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Alternative cleavage and polyadenylation within introns (intronic APA) generate shorter mRNA isoforms; however, their physiological significance remains elusive. In this study, we developed a comprehensive workflow to analyze intronic APA profiles using the mammalian target of rapamycin (mTOR)-regulated transcriptome as a model system. Our investigation revealed two contrasting effects within the transcriptome in response to fluctuations in cellular mTOR activity: an increase in intronic APA for a subset of genes and a decrease for another subset of genes. The application of this workflow to RNA-seq data from The Cancer Genome Atlas demonstrated that this dichotomous intronic APA pattern is a consistent feature in transcriptomes across both normal tissues and various cancer types. Notably, our analyses of protein length changes resulting from intronic APA events revealed two distinct phenomena in proteome programming: a loss of functional domains due to significant changes in protein length or minimal alterations in C- terminal protein sequences within unstructured regions. Focusing on conserved intronic APA events across 10 different cancer types highlighted the prevalence of the latter cases in cancer transcriptomes, whereas the former cases were relatively enriched in normal tissue transcriptomes. These observations suggest potential, yet distinct, roles for intronic APA events during pathogenic processes and emphasize the abundance of protein isoforms with similar lengths in the cancer proteome. Furthermore, our investigation into the isoform-specific functions of JMJD6 intronic APA events supported the hypothesis that alterations in unstructured C-terminal protein regions lead to functional differences. Collectively, our findings underscore intronic APA events as a discrete molecular signature present in both normal tissues and cancer transcriptomes, highlighting the contribution of APA to the multifaceted functionality of the cancer proteome. 

Abstract Alternative cleavage and polyadenylation within introns (intronic APA) generate shorter mRNA isoforms; however, their physiological significance remains elusive. In this study, we developed a comprehensive workflow to analyze intronic APA profiles using the mammalian target of rapamycin (mTOR)-regulated transcriptome as a model system. Our investigation revealed two contrasting effects within the transcriptome in response to fluctuations in cellular mTOR activity: an increase in intronic APA for a subset of genes and a decrease for another subset of genes. The application of this workflow to RNA-seq data from The Cancer Genome Atlas demonstrated that this dichotomous intronic APA pattern is a consistent feature in transcriptomes across both normal tissues and various cancer types. Notably, our analyses of protein length changes resulting from intronic APA events revealed two distinct phenomena in proteome programming: a loss of functional domains due to significant changes in protein length or minimal alterations in C-terminal protein sequences within unstructured regions. Focusing on conserved intronic APA events across 10 different cancer types highlighted the prevalence of the latter cases in cancer transcriptomes, whereas the former cases were relatively enriched in normal tissue transcriptomes. These observations suggest potential, yet distinct, roles for intronic APA events during pathogenic processes and emphasize the abundance of protein isoforms with similar lengths in the cancer proteome. Furthermore, our investigation into the isoform-specific functions of JMJD6 intronic APA events supported the hypothesis that alterations in unstructured C-terminal protein regions lead to functional differences. Collectively, our findings underscore intronic APA events as a discrete molecular signature present in both normal tissues and cancer transcriptomes, highlighting the contribution of APA to the multifaceted functionality of the cancer proteome. 

Wetland shorelines around the world are susceptible to wave erosion. Previous work has suggested that the lateral erosion rate of their cliff-like edges can be predicted as a function of intercepting waves, and yet numerous field studies have shown that other factors, for example, tidal currents or mass wasting of differing soil types, induce a wide range of variability. Our objective was to isolate the unique effects of wave heights, wavelengths, and water depths on lateral erosion rates and then synthesize a mechanistic understanding that can be applied globally. We found a potentially universal relationship, where the lateral erosion rates increase exponentially as waves increase in height but decrease exponentially as waves become longer in length. These findings suggest that wetlands and other sheltered coastlines likely experience outsized quantities of erosion, as compared to oceanic-facing coastlines. 

Metal-free carbon materials have emerged as cost-effective and high-performance catalysts for the production of hydrogen peroxide (H 2 O 2 ) through the two-electron oxygen reduction reaction (ORR). Here, we show that 3D crumpled graphene with controlled oxygen and defect configurations significantly improves the electrocatalytic production of H 2 O 2 . The crumpled graphene electrocatalyst with optimal defect structures and oxygen functional groups exhibits outstanding H 2 O 2 selectivity of 92–100% in a wide potential window of 0.05–0.7 V vs. reversible hydrogen electrode (RHE) and a high mass activity of 158 A g −1 at 0.65 V vs. RHE in alkaline media. In addition, the crumpled graphene catalyst showed an excellent H 2 O 2 production rate of 473.9 mmol gcat −1 h −1 and stability over 46 h at 0.4 V vs. RHE. Moreover, density functional theory calculations revealed the role of the functional groups and defect sites in the two-electron ORR pathway through the scaling relation between OOH and O adsorption strengths. These results establish a structure-mechanism-performance relationship of functionalized carbon catalysts for the effective production of H 2 O 2 .