The molecular underpinnings of metabolic adaptation to seasons are poorly understood in long- distance migrants. We measured changes in physiology and performed de novo sequencing of RNA extracted from liver samples collected at 4-h intervals over a period of 24 h from a long-distance avian migrant, the blackheaded bunting (Emberiza melanocephala), during two states: photostimulated vernal migratory (M) state and photorefractory non-migratory (nM) state. The M state was differentiated from the nM state based on body fattening and weight gain, as well as on Zugunruhe, that is, nocturnal migratory restlessness in caged birds. We found that baseline blood glucose and triglyceride levels were significantly higher in the M state than the nM state; conversely, surface body temperature was higher in the nM state than the M state. In a total of 6 liver samples that were sequenced from each state, 11,246 genes were annotated, including 4448 genes that were cyclic over 24 h. We found 569 differentially expressed genes (DEGs) between the M and the nM state, and the M state showed 131 upregulated and 438 downregulated genes. These DEGs formed core gene hubs associated with specific biological processes in both the states. In addition, weighted gene coexpression network analysis revealed two discrete modules of coexpressed genes, with a significant difference in the expression pattern of metab olism-associated genes between M and nM states. These results demonstrate, for the first time, transcriptome-wide changes in the liver between two distinct physiological states and give molecular insights into seasonal metabolic adaptations in latitudinal migrants.

The form and synaptic fine structure of melanopsin-expressing retinal ganglion cells, also called intrinsically photosensitive retinal ganglion cells (ipRGCs), were determined using a new membrane-targeted version of a genetic probe for correlated light and electron microscopy (CLEM). ipRGCs project to multiple brain regions, and because the method labels the entire neuron, it was possible to analyze nerve terminals in multiple retinorecipient brain regions, including the suprachiasmatic nucleus (SCN), olivary pretectal nucleus (OPN), and subregions of the lateral geniculate. Although ipRGCs provide the only direct retinal input to the OPN and SCN, ipRGC terminal arbors and boutons were found to be remarkably different in each target region. A network of dendro-dendritic chemical synapses (DDCSs) was also revealed in the SCN, with ipRGC axon terminals preferentially synapsing on the DDCS-linked cells. The methods developed to enable this analysis should propel other CLEM studies of long-distance brain circuits at high resolution.

Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.