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Analysis of estrogen-regulated enhancer rnas identifies a functional motif required for enhancer assembly and gene expression

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CELL REPORTS 2022年第11期39卷 000-000页

作者： Hou, Tim Y. Kraus, W. Lee Univ Texas Southwestern Med Ctr Dallas Cecil H & Ida Green Ctr Reprod Biol Sci Lab Signaling & Gene Regulat 5323 Harry Hines Blvd Dallas TX 75390 USA Univ Texas Southwestern Med Ctr Dallas Dept Obstet & Gynecol Div Basic Res 5323 Harry Hines Blvd Dallas TX 75390 USA

To better understand the functions of non-coding enhancer rnas (ernas), we annotated the estrogen-regulated erna transcriptome in estrogen receptor alpha (ER alpha)-positive breast cancer cells using PRO-cap and rna sequencing. We then cloned a subset of the ernas identified, fused them to single guide rnas, and targeted them to their ER alpha enhancers of origin using CRISPR/dCas9. Some of the ernas tested modulated the expression of cognate, but not heterologous, target genes after estrogen treatment by increasing ER alpha recruitment and stimulating p300-catalyzed H3K27 acetylation at the enhancer. We identified a similar to 40 nucleotide functional erna regulatory motif (FERM) present in many ernas that was necessary and sufficient to modulate gene expression, but not the specificity of activation, after estrogen treatment. The FERM interacted with BCAS2, an rna-binding protein amplified in breast cancers. The ectopic expression of a targeted erna controlling the expression of an oncogene resulted in increased cell proliferation, demonstrating the regulatory potential of ernas in breast cancer.

关键词： Breast cancer coregulator enhancer enhancer rna (erna) estrogen receptor alpha (ERα) H3K27 acetylation noncoding rna p300/CBP pre-mrna-splicing factor (SPF27/BCAS2) transcription

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The whole transcriptome analysis and the circrna-lncrna network construction in arsenic trioxide-treated mice myocardium

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BIOMEDICINE & PHARMACOTHERAPY 2022年 151卷 113183-113183页

作者： Jiang, Yanan Shen, Xiuyun Dong, Chaorun Zhi, Fengnan Gao, Yang Shi, Chunpeng Chao, Yuqiu Xu, Jincheng Shang, Desi Xu, Juan Yang, Baofeng Li, Xia Bai, Yunlong Harbin Med Univ Coll Pharm Dept Pharmacol State Prov Key Labs Biomed Harbin Peoples R China Heilongjiang Acad Med Sci Translat Med Res & Cooperat Ctr Northern China Harbin Peoples R China Harbin Med Univ Coll Bioinformat Sci & Technol Harbin Peoples R China Harbin Med Univ Affiliated Hosp 2 Dept Gastroenterol & Hepatol Harbin Peoples R China Univ South China Affiliated Hosp 1 Hengyang Med Sch Hengyang Hunan Peoples R China

Background/Aims: Arsenic trioxide (ATO) is an effective anti-cancer drug. Nonetheless, it possesses cardiotoxic effects which limit its clinical application. The present study aims to elucidate the molecular basis of ATOinduced cardiotoxicity through using whole transcriptome analysis. Methods: The whole transcriptome in ATO-treated mice myocardium was analyzed using rna sequencing technique. These results were confirmed by real-time PCR. The lncrna-mrna and circrna-mrna co-expression networks were constructed. Finally, a circrna-lncrna co-regulated competing endogenous rna (cerna) network was constructed. GO and KEGG pathway analyses were performed. The expression levels of Txnip and Spp1 in ATO-treated neonatal mouse cardiomyocytes were validated by real-time PCR. Results: A total of 113 mrnas, 159 lncrnas, 35 mirnas, and 94 circrnas were differentially expressed in ATOtreated mice myocardium. A lncrna-circrna co-regulation network was constructed. Function annotation revealed that aberrantly expressed genes may be enriched in the 'Wnt signaling pathway', 'Hippo signaling pathway', 'Notch signaling pathway', etc. Finally, the expression levels of Txnip and Spp1 were validated in ATO-treated cardiomyocytes, which was in accordance with the rna-sequencing results. Conclusion: ATO altered coding and noncoding rna profiles in myocardium of mice. The ATO-related lncrnacircrna co-regulation network was constructed. Genes in the co-regulation network are likely to play important roles in the cardiotoxicity of ATO. This study provides new insights into the prevention and treatment of ATOinduced cardiotoxicity.

关键词： Arsenic trioxide Cardiotoxicity rna sequencing noncoding rna

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C-value paradox: Genesis in misconception that natural selection follows anthropocentric parameters of 'economy' and 'optimum'

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BBA ADVANCES 2023年 4卷 100107页

作者： Lakhotia, Subhash C. Banaras Hindu Univ Inst Sci Dept Zool Cytogenet Lab Varanasi 221005 India

C-value paradox refers to the lack of correlation between biological complexity and the intuitively expected protein-coding genomic information or DNA content. Here I discuss five questions about this paradox: i) Do biologically complex organisms carry more protein-coding genes? ii) Does variable accumulation of selfish/ junk/ parasitic DNA underlie the c-value paradox? iii) Can nucleoskeletal or nucleotypic function of DNA explain the enigma of orders of magnitude high levels of DNA in some 'lower' taxa or in taxonomically related species? iv) Can the newly understood noncoding but functional DNA explain the c-value paradox? and, v) Does natural selection uniformly apply the anthropocentric parameters for 'optimum' and 'economy'? Answers to Q.1-5 are largely negative. Biology presents numerous 'anomalous' examples where the same end function/ phenotype is attained in different organisms through astoundingly diverse ways that appear 'illogical' in our perceptions. Such evolutionary oddities exist because natural selection, unlike a designer, exploits random and stochastic events to modulate the existing system. Consequently, persistence of the new-found 'solution/s' often appear bizarre, uneconomic, and therefore, paradoxical to human logic. The unexpectedly high c-values in diverse organisms are irreversible evolutionary accidents that persisted, and the additional DNA often got repurposed over the evolutionary time scale. Therefore, the c-value paradox is a redundant issue. Future integrative biological studies should address evolutionary mechanisms and processes underlying sporadic DNA expansions/ contractions, and how the newly acquired DNA content has been repurposed in diverse groups.

关键词： Selfish DNA Nucleoskeletal DNA Biological complexity noncoding rna Endoreplication

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noncoding rnas: Potential players in the self-renewal of mammalian spermatogonial stem cells

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MOLECULAR REPRODUCTION AND DEVELOPMENT 2018年第8-9期85卷 720-728页

作者： Bie, Beibei Wang, Ya Li, Liang Fang, Huanle Liu, Libing Sun, Jin Xian Peihua Univ Med Sch Dept Pharm Xian Shaanxi Peoples R China Xi An Jiao Tong Univ Affiliated Hosp 2 Natl & Local Joint Engn Res Ctr Biodiag & Biother 157 West 5th Rd Xian 710004 Shaanxi Peoples R China

Spermatogonial stem cells (SSCs), a unique population of male germ cells with self-renewal ability, are the foundation for maintenance of spermatogenesis throughout the life of the male. Although many regulatory molecules essential for SSC self-renewal have been identified, the fundamental mechanism underlying how SSCs acquire and maintain their self-renewal activity remains largely to be elucidated. In recent years, many types of noncoding rnas (ncrnas) have been suggested to regulate the SSC self-renewal through multiple ways, indicating ncrnas play crucial roles in SSC self-renewal. In this paper, we mainly focus on four types of ncrnas including microrna, long ncrna, piwi-interacting rna, as well as circular rnas, and reviewed their potential roles in SSC self-renewal that discovered recently to help us gain a better understanding of molecular mechanisms by which ncrnas perform their function in regulating SSC self-renewal.

关键词： noncoding rna self-renewal spermatogonial stem cell

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The epigenetic regulatory mechanisms of ferroptosis and its implications for biological processes and diseases

MEDCOMM

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MEDCOMM 2023年第3期4卷 e267页

作者： Yang, Molin Luo, Hanshen Yi, Xin Wei, Xiang Jiang, Ding-Sheng Huazhong Univ Sci & Technol Tongji Hosp Tongji Med Coll Div Cardiothorac & Vasc Surg 1095 Jiefang Ave Wuhan 430030 Hubei Peoples R China Wuhan Univ Dept Cardiol Renmin Hosp Wuhan Hubei Peoples R China Minist Educ Key Lab Organ Transplantat Wuhan Hubei Peoples R China NHC Key Lab Organ Transplantat Wuhan Hubei Peoples R China Chinese Acad Med Sci Key Lab Organ Transplantat Wuhan Hubei Peoples R China

Ferroptosis is a form of regulated cell death triggered by the iron-dependent peroxidation of phospholipids. Interactions of iron and lipid metabolism factors jointly promote ferroptosis. Ferroptosis has been demonstrated to be involved in the development of various diseases, such as tumors and degenerative diseases (e.g., aortic dissection), and targeting ferroptosis is expected to be an effective strategy for the treatment of these diseases. Recent studies have shown that the regulation of ferroptosis is affected by multiple mechanisms, including genetics, epigenetics, posttranscriptional modifications, and protein posttranslational modifications. Epigenetic changes have garnered considerable attention due to their importance in regulating biological processes and potential druggability. There have been many studies on the epigenetic regulation of ferroptosis, including histone modifications (e.g., histone acetylation and methylation), DNA methylation, and noncoding rnas (e.g., mirnas, circrnas, and lncrnas). In this review, we summarize recent advances in research on the epigenetic mechanisms involved in ferroptosis, with a description of rna N-6-methyladenosine (m(6)A) methylation included, and the importance of epigenetic regulation in biological processes and ferroptosis-related diseases, which provides reference for the clinical application of epigenetic regulators in the treatment of related diseases by targeting ferroptosis.

关键词： DNA methylation epigenetics ferroptosis histone modifications noncoding rna rna m(6)A methylation

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Dynamic rna Fitness Landscapes of a Group I Ribozyme during Changes to the Experimental Environment

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MOLECULAR BIOLOGY AND EVOLUTION 2022年第3期39卷 msab373-msab373页

作者： Peri, Gianluca Gibard, Clementine Shults, Nicholas H. Crossin, Kent Hayden, Eric J. Boise State Univ Biomol Sci Grad Programs Boise ID 83725 USA Boise State Univ Dept Biol Sci Boise ID 83725 USA FACible Biodiagnost 366 SW 5th AveSuite 104 Meridian ID USA

Fitness landscapes of protein and rna molecules can be studied experimentally using high-throughput techniques to measure the functional effects of numerous combinations of mutations. The rugged topography of these molecular fitness landscapes is important for understanding and predicting natural and experimental evolution. Mutational effects are also dependent upon environmental conditions, but the effects of environmental changes on fitness landscapes remains poorly understood. Here, we investigate the changes to the fitness landscape of a catalytic rna molecule while changing a single environmental variable that is critical for rna structure and function. Using high-throughput sequencing of in vitro selections, we mapped a fitness landscape of the Azoarcus group I ribozyme under eight different concentrations of magnesium ions (1-48 mM MgCl2). The data revealed the magnesium dependence of 16,384 mutational neighbors, and from this, we investigated the magnesium induced changes to the topography of the fitness landscape. The results showed that increasing magnesium concentration improved the relative fitness of sequences at higher mutational distances while also reducing the ruggedness of the mutational trajectories on the landscape. As a result, as magnesium concentration was increased, simulated populations evolved toward higher fitness faster. Curve-fitting of the magnesium dependence of individual ribozymes demonstrated that deep sequencing of in vitro reactions can be used to evaluate the structural stability of thousands of sequences in parallel. Overall, the results highlight how environmental changes that stabilize structures can also alter the ruggedness of fitness landscapes and alter evolutionary processes.

关键词： fitness landscape gene-environment interactions molecular evolution ribozyme noncoding rna

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H19 may regulate the immune cell infiltration in carcinogenesis of gastric cancer through miR-378a-5p/SERPINH1 signaling

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WORLD JOUrnaL OF SURGICAL ONCOLOGY 2022年第1期20卷 295-295页

作者： Li, Jianxin Han, Ting Wang, Xin Wang, Yinchun Chen, Xuan Chen, Wangsheng Yang, Qingqiang Southwest Med Univ Dept Gen Surg Gastrointestinal Surg Affiliated Hosp Luzhou 646000 Sichuan Peoples R China

Background Increasing studies have indicated that noncoding rna (ncrna)-mediated competing endogenous rna (cerna) network serves as a significant role in cancer progression, but the underlying regulatory mechanisms of which in gastric cancer (GC) remain largely unclear. Methods Based on Gene Expression Omnibus and The Cancer Genome Atlas datasets, potential biomarkers for GC were screened and validated by machine learning. Then, upstream regulatory ncrna of potential biomarkers was identified to construct a novel cerna network in GC through means of stepwise reverse prediction and validation. Ultimately, tumor immune cell infiltration analysis was performed based on the EPIC algorithm. Results A total of 188 differentially expressed genes (DEGs) were screened, and three candidate diagnostic biomarkers (FAP, PSAPL1, and SERPINH1) for GC were identified and validated. Subsequently, H19 and miR-378a-5p were identified as upstream regulatory ncrnas that could potentially bind SERPINH1 in GC. Moreover, Immune infiltration analysis revealed that each component in the cerna network (H19/miR-378a-5p/SERPINH1) was significantly correlated with the infiltration abundances of diverse tumor-infiltrating immune cells. Conclusions H19 may regulate the immune cell infiltration in carcinogenesis of GC through miR-378a-5p/SERPINH1 signaling.

关键词： Gastric cancer noncoding rna Competing endogenous rna Biomarker Immune cell infiltration

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Biogenesis and Regulatory Roles of Circular rnas

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ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY 2022年第1期38卷 263-289页

作者： Yang, Li Wilusz, Jeremy E. Chen, Ling-Ling Fudan Univ Childrens Hosp Ctr Mol Med Shanghai Peoples R China Fudan Univ Shanghai Key Lab Med Epigenet Int Lab Med Epigenet & Metab Minist Sci & TechnolInst Biomed Sci Shanghai Peoples R China Baylor Coll Med Verna & Marrs McLean Dept Biochem & Mol Biol Therapeut Innovat Ctr Houston TX 77030 USA Chinese Acad Sci Univ Chinese Acad Sci CAS Ctr Excellence Mol Cell SciShanghai Key Lab Shanghai Inst Biochem & Cell BiolState Key Lab M Shanghai Peoples R China ShanghaiTech Univ Sch Life Sci & Technol Shanghai Peoples R China Univ Chinese Acad Sci Sch Life Sci Hangzhou Inst Adv Study Hangzhou Peoples R China

Covalently closed, single-stranded circular rnas can be produced from viral rna genomes as well as from the processing of cellular housekeeping noncoding rnas and precursor messenger rnas. Recent transcriptomic studies have surprisingly uncovered that many protein-coding genes can be subjected to backsplicing, leading to widespread expression of a specific type of circular rnas (circrnas) in eukaryotic cells. Here, we discuss experimental strategies used to discover and characterize diverse circrnas at both the genome and individual gene scales. We further highlight the current understanding of how circrnas are generated and how the mature transcripts function. Some circrnas act as noncoding rnas to impact gene regulation by serving as decoys or competitors for micrornas and proteins. Others form extensive networks of ribonucleoprotein complexes or encode functional peptides that are translated in response to certain cellular stresses. Overall, circrnas have emerged as an important class of rna molecules in gene expression regulation that impact many physiological processes, including early development, immune responses, neurogenesis, and tumorigenesis.

关键词： backsplicing circrna microrna noncoding rna pre-mrna splicing translation

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Whole-transcriptome analysis of periodontal tissue and construction of immune-related competitive endogenous rna network

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BMC ORAL HEALTH 2022年第1期22卷 370-370页

作者： Zhao, Quanquan Wen, Jing Ouyang, Xiangying Liu, Jianru Liu, Wenyi Zhang, Shengnan Lv, Peiying Lou, Xinzhe Peking Univ Sch & Hosp Stomatol Beijing Key Lab Digital Stomatol Dept PeriodontolNatl Clin Res Ctr Oral DisNatl 22 Zhongguancun South Ave Beijing 100081 Peoples R China

Background In periodontitis, noncoding rnas may play a regulatory role in the immune microenvironment through competitive endogenous rna. We aimed to profile noncoding rna expression and construct immune-related cerna network in periodontitis. Methods Five inflamed periodontal tissue and five healthy gingivae were collected for whole-transcriptome sequencing. Differential gene, functional enrichment, and protein-protein interaction network analysis were performed to explore the function of differentially expressed genes. CIBERSORTx was used to analyze level of immune cell infiltration in the periodontal tissue. An immune-related competitive endogenous rna network was constructed and expression of key regulators in the network was validated. Results Compared with healthy gingiva, 200 mrnas, 90 long noncoding rnas, 65 micrornas, and 518 circular rnas were differentially expressed, and cell chemotaxis was significantly enhanced in inflamed periodontal tissue. Immune cell infiltration analysis showed that neutrophils, macrophages M1, T follicular helper cells, and naive B cells were significantly increased in periodontitis. Key regulators including JUN, FOS, THBS1, KLF2, WIF1, were identified and their expression was then validated. Conclusion We constructed an immune-related competitive endogenous rna network in periodontal tissue, which provided new insights into immune homeostasis in periodontitis and laid a foundation for further study of noncoding rnas. Key regulators in this network may be promising targets for future periodontitis treatment.

关键词： Periodontitis Immunomodulation noncoding rna Gene expression profiling rna-seq

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Early termination of the Shiga toxin transcript generates a regulatory small rna

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2020年第40期117卷 25055-25065页

作者： Sy, Brandon M. Lan, Ruiting Tree, Jai J. Univ New South Wales Sch Biotechnol & Biomol Sci Sydney NSW 2052 Australia

Enterohemorrhagic Escherichia coli is a significant human pathogen that causes disease ranging from hemorrhagic colitis to hemolytic uremic syndrome. The latter can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by anti-termination of the P-R' late promoter during lytic induction of the phage. During lysogeny, the late transcript is prematurely terminated at t(R)' immediately downstream of P-R', generating a short rna that is a byproduct of antitermination regulation. We demonstrate that this short transcript binds the small rna chaperone Hfq, and is processed into a stable 74-nt regulatory small rna that we have termed StxS. StxS represses expression of Shiga toxin 1 under lysogenic conditions through direct interactions with the stx1AB transcript. StxS acts in trans to activate expression of the general stress response sigma factor, RpoS, through direct interactions with an activating seed sequence within the 5 ' UTR. Activation of RpoS promotes high cell density growth under nutrient-limiting conditions. Many phages utilize antitermination to regulate the lytic/lysogenic switch and our results demonstrate that short rnas generated as a byproduct of this regulation can acquire regulatory small rna functions that modulate host fitness.

关键词： srna lambda phage Shiga toxin ncrna noncoding rna

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