Article
Biochemistry & Molecular Biology
Amy L. Pashler, Benjamin P. Towler, Christopher Jones, Hope J. Haime, Tom Burgess, Sarah F. Newbury
Summary: XRN1 is a crucial exoribonuclease involved in various cellular and developmental processes as well as human diseases, such as osteosarcoma. Its down-regulation in osteosarcoma cells suggests potential implications in disease progression. The identification of XRN1-sensitive transcripts, particularly long noncoding RNAs, sheds light on its specific regulatory roles in human cells.
Article
Biochemistry & Molecular Biology
Karin Broennimann, Inna Ricardo-Lax, Julia Adler, Eleftherios Michailidis, Ype P. de Jong, Nina Reuven, Yosef Shaul
Summary: Research has shown that hepatitis B virus (HBV) can promote RNR-R2 expression by a small conserved region within its transcript when infecting non-dividing cells, leading to an increase in dNTP levels. This demonstrates a non-coding function of HBV transcripts to support its propagation in non-cycling cells.
Review
Biochemistry & Molecular Biology
Radu Pirlog, Rares Drula, Andreea Nutu, George Adrian Calin, Ioana Berindan-Neagoe
Summary: CCAT2 is a highly studied lncRNA with diverse functions in cancer regulation, including interactions with various RNA binding proteins and transcription factors. It has been shown to play a role in promoting chromosome instability and altering glutamine metabolism, potentially affecting cancer therapy resistance and metastasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Medicine, General & Internal
Shuoshuo Ma, Wenjing Wang, Dengyong Zhang, Guanru Zhao, Zheng Lu
Summary: Long non-coding RNAs (lncRNAs) are a family of non-protein-coding RNAs that have a length of over 200 nucleotides. Abnormal expression of lncRNA CCAT2 has been found in various tumors and is associated with cell behaviors and prognostic factors. This article provides a comprehensive review of the biological functions and mechanisms of action of CCAT2 in tumors, aiming to support its future clinical applications.
CHINESE MEDICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Matthew Bennett, Igor Ulitsky, Iraide Alloza, Koen Vandenbroeck, Vladislav Miscianinov, Amira Dia Mahmoud, Margaret Ballantyne, Julie Rodor, Andrew H. Baker
Summary: This study improved the representation of lncRNAs in pathological states of VSMCs by analyzing non-reference transcripts, discovering that non-reference lncRNAs contributed 21-32% in responding to pro-mitogenic stimuli and showed particular relevance to VSMC processes and regulation of neighboring protein-coding genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Fawzeyah A. Alnajjar, Archana Sharma-Oates, Susanne N. Wijesinghe, Hussein Farah, Dominika E. Nanus, Tom Nicholson, Edward T. Davis, Simon W. Jones
Summary: The study reveals that MALAT1 expression in subchondral bone of osteoarthritis (OA) joints is associated with parameters of joint health and biomarkers of joint inflammation, and it plays a functional role in regulating inflammation in human OA osteoblasts. The induction of MALAT1 in human OA osteoblasts upon inflammatory challenge and its modulation of PGE2 production suggests that MALAT1 may play a role in regulating inflammation in OA subchondral bone.
Article
Genetics & Heredity
Siqi Wang, Shengwei Ke, Yueming Wu, Duo Zhang, Baowei Liu, Yao-hui He, Wen Liu, Huawei Mu, Xiaoyuan Song
Summary: Studies have shown that GAS5 plays a crucial role in brain aging, affecting processes such as cell proliferation and apoptosis. GAS5 may also be associated with senescence-related diseases such as Parkinson's and Alzheimer's.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Koushiki Basu, Anubha Dey, Manjari Kiran
Summary: Recent reports have shown that long non-coding RNAs (lncRNAs) have lower splicing efficiency and fewer alternative splice variants than mRNAs. However, our study found that lncRNAs actually produce more splice variants per exon, known as Transcript Complexity, compared to mRNAs. Furthermore, inefficient splicing of lncRNAs may facilitate multiple introns splicing and lead to more spliced products per exon.
Review
Biochemistry & Molecular Biology
Anshika Goenka, Deanna Marie Tiek, Xiao Song, Rebeca Piatniczka Iglesia, Minghui Lu, Bo Hu, Shi-Yuan Cheng
Summary: Research in cancer biology has predominantly focused on protein-coding genes, but the discovery of non-coding RNAs (ncRNAs) has shed light on their crucial role in various biological processes and human diseases including cancer. Dysregulated ncRNA expression affects cancer initiation, progression, and therapy resistance. This review emphasizes the recent developments and advances in ncRNA biology relevant to glioma tumorigenesis and therapy response, highlighting the potential of ncRNAs as biomarkers and therapeutic agents in glioma.
Review
Endocrinology & Metabolism
Guanqing Zhou, Mimi Zhang, Jingzhi Zhang, Yaofeng Feng, Zhishen Xie, Siyi Liu, Detu Zhu, Yumei Luo
Summary: Non-coding RNAs play important roles in cell differentiation, proliferation, apoptosis, and the pathogenesis of various diseases. Especially in non-obstructive azoospermia, the expression of non-coding RNAs is associated with pathological conditions.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Cell Biology
Chaohua Si, Chen Chen, Yaxin Guo, Qiaozhen Kang, Zhenqiang Sun
Summary: This review discusses the significant role of m6A RNA modifications in the tumor microenvironment, highlighting their potential as biomarkers and therapeutic targets for cancer therapy. Understanding the relationship between TME and m6A RNA modifications may lead to new approaches for future cancer treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hema P. Narra, Jessica Alsing, Abha Sahni, Michelle Montini, Yasim Zafar, Sanjeev K. Sahni
Summary: This study investigates the role of sRNA in regulating the expression of cydA and cydB genes in Rickettsia conorii infection. The results show that the binding of sRNA is required for the regulation of cydA but not cydB. The expression of sRNA and its cognate target gene transcripts also exhibit tissue-specific differences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Letizia Messa, Bianca Barzaghini, Federica Rey, Cecilia Pandini, Gian Vincenzo Zuccotti, Cristina Cereda, Stephana Carelli Carelli, Manuela Teresa Raimondi
Summary: This study investigated the transcriptional dysregulation of 357 non-coding genes in murine neural precursor cells and highlighted their role in altering the expression of coding genes involved in mechanotransduction, stemness, and neural differentiation. Furthermore, computational characterization of non-coding RNAs with human homologue sequences was performed to explore their mechanisms of action.
Review
Biochemistry & Molecular Biology
Carlos Garcia-Padilla, Estefania Lozano-Velasco, Virginio Garcia-Lopez, Amelia Aranega, Diego Franco, Virginio Garcia-Martinez, Carmen Lopez-Sanchez
Summary: Heart failure is a complex clinical syndrome with increasing prevalence, and finding new molecular biomarkers is an interesting tool to improve its prevention, diagnosis, treatment, and prognosis. This review emphasizes the relevance of microRNAs, long non-coding RNAs, and circular RNAs as potential biomarkers in heart failure. Further studies in this field are crucial to support their widespread clinical use.
Article
Biochemical Research Methods
Lars Gabriel, Katharina J. Hoff, Tomas Bruna, Mark Borodovsky, Mario Stanke
Summary: TSEBRA is a software tool that selects gene predictions from BRAKER1 and BRAKER2 sets based on RNA-seq and homologous protein evidence support. Computational experiments show that TSEBRA achieves higher accuracy compared to running BRAKER1 and BRAKER2 alone, and it performs favorably against EVidenceModeler.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Camille Sayou, Gonzalo Millan-Zambrano, Helena Santos-Rosa, Elisabeth Petfalski, Samuel Robson, Jonathan Houseley, Tony Kouzarides, David Tollervey
MOLECULAR AND CELLULAR BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Ryan M. Hull, Cristina Cruz, Carmen V. Jack, Jonathan Houseley
Article
Geriatrics & Gerontology
Stephen Frenk, Jonathan Houseley
Article
Biology
Cristina Cruz, Monica Della Rosa, Christel Krueger, Qian Gao, Dorottya Horkai, Michelle King, Lucy Field, Jonathan Houseley
Article
Biochemistry & Molecular Biology
Ryan M. Hull, Michelle King, Grazia Pizza, Felix Krueger, Xabier Vergara, Jonathan Houseley
Review
Genetics & Heredity
Ryan M. Hull, Jonathan Houseley
Article
Biochemistry & Molecular Biology
Inigo Prada-Luengo, Henrik D. Moller, Rasmus A. Henriksen, Qian Gao, Camilla Eggert Larsen, Sefa Alizadeh, Lasse Maretty, Jonathan Houseley, Birgitte Regenberg
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Prasanna Channathodiyil, Jonathan Houseley
Summary: Replacing formaldehyde with glyoxal for cell fixation allows for easy extraction of high quality RNA from stained and sorted mammalian cells, maintaining the integrity of RNA and enabling routine transcriptome analysis. Glyoxal fixation does not impair RNA extraction and ensures accessibility of RNA for enzymatic manipulation, making it a suitable method for transcriptomic studies on fixed cells.
Article
Biochemistry & Molecular Biology
Neesha Kara, Felix Krueger, Peter Rugg-Gunn, Jonat Houseley
Summary: TrAEL-seq is a method that captures single-stranded DNA 3' ends genome-wide with high sensitivity and resolution, providing maps of replication fork progression and stalling sites. It offers a flexible and robust approach for studying DNA replication and repair, with the ability to accurately detect double-strand break sites.
Article
Biochemistry & Molecular Biology
Alex J. Whale, Michelle King, Ryan M. Hull, Felix Krueger, Jonathan Houseley
Summary: Adaptive mutations can cause drug resistance and increase tolerance to chemical treatment. The study investigates the transcription mechanism of the copper resistance gene CUP1 in budding yeast and its impact on copy number variation. The results demonstrate that CUP1 transcription requires TREX-2 and Mediator, and that replication stress and homologous recombination contribute to the amplification of CUP1 gene. The study also highlights the critical role of late-firing replication origins in CUP1 amplification.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Andre Zylstra, Hanane Hadj-Moussa, Dorottya Horkai, Alex J. Whale, Baptiste Piguet, Jonathan Houseley
Summary: The accumulation of extrachromosomal ribosomal DNA circles (ERCs) has long been considered as the main cause of replicative ageing in yeast mother cells. However, this study found that ERCs have little molecular effects and do not induce gene expression differences that suggest stress responses or metabolic feedback. The driver of senescence during yeast ageing was found to be copy number amplification of a region of chromosome XII, rather than ERCs.
Article
Biochemistry & Molecular Biology
Dorottya Horkai, Hanane Hadj-Moussa, Alex J. Whale, Jonathan Houseley
Summary: This study found that an unrestricted galactose diet in early life can minimize changes during replicative aging in yeast, regardless of later diet. The average mother cell division rate is comparable between glucose and galactose diets, but senescence markers and dysregulation of gene expression are minimal on galactose. These findings support the existence of two separable aging trajectories in yeast and suggest that a shift to a healthy aging mode can be achieved through dietary change in early life.
Overall importance rating: 8/10
Article
Biochemistry & Molecular Biology
Prasanna Channathodiyil, Kieron May, Anne Segonds-Pichon, Paul D. Smith, Simon J. Cook, Jonathan Houseley
Summary: Mutations and gene amplifications that cause drug resistance frequently occur during chemotherapy. This study investigates BRAF amplification as the main cause of resistance to the MEK inhibitor selumetinib. They find that selumetinib induces G1 arrest and reduces the expression of DNA replication and repair genes, but cells can still re-enter the cell cycle during treatment. By impeding cell cycle entry, de novo gene amplification can be suppressed.
Article
Cell Biology
Stephen Frenk, Grazia Pizza, Rachael V. Walker, Jonathan Houseley
Article
Biotechnology & Applied Microbiology
Thomas M. Stubbs, Marc Jan Bonder, Anne-Katrien Stark, Felix Krueger, Ferdinand von Meyenn, Oliver Stegle, Wolf Reik
