Li, S.-X. | bioRxiv Science

bioRxiv2022

Extensive RNA editing in tomato nuclear genes

MicroTom tomato has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g., arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on microTom, and this database should be of great value to those who wants to adopt microTom as a model plant for research.

genomics↗

bioRxiv2021

Clock genes Period1 and Period2 in the hippocampal CA1 mediate depression-like behaviors and rapid antidepressant response

Accumulated reports have indicated that circadian rhythm is closely related to the pathogenesis of major depressive disorder (MDD). Recently, adenosine has been identified to modulate circadian clock via adenosine A1 and A2A receptor signaling pathways. Cyclic AMP-response element binding protein (CREB) is a convergent point that plays a critical role in the pathogenesis of depression and is a downstream molecule of adenosine A1 receptor signaling pathway as an endpoint that can regulate the expression of circadian genes Period1 (Per1) and Period2 (Per2). However, whether Per mediates the development of MDD via CREB has not been elucidated. We used chronic unpredictable stress (CUS) to induce depression-like behaviors and found that it could induce decrease in p-CREB and PER1 levels in the hippocampal CA1 region in rats. Both depression-like behaviors and the decreased protein levels could be rapidly rescued by the administration of adenosine A1 receptor agonist 2-Choro-N6-cyclopentyladenosine (CCPA). Furthermore, knockdown of Per1 in hippocampal CA1 region could also induce depression-like behaviors, which could also be rescued by CCPA. Interestingly, Per2 knockdown in hippocampal CA1 region resulted in potential antidepressant-like effect. In addition, knockout of CRE sequence in the promoter regions of either Per1 or Per2 led to depression-like behaviors, which could not be rescued by CCPA. These results indicated that clock genes Per1 and Per2 play critical roles in the pathophysiology of depression and CRE sequences in the promoter regions of Per1 and Per2 may be a critical antidepressant target. HighlightsO_LICUS induces both depression-like behaviors and decreases in the expression of p-CREB and PER1 levels in the hippocampal CA1 region in rats, which can be rapidly rescued by 2-Choro-N6-cyclopentyladenosine (CCPA). C_LIO_LIKnockdown of clock gene Per1 in the hippocampal CA1 brain region leads to depression-like behaviors in rats, which can be also rescued by CCPA. C_LIO_LIKnockdown of clock gene Per2 in the hippocampal CA1 brain region may have potential antidepressant-like effect. C_LIO_LIKnockout of the CRE sequence on the promoter region of the clock genes Per1 and Per2 produces depression-like behaviors, which cannot be rescued by CCPA. C_LI

neuroscience↗