Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.

Most phenotype-associated genetic variants map to non-coding regulatory regions of the human genome. Moreover, variants associated with blood cell phenotypes are enriched in regulatory regions active during hematopoiesis. To systematically explore the nature of these regions, we developed a highly efficient strategy, Perturb-multiome, that makes it possible to simultaneously profile both chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of a range of master transcription factors (TFs). This approach allowed us to examine the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within the TF-sensitive accessible chromatin regions, while representing less than 0.3% of the genome, show a ~100-fold enrichment in heritability across certain blood cell phenotypes; this enrichment is strikingly higher than for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.

Control over attentional capture within 170 ms by long-term memory control settings: Evidence from the N2pc.

Observers adopt attentional control settings (ACSs) based on their goals that guide the capture of attention: Searched-for stimuli capture attention, and stimuli that are not searched for do not. While previous behavioural research indicates that observers can adopt long-term memory (LTM) ACSs (Giammarco et al. Visual Cognition, 24, 78-101, 2016), it seems surprising that representations in LTM could guide attention quickly enough to control attentional capture. To assess the claim that LTM ACSs exert control over early attentional orienting, we recorded electroencephalography while participants studied and searched for 30 target objects in an attention cueing task. Participants reported the studied target and ignored the preceding cues. To control for perceptual evoked responses, on each trial we presented two cue objects (one studied and one nonstudied). Even though participants were instructed to ignore the cues, studied cues produced the N2pc event-related potential, indicating early attentional orienting that was preferentially directed towards the studied cue versus the nonstudied cue. Critically, the N2pc was detectable within 170 ms, confirming that LTM ACSs rapidly control early capture. We propose an update to contemporary models of attentional capture to account for rapid attentional guidance by LTM ACSs.

Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs.

The mechanisms and regulation of RNA degradation in mycobacteria have been subject to increased interest following the identification of interplay between RNA metabolism and drug resistance. Mycobacteria encode multiple ribonucleases predicted to participate in mRNA degradation and/or processing of stable RNAs. RNase E is hypothesized to play a major role in mRNA degradation because of its essentiality in mycobacteria and its role in mRNA degradation in gram-negative bacteria. Here, we defined the impact of RNase E on mRNA degradation rates transcriptome-wide in the nonpathogenic model Mycolicibacterium smegmatis. RNase E played a rate-limiting role in degradation of the transcripts encoded by at least 89% of protein-coding genes, with leadered transcripts often being more affected by RNase E repression than leaderless transcripts. There was an apparent global slowing of transcription in response to knockdown of RNase E, suggesting that M. smegmatis regulates transcription in responses to changes in mRNA degradation. This compensation was incomplete, as the abundance of most transcripts increased upon RNase E knockdown. We assessed the sequence preferences for cleavage by RNase E transcriptome-wide in M. smegmatis and Mycobacterium tuberculosis and found a consistent bias for cleavage in C-rich regions. Purified RNase E had a clear preference for cleavage immediately upstream of cytidines, distinct from the sequence preferences of RNase E in gram-negative bacteria. We furthermore report a high-resolution map of mRNA cleavage sites in M. tuberculosis, which occur primarily within the RNase E-preferred sequence context, confirming that RNase E has a broad impact on the M. tuberculosis transcriptome.

Getting an aMPLe grasp on hematopoiesis.

Hematopoiesis requires balance between self-renewal of stem cells and differentiation into mature blood cells, orchestrated by pathways such as thrombopoietin signaling. In this issue of Cell, Tsutsumi et al. report the structure of the thrombopoietin ligand-receptor complex and demonstrate the potential to decouple its roles in self-renewal and hematopoietic differentiation.

Massively parallel base editing to map variant effects in human hematopoiesis.

Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow for rich phenotyping through single-cell RNA sequencing readouts and separately for characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.

Repetition enhances the effects of activated long-term memory.

Recent research indicates that visual long-term memory (vLTM) representations directly interface with perception and guide attention. This may be accomplished through a state known as activated LTM, however, little is known about the nature of activated LTM. Is it possible to enhance the attentional effects of these activated representations? And furthermore, is activated LTM discrete (i.e., a representation is either active or not active, but only active representations interact with perception) or continuous (i.e., there are different levels within the active state that all interact with perception)? To answer these questions, in the present study, we measured intrusion effects during a modified Sternberg task. Participants saw two lists of three complex visual objects, were cued that only one list was relevant for the current trial (the other list was, thus, irrelevant), and then their memory for the cued list was probed. Critically, half of the trials contained repeat objects (shown 10 times each), and half of the trials contained non-repeat objects (shown only once each). Results indicated that repetition enhanced activated LTM, as the intrusion effect (i.e., longer reaction times to irrelevant list objects than novel objects) was larger for repeat trials compared with non-repeat trials. These initial findings provide preliminary support that LTM activation is continuous, as the intrusion effect was not the same size for repeat and non-repeat trials. We conclude that researchers should repeat stimuli to increase the size of their effects and enhance how LTM representations interact with perception.

MamA essentiality in Mycobacterium smegmatis is explained by the presence of an apparent cognate restriction endonuclease.

OBJECTIVE: Restriction-Modification (R-M) systems are ubiquitous in bacteria and were considered for years as rudimentary immune systems that protect bacterial cells from foreign DNA. Currently, these R-M systems are recognized as important players in global gene expression and other cellular processes such us virulence and evolution of genomes. Here, we report the role of the unique DNA methyltransferase in Mycobacterium smegmatis, which shows a moderate degree of sequence similarity to MamA, a previously characterized methyltransferase that affects gene expression in Mycobacterium tuberculosis and is important for survival under hypoxic conditions. RESULTS: We found that depletion of mamA levels impairs growth and produces elongated cell bodies. Microscopy revealed irregular septation and unevenly distributed DNA, with large areas devoid of DNA and small DNA-free cells. Deletion of MSMEG_3214, a predicted endonuclease-encoding gene co-transcribed with mamA, restored the WT growth phenotype in a mamA-depleted background. Our results suggest that the mamA-depletion phenotype can be explained by DNA cleavage by the apparent cognate restriction endonuclease MSMEG_3214. In addition, in silico analysis predicts that both MamA methyltransferase and MSMEG_3214 endonuclease recognize the same palindromic DNA sequence. We propose that MamA and MSMEG_3214 constitute a previously undescribed R-M system in M. smegmatis.