Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity.

Limited knowledge is available on the relationship between antigen-specific immune responses and COVID-19 disease severity. We completed a combined examination of all three branches of adaptive immunity at the level of SARS-CoV-2-specific CD4+ and CD8+ T cell and neutralizing antibody responses in acute and convalescent subjects. SARS-CoV-2-specific CD4+ and CD8+ T cells were each associated with milder disease. Coordinated SARS-CoV-2-specific adaptive immune responses were associated with milder disease, suggesting roles for both CD4+ and CD8+ T cells in protective immunity in COVID-19. Notably, coordination of SARS-CoV-2 antigen-specific responses was disrupted in individuals ≥ 65 years old. Scarcity of naive T cells was also associated with aging and poor disease outcomes. A parsimonious explanation is that coordinated CD4+ T cell, CD8+ T cell, and antibody responses are protective, but uncoordinated responses frequently fail to control disease, with a connection between aging and impaired adaptive immune responses to SARS-CoV-2.

Bcl-6 is the nexus transcription factor of T follicular helper cells via repressor-of-repressor circuits.

T follicular helper (TFH) cells are a distinct type of CD4+ T cells that are essential for most antibody and B lymphocyte responses. TFH cell regulation and dysregulation is involved in a range of diseases. Bcl-6 is the lineage-defining transcription factor of TFH cells and its activity is essential for TFH cell differentiation and function. However, how Bcl-6 controls TFH biology has largely remained unclear, at least in part due to the intrinsic challenges of connecting repressors to gene upregulation in complex cell types with multiple possible differentiation fates. Multiple competing models were tested here by a series of experimental approaches to determine that Bcl-6 exhibits negative autoregulation and controls pleiotropic attributes of TFH differentiation and function, including migration, costimulation, inhibitory receptors and cytokines, via multiple repressor-of-repressor gene circuits.

Id2 reinforces TH1 differentiation and inhibits E2A to repress TFH differentiation.

The differentiation of helper T cells into effector subsets is critical to host protection. Transcription factors of the E-protein and Id families are important arbiters of T cell development, but their role in the differentiation of the TH1 and TFH subsets of helper T cells is not well understood. Here, TH1 cells showed more robust Id2 expression than that of TFH cells, and depletion of Id2 via RNA-mediated interference increased the frequency of TFH cells. Furthermore, TH1 differentiation was blocked by Id2 deficiency, which led to E-protein-dependent accumulation of effector cells with mixed characteristics during viral infection and severely impaired the generation of TH1 cells following infection with Toxoplasma gondii. The TFH cell-defining transcriptional repressor Bcl6 bound the Id2 locus, which provides a mechanism for the bimodal Id2 expression and reciprocal development of TH1 cells and TFH cells.

Seafloor primary production in a changing Arctic Ocean.

Phytoplankton and sea ice algae are traditionally considered to be the main primary producers in the Arctic Ocean. In this Perspective, we explore the importance of benthic primary producers (BPPs) encompassing microalgae, macroalgae, and seagrasses, which represent a poorly quantified source of Arctic marine primary production. Despite scarce observations, models predict that BPPs are widespread, colonizing ~3 million km2 of the extensive Arctic coastal and shelf seas. Using a synthesis of published data and a novel model, we estimate that BPPs currently contribute ~77 Tg C y-1 of primary production to the Arctic, equivalent to ~20 to 35% of annual phytoplankton production. Macroalgae contribute ~43 Tg C y-1, seagrasses contribute ~23 Tg C y-1, and microalgae-dominated shelf habitats contribute ~11 to 16 Tg C y-1. Since 2003, the Arctic seafloor area exposed to sunlight has increased by ~47,000 km2 y-1, expanding the realm of BPPs in a warming Arctic. Increased macrophyte abundance and productivity is expected along Arctic coastlines with continued ocean warming and sea ice loss. However, microalgal benthic primary production has increased in only a few shelf regions despite substantial sea ice loss over the past 20 y, as higher solar irradiance in the ice-free ocean is counterbalanced by reduced water transparency. This suggests complex impacts of climate change on Arctic light availability and marine primary production. Despite significant knowledge gaps on Arctic BPPs, their widespread presence and obvious contribution to coastal and shelf ecosystem production call for further investigation and for their inclusion in Arctic ecosystem models and carbon budgets.

The Chromatin Regulator Mll1 Supports T Follicular Helper Cell Differentiation by Controlling Expression of Bcl6, LEF-1, and TCF-1.

T follicular helper (TFH) cells are essential for developing protective Ab responses following vaccination. Greater understanding of the genetic program leading to TFH differentiation is needed. Chromatin modifications are central in the control of gene expression. However, detailed knowledge of how chromatin regulators (CRs) regulate differentiation of TFH cells is limited. We screened a large short hairpin RNA library targeting all known CRs in mice and identified the histone methyltransferase mixed lineage leukemia 1 (Mll1) as a positive regulator of TFH differentiation. Loss of Mll1 expression reduced formation of TFH cells following acute viral infection or protein immunization. In addition, expression of the TFH lineage-defining transcription factor Bcl6 was reduced in the absence of Mll1. Transcriptomics analysis identified Lef1 and Tcf7 as genes dependent on Mll1 for their expression, which provides one mechanism for the regulation of TFH differentiation by Mll1. Taken together, CRs such as Mll1 substantially influence TFH differentiation.

The Transcription Factor YY-1 Is an Essential Regulator of T Follicular Helper Cell Differentiation.

T follicular helper (TFH) cells are a specialized subset of CD4 T cells that deliver critical help signals to B cells for the production of high-affinity Abs. Understanding the genetic program regulating TFH differentiation is critical if one wants to manipulate TFH cells during vaccination. A large number of transcription factor (TFs) involved in the regulation of TFH differentiation have been characterized. However, there are likely additional unknown TFs required for this process. To identify new TFs, we screened a large short hairpin RNA library targeting 353 TFs in mice using an in vivo RNA interference screen. Yin Yang 1 (YY-1) was identified as a novel positive regulator of TFH differentiation. Ablation of YY-1 severely impaired TFH differentiation following acute viral infection and protein immunization. We found that the zinc fingers of YY-1 are critical to support TFH differentiation. Thus, we discovered a novel TF involved in the regulation of TFH cells.

Optical closure in highly absorptive coastal waters: significance of inelastic scattering processes.

In hydrological optics, "optical closure" means consistency between the apparent optical properties (AOPs) determined from radiometric measurements and those derived from radiative transfer modelling based on concurrently measured inherent optical properties (IOPs) and boundary conditions (sea and sky states). Good optical closure not only provides confidence in the data quality but also informs on the adequacy of the radiative transfer parameterization. Achieving optical closure in highly absorptive coastal waters is challenging due to the low signal-to-noise ratio of radiometric measurements and uncertainties in the measurements of IOPs, namely the spectral absorption and backscattering coefficients. Here, we present an optical closure assessment using a comprehensive set of in situ IOPs acquired in highly absorptive coastal waters optically dominated by chromophoric dissolved organic matter (CDOM). The spectral remote sensing reflectance, Rrs(λ), was modeled using the software HydroLight (HL) with measured IOPs and observed boundary conditions. Corresponding in-water in situ Rrs(λ) was derived from radiometric measurements made with a Compact Optical Profiling System (C-OPS; Biospherical). The assessment revealed that the inclusion of inelastic scattering processes in the model, specifically sun-induced CDOM fluorescence (fDOM) and sun-induced chlorophyll fluorescence (SICF) from Chlorophyll-a ([chl]), significantly improved the optical closure and led to good agreement between measured and modeled Rrs (i.e., for 440 ≤ λ ≤ 710 nm with no inelastic processes: R2=0.90, slope=0.64; with inelastic processes: R2=0.96, slope=0.90). The analysis also indicated that fDOM and SICF contributed a substantial fraction of the green-red wavelength Rrs in these waters. Specifically, fDOM contributed ∼18% of the modeled Rrs in the green region and SICF accounted for ∼20% of the modeled Rrs in the red region. Overall, this study points out the importance of accounting for fDOM in remote sensing applications in CDOM-dominated waters.

In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation.

Classical genetic approaches to examine the requirements of genes for T cell differentiation during infection are time consuming. Here we developed a pooled approach to screen 30-100+ genes individually in separate antigen-specific T cells during infection using short hairpin RNAs in a microRNA context (shRNAmir). Independent screens using T cell receptor (TCR)-transgenic CD4(+) and CD8(+) T cells responding to lymphocytic choriomeningitis virus (LCMV) identified multiple genes that regulated development of follicular helper (Tfh) and T helper 1 (Th1) cells, and short-lived effector and memory precursor cytotoxic T lymphocytes (CTLs). Both screens revealed roles for the positive transcription elongation factor (P-TEFb) component Cyclin T1 (Ccnt1). Inhibiting expression of Cyclin T1, or its catalytic partner Cdk9, impaired development of Th1 cells and protective short-lived effector CTL and enhanced Tfh cell and memory precursor CTL formation in vivo. This pooled shRNA screening approach should have utility in numerous immunological studies.

Shells of the bivalve Astarte moerchi give new evidence of a strong pelagic-benthic coupling shift occurring since the late 1970s in the North Water polynya.

Climate changes in the Arctic may weaken the currently tight pelagic-benthic coupling. In response to decreasing sea ice cover, arctic marine systems are expected to shift from a 'sea-ice algae-benthos' to a 'phytoplankton-zooplankton' dominance. We used mollusc shells as bioarchives and fatty acid trophic markers to estimate the effects of the reduction of sea ice cover on the food exported to the seafloor. Bathyal bivalve Astarte moerchi living at 600 m depth in northern Baffin Bay reveals a clear shift in growth variations and Ba/Ca ratios since the late 1970s, which we relate to a change in food availability. Tissue fatty acid compositions show that this species feeds mainly on microalgae exported from the euphotic zone to the seabed. We, therefore, suggest that changes in pelagic-benthic coupling are likely due either to local changes in sea ice dynamics, mediated through bottom-up regulation exerted by sea ice on phytoplankton production, or to a mismatch between phytoplankton bloom and zooplankton grazing due to phenological change. Both possibilities allow a more regular and increased transfer of food to the seabed. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

CXCL13 is a plasma biomarker of germinal center activity.

Significantly higher levels of plasma CXCL13 [chemokine (C-X-C motif) ligand 13] were associated with the generation of broadly neutralizing antibodies (bnAbs) against HIV in a large longitudinal cohort of HIV-infected individuals. Germinal centers (GCs) perform the remarkable task of optimizing B-cell Ab responses. GCs are required for almost all B-cell receptor affinity maturation and will be a critical parameter to monitor if HIV bnAbs are to be induced by vaccination. However, lymphoid tissue is rarely available from immunized humans, making the monitoring of GC activity by direct assessment of GC B cells and germinal center CD4(+) T follicular helper (GC Tfh) cells problematic. The CXCL13-CXCR5 [chemokine (C-X-C motif) receptor 5] chemokine axis plays a central role in organizing both B-cell follicles and GCs. Because GC Tfh cells can produce CXCL13, we explored the potential use of CXCL13 as a blood biomarker to indicate GC activity. In a series of studies, we found that plasma CXCL13 levels correlated with GC activity in draining lymph nodes of immunized mice, immunized macaques, and HIV-infected humans. Furthermore, plasma CXCL13 levels in immunized humans correlated with the magnitude of Ab responses and the frequency of ICOS(+) (inducible T-cell costimulator) Tfh-like cells in blood. Together, these findings support the potential use of CXCL13 as a plasma biomarker of GC activity in human vaccine trials and other clinical settings.

Evaluation of sea-surface photosynthetically available radiation algorithms under various sky conditions and solar elevations.

In this study, we report on the performance of satellite-based photosynthetically available radiation (PAR) algorithms used in published oceanic primary production models. The performance of these algorithms was evaluated using buoy observations under clear and cloudy skies, and for the particular case of low sun angles typically encountered at high latitudes or at moderate latitudes in winter. The PAR models consisted of (i) the standard one from the NASA-Ocean Biology Processing Group (OBPG), (ii) the Gregg and Carder (GC) semi-analytical clear-sky model, and (iii) look-up-tables based on the Santa Barbara DISORT atmospheric radiative transfer (SBDART) model. Various combinations of atmospheric inputs, empirical cloud corrections, and semi-analytical irradiance models yielded a total of 13 (11 + 2 developed in this study) different PAR products, which were compared with in situ measurements collected at high frequency (15 min) at a buoy site in the Mediterranean Sea (the "BOUée pour l'acquiSition d'une Série Optique à Long termE," or, "BOUSSOLE" site). An objective ranking method applied to the algorithm results indicated that seven PAR products out of 13 were well in agreement with the in situ measurements. Specifically, the OBPG method showed the best overall performance with a root mean square difference (RMSD) (bias) of 19.7% (6.6%) and 10% (6.3%) followed by the look-up-table method with a RMSD (bias) of 25.5% (6.8%) and 9.6% (2.6%) at daily and monthly scales, respectively. Among the four methods based on clear-sky PAR empirically corrected for cloud cover, the Dobson and Smith method consistently underestimated daily PAR while the Budyko formulation overestimated daily PAR. Empirically cloud-corrected methods using cloud fraction (CF) performed better under quasi-clear skies (CF<0.3) with an RMSD (bias) of 9.7%-14.8% (3.6%-11.3%) than under partially clear to cloudy skies (0.30.7), however, all methods showed larger RMSD differences (biases) ranging between 32% and 80.6% (-54.5%-8.7%). Finally, three methods tested for low sun elevations revealed systematic overestimation, and one method showed a systematic underestimation of daily PAR, with relative RMSDs as large as 50% under all sky conditions. Under partially clear to overcast conditions all the methods underestimated PAR. Model uncertainties predominantly depend on which cloud products were used.

Bcl6 middle domain repressor function is required for T follicular helper cell differentiation and utilizes the corepressor MTA3.

T follicular helper (Tfh) cells are essential providers of help to B cells. The transcription factor B-cell CLL/lymphoma 6 (Bcl6) is a lineage-defining regulator of Tfh cells and germinal center B cells. In B cells, Bcl6 has the potential to recruit distinct transcriptional corepressors through its BTB domain or its poorly characterized middle domain (also known as RDII), but in Tfh cells the roles of the Bcl6 middle domain have yet to be clarified. Mimicked acetylation of the Bcl6 middle domain (K379Q) in CD4 T cells results in significant reductions in Tfh differentiation in vivo. Blimp1 (Prdm1) is a potent inhibitor of Tfh cell differentiation. Although Bcl6 K379Q still bound to the Prdm1 cis-regulatory elements in Tfh cells, Prdm1 expression was derepressed. This was a result of the failure of Bcl6 K379Q to recruit metastasis-associated protein 3 (MTA3). The loss of Bcl6 function in Bcl6 K379Q-expressing CD4 T cells could be partially rescued by abrogating Prdm1 expression. In addition to Prdm1, we found that Bcl6 recruits MTA3 to multiple genes involved in Tfh cell biology, including genes important for cell migration, cell survival, and alternative differentiation pathways. Thus, Bcl6 middle domain mediated repression is a major mechanism of action by which Bcl6 controls CD4 T-cell fate and function.

Cutting edge: T follicular helper cell differentiation is defective in the absence of Bcl6 BTB repressor domain function.

T follicular helper (Tfh) cells are essential for germinal centers (GCs) and most long-term humoral immunity. Differentiation of Tfh cells depends on the transcriptional repressor B cell CLL/lymphoma 6 (Bcl6). Bcl6 mediates gene repression via the recruitment of corepressors. Currently, it is unknown how Bcl6 recruits corepressors to regulate gene expression of Tfh cells. In this article, we demonstrate, using a mutant form of Bcl6 with two BTB (bric-a-brac, tramtrack, broad-complex) mutations that abrogate corepressor binding, that the Bcl6 BTB domain is required for proper differentiation of Tfh and GC-Tfh cells in vivo. Importantly, we also observe a significant defect in GC B cell development. These results are consistent in multiple contexts, including a novel lymphocytic choriomeningitis virus nucleoprotein-specific TCR-transgenic mouse model. Taken together, these data suggest that the Bcl6 BTB domain is a key mediator of the differentiation of Tfh cells.

Climate change enhances primary production in the western Antarctic Peninsula.

Intense regional warming was observed in the western Antarctic Peninsula (WAP) over the last 50 years. Here, we investigate the impact of climate change on primary production (PP) in this highly productive region. This study is based on temporal data series of ozone thickness (1972-2010), sea ice concentration (1978-2010), sea-surface temperature (1990-2010), incident irradiance (1988-2010) and satellite-derived chlorophyll a concentration (Chl-a, 1997-2010) for the coastal WAP. In addition, we apply a photosynthesis/photoinhibition spectral model to satellite-derived data (1997-2010) to compute PP and examine the separate impacts of environmental forcings. Since 1978, sea ice retreat has been occurring earlier in the season (in March in 1978 and in late October during the 2000s) while the ozone hole is present in early spring (i.e. August to November) since the early 1990s, increasing the intensity of ultraviolet-B radiation (UVBR, 280-320 nm). The WAP waters have also warmed over 1990-2010. The modelled PP rates are in the lower range of previously reported PP rates in the WAP. The annual open water PP in the study area increased from 1997 to 2010 (from 0.73 to 1.03 Tg C yr(-1) ) concomitantly with the increase in the production season length. The coincidence between the earlier sea ice retreat and the presence of the ozone hole increased the exposure to incoming radiation (UVBR, UVAR and PAR) and, thus, increased photoinhibition during austral spring (September to November) in the study area (from 0.014 to 0.025 Tg C yr(-1) ). This increase in photoinhibition was minor compared to the overall increase in PP, however. Climate change hence had an overall positive impact on PP in the WAP waters.

The activating receptor NKG2D of natural killer cells promotes resistance against enterovirus-mediated inflammatory cardiomyopathy.

In enterovirus-induced cardiomyopathy, information regarding the detailed impact of natural killer (NK) cells on the outcome of the disease is limited. We therefore hypothesized that NK cells and certain NK cell receptors determine the different outcome of coxsackievirus B3 (CVB3) myocarditis. Here, we demonstrate in murine models that resistance to chronic CVB3 myocarditis in immunocompetent C57BL/6 mice is characterized by significantly more mature CD11b(high) NK cells, the presence of NKG2D on NK cells, and enhanced NKG2D-dependent cytotoxicity compared to CVB3-susceptible A.BY/SnJ mice. The highly protective role of NKG2D in myocarditis was further proven by in vivo neutralization of NKG2D as well as in NKG2D-deficient mice but was shown to be independent of CD8(+) T-cell-dependent immunity. Moreover, the adoptive transfer of immunocompetent C57BL/6 NK cells pre- (day -1) as well as post-infectionem (day +2) displayed the potential to prevent permissive A.BY/SnJ mice from a progressive outcome of CVB3 myocarditis reflected by significantly improved cardiopathology and heart function. Altogether, our results provide firm evidence for a protective role of NKG2D-activated NK cells in CVB3 myocarditis leading to an effective virus clearance, thus offering novel therapeutic options in the treatment of virus-induced myocarditis.

Optimized tetramer analysis reveals Ly49 promiscuity for MHC ligands.

Murine Ly49 receptors, which are expressed mainly on NK and NKT cells, interact with MHC class I (MHC-I) molecules with varying specificity. Differing reports of Ly49/MHC binding affinities may be affected by multiple factors, including cis versus trans competition and species origin of the MHC-I L chain (ß2-microglobulin). To determine the contribution of each of these factors, Ly49G, Ly49I, Ly49O, Ly49V, and Ly49Q receptors from the 129 mouse strain were expressed individually on human 293T cells or the mouse cell lines MHC-I-deficient C1498, H-2(b)-expressing MC57G, and H-2(k)-expressing L929. The capacity to bind to H-2D(b)- and H-2K(b)-soluble MHC-I tetramers containing either human or murine ß2-microglobulin L chains was tested for all five Ly49 receptors in all four cell lines. We found that most of these five inhibitory Ly49 receptors show binding for one or both self-MHC-I molecules in soluble tetramer binding assays when three conditions are fulfilled: 1) lack of competing cis interactions, 2) tetramer L chain is of mouse origin, and 3) Ly49 is expressed in mouse and not human cell lines. Furthermore, Ly49Q, the single known MHC-I receptor on plasmacytoid dendritic cells, was shown to bind H-2D(b) in addition to H-2K(b) when the above conditions were met, suggesting that Ly49Q functions as a pan-MHC-Ia receptor on plasmacytoid dendritic cells. In this study, we have optimized the parameters for soluble tetramer binding analyses to enhance future Ly49 ligand identification and to better evaluate specific contributions by different Ly49/MHC-I pairs to NK cell education and function.

Impaired natural killer cell self-education and "missing-self" responses in Ly49-deficient mice.

Ly49-mediated recognition of MHC-I molecules on host cells is considered vital for natural killer (NK)-cell regulation and education; however, gene-deficient animal models are lacking because of the difficulty in deleting this large multigene family. Here, we describe NK gene complex knockdown (NKC(KD)) mice that lack expression of Ly49 and related MHC-I receptors on most NK cells. NKC(KD) NK cells exhibit defective killing of MHC-I-deficient, but otherwise normal, target cells, resulting in defective rejection by NKC(KD) mice of transplants from various types of MHC-I-deficient mice. Self-MHC-I immunosurveillance by NK cells in NKC(KD) mice can be rescued by self-MHC-I-specific Ly49 transgenes. Although NKC(KD) mice display defective recognition of MHC-I-deficient tumor cells, resulting in decreased in vivo tumor cell clearance, NKG2D- or antibody-dependent cell-mediated cytotoxicity-induced tumor cell cytotoxicity and cytokine production induced by activation receptors was efficient in Ly49-deficient NK cells, suggesting MHC-I education of NK cells is a single facet regulating their total potential. These results provide direct genetic evidence that Ly49 expression is necessary for NK-cell education to self-MHC-I molecules and that the absence of these receptors leads to loss of MHC-I-dependent "missing-self" immunosurveillance by NK cells.

The apparent quantum yield matrix (AQY-M) of CDOM photobleaching in estuarine, coastal, and oceanic surface waters.

The photochemical degradation of chromophoric dissolved organic matter (CDOM) upon solar exposure, known as photobleaching, can significantly alter the optical properties of the surface ocean. By leading to the breakdown of UV- and visible-radiation-absorbing moieties within dissolved organic matter, photobleaching regulates solar heating, the vertical distribution of photochemical processes, and UV exposure and light availability to the biota in surface waters. Despite its biogeochemical and ecological relevance, this sink of CDOM remains poorly quantified. Efforts to quantify photobleaching globally have long been hampered by the inherent challenge of determining representative apparent quantum yields (AQYs) for this process, and by the resulting lack of understanding of their variability in natural waters. Measuring photobleaching AQY is made challenging by the need to determine AQY matrices (AQY-M) that capture the dual spectral dependency of this process (i.e., magnitude varies with both excitation wavelength and response wavelength). A new experimental approach now greatly facilitates the quantification of AQY-M for natural waters, and can help address this problem. Here, we conducted controlled photochemical experiments and applied this new approach to determine the AQY-M of 27 contrasting water samples collected globally along the land-ocean aquatic continuum (i.e., rivers, estuaries, coastal ocean, and open ocean). The experiments and analyses revealed considerable variability in the magnitude and spectral characteristics of the AQY-M among samples, with strong dependencies on CDOM composition/origin (as indicated by the CDOM 275-295-nm spectral slope coefficient, S275-295), solar exposure duration, and water temperature. The experimental data facilitated the development and validation of a statistical model capable of accurately predicting the AQY-M from three simple predictor variables: 1) S275-295, 2) water temperature, and 3) a standardized measure of solar exposure. The model will help constrain the variability of the AQY-M when modeling photobleaching rates on regional and global scales.

Mll1 pioneers histone H3K4me3 deposition and promotes formation of CD8 + T stem cell memory.

CD8 + T cells with stem cell-like properties (T SCM ) 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 T SCM precursor state and mature memory (T MEM ) 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 T MEM cells. Mll1 promoted both H3K4me3 deposition and reduced TCR-induced Pol II pausing at genes whose single-cell transcriptional dynamics explained trajectories into nascent T SCM precursor states during viral infection. Our results suggest Mll1-dependent control of Pol II elongation and H3K4me3 establishes and maintains differentiation of CD8 + T SCM cell states.