establishes and maintains differentiation of CD8+ TSCM cell states.

immunology↗

bioRxiv2022

The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage

The 18S rRNA sequence is highly conserved, particularly at its 3-end. In contrast, the sequence around the 3-end is degenerate with similar sites nearby. How RNA is correctly processed by the endonuclease Nob1 is not known, especially because in vitro experiments have shown it to be error-prone. Here we used yeast genetics, biochemistry, and next generation sequencing to investigate a role for Rio1 in monitoring the 3-end of 18S rRNA. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-mediated quality control step, but not in healthy cells with intact quality control mechanisms. Mechanistically, we show that Rio1 binding to miscleaved rRNA is weakened. Accordingly, excess Pno1 results in accumulation of miscleaved rRNA. Ribosomes containing miscleaved rRNA enter the polysomes and produce dominant negative growth defects, suggesting that they cause defects during translation. Our data strongly suggest that ribosome collisions identify these miscleaved 18S rRNA-containing ribosomes as partially functional and target them for degradation. Altogether, the data support a model in which Rio1 inspects the 3-end of the nascent 18S rRNA, only removing Nob1 and Pno1 from the ribosomes with precisely cleaved 18S rRNA to prevent miscleaved 18S rRNA-containing ribosomes from erroneously engaging in translation, where they induce ribosome collisions. The data also demonstrate how ribosome collisions "purify" the cells of altered ribosomes with different functionalities, with important implications for the concept of ribosome heterogeneity.

molecular biology↗

bioRxiv2021

Single-cell lineage trajectories and chromatin regulators that initialize antiviral CD8 T cell ontogeny

Individual naive CD8 T cells activated in lymphoid organs differentiate into functionally diverse and anatomically distributed T cell phylogenies in response to intracellular microbes. During infections that resolve rapidly, including live viral vaccines1, distinct effector (TEFF) and memory (TMEM) cell populations develop that ensure long term immunity2. During chronic infections, responding cells progressively become dysfunctional and "exhaust"3. A diverse taxonomy of TEFF, TMEM and exhausted (TEX) CD8 T cell populations is known, but the initial developmental basis of this phenotypic variation remains unclear4-10. Here, we defined single-cell trajectories and identified chromatin regulators that establish antiviral CD8 T cell heterogeneity using unsupervised analyses of single-cell RNA dynamics11-13 and an in vivo RNAi screen14. Activated naive cells differentiate linearly into uncommitted effector-memory progenitor (EMP) cells, which initially branch into an analogous manifold during either acute or chronic infection. Disparate RNA velocities in single EMP cells initiate divergence into stem, circulating, and tissue-resident memory lineages that generate diverse TMEM and TEX precursor states in specific developmental orders. Interleukin-2 receptor (IL-2R) signals are essential for formation and transcriptional heterogeneity of EMP cells, and promote trajectories toward TEFF rather than TEX states. Nucleosome remodelers Smarca4 and Chd7 differentially promote transcription that delineates divergent TMEM lineages before cooperatively driving terminal TEFF cell differentiation. Thus, the lineage architecture is established by specific chromatin regulators that stabilize diverging transcription in uncommitted progenitors.

immunology↗