Article
Biochemistry & Molecular Biology
Anna Talyzina, Yan Han, Chiranjib Banerjee, Susan Fishbain, Alexis Reyes, Reza Vafabakhsh, Yuan He
Summary: RNA polymerase III (Pol III) transcribes 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Transcription factors TFIIIA, TFIIIC, and TFIIIB are required for its recruitment to the 5S rRNA promoter. Cryo-EM visualization of a S. cerevisiae complex reveals the interaction of TFIIIA and TFIIIC with the promoter, and the DNA binding of TFIIIB subunits. smFRET study confirms the bending and dissociation of DNA within the complex. These findings provide new insights into transcription initiation on the 5S rRNA promoter and comparative analysis between Pol III and Pol II.
Article
Multidisciplinary Sciences
Wolfram Seifert-Davila, Mathias Girbig, Luis Hauptmann, Thomas Hoffmann, Sebastian Eustermann, Christoph W. Mueller
Summary: Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to target genes by recognizing intragenic A- and B-box motifs. Cryo-electron microscopy structures revealed that the tau B module of TFIIIC recognizes the B-box through DNA shape and sequence readout. TFIIIC220 acts as a linker connecting the tau A and tau B subcomplexes, facilitating scanning for A-boxes and Pol III activation by TFIIIB.
Article
Oncology
Stephanie Cabarcas-Petroski, Laura Schramm
Summary: This study analyzed clinical breast cancer datasets and found that BDP1 copy number and mRNA expression correlate with clinical outcomes in breast cancer, particularly with invasive ductal carcinoma, high grade, and advanced stage. Decreased BDP1 expression is associated with poor clinical outcomes such as metastasis, cancer recurrence, and patient death. Additionally, BDP1 alterations are observed in triple-negative invasive breast cancer, suggesting a potential role for BDP1 as a biomarker in breast cancer.
Article
Genetics & Heredity
Ofri Levi, Monalisha Mallik, Yoav S. Arava
Summary: Aminoacyl tRNA synthetases (aaRSs) have a canonical role in charging tRNAs with amino acids, but they also have non-canonical roles in post-transcriptional regulation of mRNA expression. This study focused on yeast cytosolic threonine tRNA synthetase (ThrRS) and discovered its preference for binding mRNAs encoding RNA polymerase subunits. The mRNA encoding RPC10, a small subunit of RNA polymerase III, showed the highest binding affinity. Mutations in an ASL-like structure within this mRNA sequence led to reduced binding by ThrRS and decreased RPC10 protein levels. This suggests a novel regulatory mechanism involving a mimicking element within an RNA polymerase III subunit in the regulation of cellular tRNA levels through the tRNA cognate aaRS.
Article
Biochemical Research Methods
Paul D. Donovan, Natalie M. McHale, Morten T. Veno, Jochen H. M. Prehn
Summary: This study introduces a pipeline called tsRNAsearch for identifying tRNA fragments and other non-coding RNAs from small RNA sequencing data. By comparing two groups of datasets, this tool can effectively identify RNA fragments with irregular read distribution, serving as a proxy for RNA cleavage. The results demonstrate the successful application of tsRNAsearch to small RNA sequencing data from different diseases, potentially discovering new biomarkers.
Article
Genetics & Heredity
Rebecca E. Sizer, Nisreen Chahid, Sienna P. Butterfield, David Donze, Nia J. Bryant, Robert J. White
Summary: Eukaryotic chromosomes are divided into domains with distinct properties, and tRNA genes can function as insulators to block the spread of silencing activities. The function of tDNAs as insulators is dependent on the transcription factor TFIIIC. This mechanism is conserved across different species.
Article
Genetics & Heredity
Rebecca E. Sizer, Nisreen Chahid, Sienna P. Butterfield, David Donze, Nia J. Bryant, Robert J. White
Summary: This study explores the conservation and diversity of tRNA genes (tDNAs) in insulation functions across different species, as well as the crucial role of the transcription factor TFIIIC in insulators. The research shows that tDNAs can effectively function as insulators in distantly-related yeast species, and the transcription factor USF1 in human tDNAs plays a key role in insulation activity.
Article
Oncology
Hitha Gopalan Nair, Aneta Jurkiewicz, Damian Graczyk
Summary: Tumour necrosis factor alpha (TNF-alpha) is a multifunctional cytokine that plays a pivotal role in apoptosis, cell survival, inflammation, and immunity. While it is known for its antitumor properties, TNF-alpha also has tumor-promoting effects. This study shows that inhibiting RNA polymerase III (Pol III) enhances the cytotoxic and cytostatic effects of TNF-alpha in colorectal cancer cells, suggesting that targeting Pol III may be a potential therapeutic intervention to sensitize cancer cells to TNF-alpha.
Article
Oncology
Sienna P. Butterfield, Rebecca E. Sizer, Emma Rand, Robert J. White
Summary: High expression of tRNA is a common feature of breast cancer, but the activated gene family members vary between tumors while familial patterns show consistency. Specific tRNA expression levels are significantly correlated with patient prognosis.
Article
Oncology
Stephanie Cabarcas-Petroski, Gabriella Olshefsky, Laura Schramm
Summary: Through the analysis of clinical data, the study found that BDP1 expression was decreased in serous ovarian cancer and correlated with higher and advanced stages. Further analysis showed that high BDP1 expression was unfavorable for overall survival and occurred in stages 2, 3, and 4 of serous ovarian cancer. Additionally, high BDP1 expression was disadvantageous for progression-free survival. Finally, BDP1 expression significantly decreased in patients treated with first-line chemotherapy. The study suggests that BDP1 could be a predictive biomarker of clinical relevance in serous ovarian cancer.
Article
Multidisciplinary Sciences
Emilio Merheb, Min-Hui Cui, Juwen C. DuBois, Craig A. Branch, Maria Gulinello, Bridget Shafit-Zagardo, Robyn D. Moir, Ian M. Willis
Summary: Mice expressing pathogenic mutations in the largest Pol III subunit, Polr3a, show impaired growth, developmental delay, cognitive deficits, and hypomyelination in certain brain regions, resembling some clinical features of patients with Pol III-related leukodystrophy. The disease pathogenesis in the mice involves defects in oligodendrogenesis and myelination processes sensitive to perturbations of Pol III transcription.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Immunology
Victor E. Nava, Pin-Yu Perera, Nirbhay Kumar, Maneesh Jain
Summary: Noncoding RNAs (ncRNAs) are RNA molecules that are not translated into protein but can convey information encoded in their DNA. Research on the exact function of ncRNAs is challenging but understanding their importance holds great potential for basic and translational research as well as therapeutic progress.
Article
Multidisciplinary Sciences
Dhenugen Logeswaran, Yang Li, Khadiza Akhter, Joshua D. Podlevsky, Tamara L. Olson, Katherine Forsberg, Julian J-L Chen
Summary: A previously unknown messenger RNA-derived biogenesis pathway for telomerase RNA has been discovered in the basidiomycete fungus Ustilago maydis. This pathway involves the processing of a larger RNA precursor, which possesses mRNA characteristics, to produce a mature telomerase RNA. This finding expands our understanding of telomerase biogenesis mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Nayef Jarrous, Dhivakar Mani, Aravind Ramanathan
Summary: The article discusses the coordination of transcription and processing of RNA in eukaryotes as a basic principle of gene expression regulation. It presents a model of high molecular weight initiation complexes of human RNA polymerase III on tRNA genes, highlighting their role in co-transcriptional processing of tRNA precursors to mature forms.
Review
Biochemistry & Molecular Biology
Tomasz W. Turowski, Magdalena Boguta
Summary: RNAPI and RNAPIII are multi-heterogenic protein complexes specialized in transcribing highly abundant non-coding RNAs, more complex than RNAPII synthesizing mRNAs. They share associated subcomplexes formed by specific subunits in yeast and establish an assembly platform co-translationally during the synthesis of the Rpb10 subunit.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Matilde Calderoni, Maddalena Altare, Luca Mastracci, Federica Grillo, Laura Cornara, Aldo Pagano
Summary: This study demonstrates a method for qualitative identification of Peganum harmala seeds using optical and electron microscopy, as well as the development of a real-time qPCR test that can detect Peganum harmala DNA in quantities as low as less than 1 pg. In addition to species specificity and high sensitivity, this method accurately quantifies the presence of Peganum harmala seeds or seed parts in complex herbal mixtures, providing an indication of the danger level of the product.
Editorial Material
Biochemistry & Molecular Biology
Elisabeth Lata, Martin Teichmann
Summary: By resolving RNA polymerase structures at the atomic level, researchers have uncovered unique properties of human RNA polymerase III and proposed built-in modules within the enzyme that mediate transcriptional activation, repression, and antirepression.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Francesca Baldini, Matilde Calderoni, Laura Vergani, Paola Modesto, Tullio Florio, Aldo Pagano
Summary: Neuroblastoma is a heterogeneous childhood tumor with unknown mechanisms and challenging treatment. Long non-coding RNAs may play a significant role in the pathogenesis and progression of neuroblastoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biology
Roberto Ferrari, Nicole Grandi, Enzo Tramontano, Giorgio Dieci
Summary: Retrotransposons, still active in humans, play a significant role in genomic innovation in mammals, particularly in relation to the evolution of unique brain morphology and function. Their involvement in gene regulation in the brain has been linked to various neurodevelopmental and neurodegenerative conditions, highlighting their crucial role in the emergence of mammalian, primate, and human brain peculiarities.
Article
Biology
Giorgio Dieci
Summary: In eukaryotes, RNA polymerase II (Pol II) is responsible for the synthesis of all mRNAs and a variety of untranslated RNAs. The Pol II CTD, with its tandem repeats of a heptapeptide sequence, allows for posttranslational modifications of each amino acid, leading to specific recognition by different protein binding partners. This organic code system plays a crucial role in coordinating RNA biogenesis with RNA synthesis by Pol II, and is integrated with other organic codes like the splicing code and histone code.
Article
Biochemistry & Molecular Biology
Patrizia Garbati, Raffaella Barbieri, Matilde Calderoni, Francesca Baldini, Mario Nizzari, Paola Modesto, Tullio Florio, Aldo Pagano
Summary: This study combined three drugs to treat HR-NB, showing that the combination was more effective than using cisplatin alone, leading to a significant decrease in the expression of malignancy markers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Elisabeth Lata, Karine Choquet, Francis Sagliocco, Bernard Brais, Genevieve Bernard, Martin Teichmann
Summary: Pol III transcribes small untranslated RNAs, and mutations in its subunits can lead to specific neurodegenerative diseases and other disorders. While the causal relationship between mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain unclear.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Marco Morselli, Giorgio Dieci
Summary: Recent investigations have revealed hidden layers of gene regulation in human cells, with a focus on the non-protein-coding transcriptome. This review highlights the relatively little attention given to the epigenetic regulation of non-protein-coding RNA genes, and suggests that further investigation could lead to a better understanding of the entire human epigenomic network.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Lara de Llobet Cucalon, Chiara Di Vona, Marco Morselli, Marco Vezzoli, Barbara Montanini, Martin Teichmann, Susana de la Luna, Roberto Ferrari
Summary: This study reveals the role of TFIIIC, a general transcription factor, in the three-dimensional organization of the genome. TFIIIC predominantly binds to specific regions corresponding to repetitive elements, such as Alu elements, depending on the cell's developmental origin. These TFIIIC-enriched regions contribute to cell type-specific DNA looping, independent of the architectural protein CTCF.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Wiebke Lautre, Elodie Richard, Jean-Paul Feugeas, Helene Dumay-Odelot, Martin Teichmann
Summary: This study reveals the importance of human RNA polymerase (Pol) III in triple-negative breast cancer (TNBC). The embryonic isoform of Pol III, POLR3G, plays a critical role in the development and spread of TNBC, as well as in the expression of tumor-specific proteins. Deletion of POLR3G inhibits tumor growth and metastasis in TNBC, and induces the expression of transcription factors characteristic of other types of breast cancer. This finding provides new potential therapeutic targets for the treatment of TNBC in the future.
Article
Biochemistry & Molecular Biology
Marco Vezzoli, Lara Isabel de Llobet Cucalon, Chiara Di Vona, Marco Morselli, Barbara Montanini, Susana de la Luna, Martin Teichmann, Giorgio Dieci, Roberto Ferrari
Summary: Regulation of histone acetylation plays a crucial role in gene expression patterns. The study uncovered a more complex picture of histone acetyltransferases (HATs) responsible for histone acetylation in hESCs. Specifically, p300 is only partially involved in acetylation of H3K18 and H3K27 in stem cells, while TFIIIC is associated with H3K18ac in stemness genes and is found near genes related to neuronal biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Federica Barbieri, Adriana Bajetto, Irene Dellacasagrande, Agnese Solari, Roberto Wuerth, Virginia Fernandez, Silvia Rancati, Davide Ceresa, Irene Appolloni, Giuseppa De Luca, Mariella Dono, Paolo Nozza, Piero Schiapparelli, Monica Gambaro, Pietro Fiaschi, Gabriele Gaggero, Nicolo Costanzo, Stefano Thellung, Paolo Malatesta, Aldo Pagano, Gianluigi Zona, Davide De Pietri Tonelli, Tullio Florio
Summary: This study isolated meningioma stem cells from human samples and identified the role of the CXCR4/CXCR7 chemokine axis in stem cell-related functions. The findings suggest that CXCR4/CXCR7 antagonists may be a useful approach for high-risk meningiomas.
Article
Biochemistry & Molecular Biology
Francesca Baldini, Lama Zeaiter, Farah Diab, Hawraa Zbeeb, Lisa Cuneo, Aldo Pagano, Piero Portincasa, Alberto Diaspro, Laura Vergani
Summary: Hypertrophy of adipocytes is the main cause of obesity. In this study, we investigated the changes in nuclear morphometry and chromatin epigenetic remodeling during adipocyte differentiation and hypertrophy. The results showed that hypertrophic adipocytes have larger nuclei with less elongated shape and reduced chromatin compaction. Additionally, hypertrophic adipocytes exhibited increased triglyceride accumulation, up-regulated expression of PPAR and gamma, reduced IL-1a release, and dysregulation of adipose tissue function markers. Furthermore, there was a remodeling of the epigenome and chromatin organization in hypertrophic adipocytes, including an increase in H3K9 acetylated domains and KAT2A expression, as well as global hypomethylation of DNA. These findings provide insights into the nuclear changes during adipocyte differentiation and hypertrophy and may contribute to the development of strategies for treating obesity and metabolic complications.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS
(2023)
Meeting Abstract
Biophysics
Francesca Baldini, Isotta Cainero, Lisa Cuneo, Irene Nepita, Chantal Usai, Paolo Bianchini, Laura Vergani, Aldo Pagano, Alberto Diaspro
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Francesca Baldini, Isotta Cainero, Chantal Usai, Paolo Bianchini, Aldo Pagano, Laura Vergani, Alberto Diaspro
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
(2021)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.