High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.

High-throughput sequencing SELEX (HT-SELEX) is a powerful technique for unbiased determination of preferred target motifs of DNA-binding proteins in vitro. The procedure depends upon selection of DNA binding sites from a random library of oligonucleotides by purifying protein-DNA complexes and amplifying bound DNA using the polymerase chain reaction. Here, we describe an optimized step-by-step protocol for HT-SELEX compatible with Illumina sequencing. We also introduce a bioinformatic pipeline (eme_selex) facilitating the detection of promiscuous DNA binding by analyzing the enrichment of all possible k-mers. For complete details on the use and execution of this protocol, please refer to Pantier et al. (2021).

Associations between postpartum depression and assistance with household tasks and childcare during the COVID-19 pandemic: evidence from American mothers.

BACKGROUND: The early postpartum period is recognized cross-culturally as being important for recovery, with new parents receiving increased levels of community support. However, COVID-19-related lockdown measures may have disrupted these support systems, with possible implications for mental health. Here, we use a cross-sectional analysis among individuals who gave birth at different stages of the pandemic to test (i) if instrumental support access in the form of help with household tasks, newborn care, and care for older children has varied temporally across the pandemic, and (ii) whether access to these forms of instrumental support is associated with lower postpartum depression scores. METHODS: This study used data from the COVID-19 And Reproductive Effects (CARE) study, an online survey of pregnant persons in the United States. Participants completed postnatal surveys between April 30 - November 18, 2020 (n = 971). Logistic regression analysis tested whether birth timing during the pandemic was associated with odds of reported sustained instrumental support. Linear regression analyses assessed whether instrumental support was associated with lower depression scores as measured via the Edinburgh Postnatal Depression survey. RESULTS: Participants who gave birth later in the pandemic were more likely to report that the pandemic had not affected the help they received with household work and newborn care (p < 0.001), while access to childcare for older children appeared to vary non-linearly throughout the pandemic. Additionally, respondents who reported that the pandemic had not impacted their childcare access or help received around the house displayed significantly lower depression scores compared to participants who reported pandemic-related disruptions to these support types (p < 0.05). CONCLUSIONS: The maintenance of postpartum instrumental support during the pandemic appears to be associated with better maternal mental health. Healthcare providers should therefore consider disrupted support systems as a risk factor for postpartum depression and ask patients how the pandemic has affected support access. Policymakers seeking to improve parental wellbeing should design strategies that reduce disease transmission, while facilitating safe interactions within immediate social networks (e.g., through investment in COVID-19 testing and contact tracing). Cumulatively, postpartum instrumental support represents a potential tool to protect against depression, both during and after the COVID-19 pandemic.

SALL4 controls cell fate in response to DNA base composition.

Mammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4, which contains multiple zinc fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely upregulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen in Sall4 null cells, including precocious differentiation of embryonic stem cells (ESCs) and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by downregulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive byproduct of genome evolution and constitutes a signal that aids control of cell fate.