SummaryRNA functions through the dynamic formation of complexes with RNA-binding proteins (RBPs) in all clades of life. We determined the RBP repertoire of beating cardiomyocytic HL-1 cells by jointly employing two in vivo proteomic methods, mRNA interactome capture and RBDmap. Together, these yielded 1,148 RBPs, 391 of which are shared with all other available mammalian RBP repertoires, while 393 are thus far unique to cardiomyocytes. RBDmap further identified 568 regions of RNA contact within 368 RBPs. The cardiomyocyte mRNA interactome composition reflects their unique biology. Proteins with roles in cardiovascular physiology or disease, mitochondrial function, and intermediary metabolism are all highly represented. Notably, we identified 73 metabolic enzymes as RBPs. RNA-enzyme contacts frequently involve Rossmann fold domains with examples in evidence of both, mutual exclusivity of, or compatibility between RNA binding and enzymatic function. Our findings raise the prospect of previously hidden RNA-mediated regulatory interactions among cardiomyocyte gene expression, physiology, and metabolism.

Cold acclimation in Arabidopsis thaliana triggers a significant transcriptional reprogramming altering the expression patterns of thousands of coldresponsive (COR) genes. Essential to this process is the C-repeat binding factor (CBF)-dependent pathway, involving the activity of AP2/ERF (APETALA2/ethylene-responsive factor)-type CBF transcription factors required for plant cold acclimation. In this study, we performed chromatin immunoprecipitation assays followed by deep sequencing (ChIP-seq) to determine the genomewide binding sites of the CBF transcription factors. Cold-induced CBF proteins specifically bind to the conserved C-repeat (CRT)/dehydrationresponsive elements (CRT/DRE; G/ACCGAC) of their target genes. A Gene Ontology enrichment analysis showed that 1,012 genes are targeted by all three CBFs. Combined with a transcriptional analysis of the cbf1,2,3 triple mutant, we define 146 CBF regulons as direct CBF targets. In addition, the CBF-target genes are significantly enriched in functions associated with hormone, light, and circadian rhythm signaling, suggesting that the CBFs act as key integrators of endogenous and external environmental cues. Our findings not only define the genome-wide binding patterns of the CBFs during the early cold response, but also provide insights into the role of the CBFs in regulating multiple biological processes of plants.

Exposure to cold triggers a spike in cytosolic calcium (Ca 2+ ) that often leads to transcriptional reprogramming in plants. However, how this Ca 2+ signal is perceived and relayed to the downstream cold signaling pathway remains unknown. Here, we show that the CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28) initiates a phosphorylation cascade to specify transcriptional reprogramming downstream of cold-induced Ca 2+ signal. Plasma membrane (PM)–localized CPK28 is activated rapidly upon cold shock within 10 seconds in a Ca 2+ -dependent manner. CPK28 then phosphorylates and promotes the nuclear translocation of NIN-LIKE PROTEIN 7 (NLP7), a transcription factor that specifies the transcriptional reprogramming of cold-responsive gene sets in response to Ca 2+ , thereby positively regulating plant response to cold stress. This study elucidates a previously unidentified mechanism by which the CPK28-NLP7 regulatory module integrates cold-evoked Ca 2+ signal and transcriptome and thus uncovers a key strategy for the rapid perception and transduction of cold signals from the PM to the nucleus.

During orchid seed culture, seeds germinate as protocorms, and protocorms normally develop into plant with leaves and roots. Orchids require many years of vegetative development for flowering. However, under a certain combination of growth cultures, we observed that protocorms can directly flower without leaves and roots. Therefore, we performed comparative transcriptome analysis to identify the different transcriptional regulators of two types of protocorms of Cymbidium ensifolium, Cymbidium sinense, and Cymbidium goeringii. Zinc finger, MYB, AP2, and bHLH were the most abundant transcription factor (TF) families in the transcriptome. Weighted gene coexpression network analysis (WGCNA) was performed to identify hub genes related to leaf and flower development. The key hubs included SPL6, SVP, SEP2, KNOX1, AP2, OFP1, COL12, MYB13, MYB36, MYB59, bHLH086, and ARF7. The hub genes were further validated through statistical tools to propose the roles of key TFs. Therefore, this study initiates to answer that why there is no leaf initiation and root development and how can protocorm bypass the vegetative phase to flower? The outcomes can direct future research on short-span flowering in orchids through protocorms.