keyword
https://read.qxmd.com/read/37526137/the-role-of-salinity-on-genome-wide-dna-methylation-dynamics-in-european-sea-bass-gills
#21
JOURNAL ARTICLE
Eva Blondeau-Bidet, Ghizlane Banousse, Thibaut L'Honoré, Emilie Farcy, Céline Cosseau, Catherine Lorin-Nebel
Epigenetic modifications, like DNA methylation, generate phenotypic diversity in fish and ultimately lead to adaptive evolutionary processes. Euryhaline marine species that migrate between salinity-contrasted habitats have received little attention regarding the role of salinity on whole-genome DNA methylation. Investigation of salinity-induced DNA methylation in fish will help to better understand the potential role of this process in salinity acclimation. Using whole-genome bisulfite sequencing, we compared DNA methylation patterns in European sea bass (Dicentrarchus labrax) juveniles in seawater and after freshwater transfer...
August 1, 2023: Molecular Ecology
https://read.qxmd.com/read/37486712/functional-role-of-sap18-protein-from-transcriptional-repression-to-splicing-regulation
#22
REVIEW
Sweta Kumari, Ayushi Rehman, Pratap Chandra, Kusum K Singh
Sin3 associated protein 18 (SAP18) is an evolutionary conserved protein, originally discovered in a complex with the transcriptional regulatory protein, Sin3. Subsequent investigations revealed SAP18 as an integral splicing component of the exon junction complex (EJC)-associated apoptosis-and splicing-associated protein (ASAP)/PNN-RNPS1-SAP18 (PSAP) complex. In association with Sin3, SAP18 contributes toward transcriptional repression of genes implicated in embryonic development, stress response, human immunodeficiency virus type 1 replication, and tumorigenesis...
July 24, 2023: Cell Biochemistry and Function
https://read.qxmd.com/read/37443320/exon-intron-boundary-inhibits-m-6-a-deposition-enabling-m-6-a-distribution-hallmark-longer-mrna-half-life-and-flexible-protein-coding
#23
JOURNAL ARTICLE
Zhiyuan Luo, Qilian Ma, Shan Sun, Ningning Li, Hongfeng Wang, Zheng Ying, Shengdong Ke
Regional bias of N6 -methyladenosine (m6 A) mRNA modification avoiding splice site region, calls for an open hypothesis whether exon-intron boundary could affect m6 A deposition. By deep learning modeling, we find that exon-intron boundary represses a proportion (12% to 34%) of m6 A deposition at adjacent exons (~100 nt to splice site). Experiments validate that m6 A signal increases once the host gene does not undergo pre-mRNA splicing to produce the same mRNA. Inhibited m6 A sites have higher m6 A enhancers and lower m6 A silencers locally and show high heterogeneity at different exons genome-widely, with only a small proportion (12% to 15%) of exons showing strong inhibition, enabling more stable mRNAs and flexible protein coding...
July 13, 2023: Nature Communications
https://read.qxmd.com/read/37340961/exon-junction-complex-modulates-the-formation-of-the-m-6-a-epitranscriptome
#24
JOURNAL ARTICLE
Peng-Hui Song, Li-Juan Ma, Dong Yan
N 6 -methyladenosine (m6 A) is one of the most abundant chemical modifications in mRNA and plays essential roles in diverse physiological and pathological processes. m6 A is highly enriched near stop codons and in long internal exons of mRNA, but the mechanism leading to this specific distribution has been unclear. Recently, three papers have solved this major problem by revealing that exon junction complexes (EJCs) act as m6 A suppressors and shape the formation of the m6 A epitranscriptome. Here, we briefly introduce the m6 A pathway, elaborate the roles of EJC on the formation of m6 A modification based on these results, and describe the effect of exon-intron structure on mRNA stability via m6 A, which will help us better understand the latest progress in the m6 A RNA modification field...
June 20, 2023: Yi Chuan, Hereditas
https://read.qxmd.com/read/37301449/genome-wide-identification-evolution-and-expression-analysis-of-tight-junction-gene-family-and-the-immune-roles-of-claudin5-gene-in-turbot-scophthalmus-maximus-l
#25
JOURNAL ARTICLE
Xin Cai, Chengbin Gao, Le Ma, Chao Li
Tight junction proteins (TJs) are important component proteins that maintaining the structure and function of TJs, connecting to each other to form a TJ complex between cells, maintaining the biological homeostasis of the internal environment. In this study, a total of 103 TJ genes were identified in turbot according to our whole-transcriptome database. Transmembrane TJs were divided into seven subfamilies, including claudin (CLDN), occludin (OCLD), tricellulin (MARVELD2), MARVEL domain containing 3 (MARVELD3), junctional adhesion molecules (JAM), immunoglobulin superfamily member 5 (IGSF5/JAM4), blood vessel epicardial substance (BVEs)...
June 8, 2023: Gene
https://read.qxmd.com/read/37294214/the-paralogues-magoh-and-magohb-are-oncogenic-factors-in-high-grade-gliomas-and-safeguard-the-splicing-of-cell-division-and-cell-cycle-genes
#26
JOURNAL ARTICLE
Rodrigo A S Barreiro, Gabriela D A Guardia, Fabiana M Meliso, Xiufen Lei, Wei-Qing Li, Andre Savio, Martin Fellermeyer, Helena B Conceição, Rafael L V Mercuri, Tesha Landry, Mei Qiao, Lorea Blazquez, Jernej Ule, Luiz O F Penalva, Pedro A F Galante
The exon junction complex (EJC) plays key roles throughout the lifespan of RNA and is particularly relevant in the nervous system. We investigated the roles of two EJC members, the paralogs MAGOH and MAGOHB, with respect to brain tumour development. High MAGOH/MAGOHB expression was observed in 14 tumour types; glioblastoma (GBM) showed the greatest difference compared to normal tissue. Increased MAGOH/MAGOHB expression was associated with poor prognosis in glioma patients, while knockdown of MAGOH/MAGOHB affected different cancer phenotypes...
January 2023: RNA Biology
https://read.qxmd.com/read/37237280/circular-rnas-arising-from-synaptic-host-genes-during-human-neuronal-differentiation-are-modulated-by-sfpq-rna-binding-protein
#27
JOURNAL ARTICLE
Michelle E Watts, Marika Oksanen, Sanna Lejerkrans, Francesca Mastropasqua, Myriam Gorospe, Kristiina Tammimies
BACKGROUND: Circular RNA (circRNA) molecules, generated through non-canonical back-splicing of exon-exon junctions, have recently been implicated in diverse biological functions including transcriptional regulation and modulation of protein interactions. CircRNAs are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored...
May 26, 2023: BMC Biology
https://read.qxmd.com/read/37204171/serine-rich-domain-of-rnps1-functions-in-activation-of-alternative-splicing
#28
JOURNAL ARTICLE
Sweta Kumari, Bhagyashree Deka, Kusum Kumari Singh
RNA-binding protein with serine-rich domain 1 (RNPS1) gets deposited on the mRNA during the process of splicing and concomitantly associates with the exon junction complex (EJC). RNPS1 participates in post-transcriptional gene regulation, including constitutive and alternative splicing, transcriptional regulation and nonsense-mediated mRNA decay. In this study, we found that the tethering of RNPS1 or its isolated serine-rich domain (S domain) causes exon inclusion of an HIV-1 splicing substrate. In contrast, overexpressing the RRM domain of RNPS1 acts in a dominant negative manner and leads to the exon skipping of endogenous apoptotic pre-mRNAs (Bcl-X and MCL-1)...
May 19, 2023: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://read.qxmd.com/read/37145092/the-long-and-short-of-ejc-independent-nonsense-mediated-rna-decay
#29
JOURNAL ARTICLE
Oscar Muñoz, Mlana Lore, Sujatha Jagannathan
Nonsense-mediated RNA decay (NMD) plays a dual role as an RNA surveillance mechanism against aberrant transcripts containing premature termination codons and as a gene regulatory mechanism for normal physiological transcripts. This dual function is possible because NMD recognizes its substrates based on the functional definition of a premature translation termination event. An efficient mode of NMD target recognition involves the presence of exon-junction complexes (EJCs) downstream of the terminating ribosome...
May 5, 2023: Biochemical Society Transactions
https://read.qxmd.com/read/37139782/the-exon-junction-complex-component-eif4a3-is-essential-for-mouse-and-human-cortical-progenitor-mitosis-and-neurogenesis
#30
JOURNAL ARTICLE
Bianca M Lupan, Rachel A Solecki, Camila Manso Musso, Fernando C Alsina, Debra L Silver
Mutations in components of the exon junction complex (EJC) are associated with neurodevelopment and disease. In particular, reduced levels of the RNA helicase EIF4A3 cause Richieri-Costa-Pereira Syndrome (RCPS) and CNVs are linked to intellectual disability. Consistent with this, Eif4a3 haploinsufficient mice are microcephalic. Altogether, this implicates EIF4A3 in cortical development; however, the underlying mechanisms are poorly understood. Here, we use mouse and human models to demonstrate that EIF4A3 promotes cortical development by controlling progenitor mitosis, cell fate, and survival...
May 4, 2023: Development
https://read.qxmd.com/read/37090609/tar-syndrome-associated-rbm8a-deficiency-causes-hematopoietic-defects-and-attenuates-wnt-pcp-signaling
#31
Agnese Kocere, Elena Chiavacci, Kevin M Mendez-Acevedo, Charlotte Soneson, Max S Hiltabidle, Azhwar Raghunath, Jacalyn S MacGowan, Jordan A Shavit, Daniela Panakova, Margot L K Williams, Mark D Robinson, Christian Mosimann, Alexa Burger
Defects in blood development frequently occur among syndromic congenital anomalies. Thrombocytopenia-Absent Radius (TAR) Syndrome is a rare congenital condition with reduced platelets (hypomegakaryocytic thrombocytopenia) and forelimb anomalies, concurrent with more variable heart and kidney defects. TAR syndrome associates with hypomorphic gene function for RBM8A/Y14 that encodes a component of the exon junction complex involved in mRNA splicing, transport, and nonsense-mediated decay. How perturbing a general mRNA-processing factor causes the selective TAR Syndrome phenotypes remains unknown...
April 20, 2023: bioRxiv
https://read.qxmd.com/read/37065448/the-ejc-disassembly-factor-pym-is-an-intrinsically-disordered-protein-and-forms-a-fuzzy-complex-with-rna
#32
JOURNAL ARTICLE
Deepshikha Verma, Veena Hegde, John Kirkpatrick, Teresa Carlomagno
The discovery of several functional interactions where one or even both partners remain disordered has demonstrated that specific interactions do not necessarily require well-defined intermolecular interfaces. Here we describe a fuzzy protein-RNA complex formed by the intrinsically unfolded protein PYM and RNA. PYM is a cytosolic protein, which has been reported to bind the exon junction complex (EJC). In the process of oskar mRNA localization in Drosophila melanogaster , removal of the first intron and deposition of the EJC are essential, while PYM is required to recycle the EJC components after localization has been accomplished...
2023: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/37058324/tcf3-gene-rearrangements-in-pediatric-b-cell-acute-lymphoblastic-leukemia-a-single-center-experience
#33
JOURNAL ARTICLE
Elena Zerkalenkova, Yaroslav Menchits, Alexandra Borkovskaia, Sophia Sokolova, Olga Soldatkina, Ekaterina Mikhailova, Alexander Popov, Alexander Komkov, Yulia Rumiantseva, Alexander Karachunskii, Yulia Olshanskaya
INTRODUCTION: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common neoplasm in children. One of the long known recurrent rearrangements in BCP-ALL is t(1;19)(q23;p13.3)/TCF3::PBX1. However, other TCF3 gene rearrangements were also described that are associated with significant difference in ALL prognosis. METHODS: The current study aimed to analyze the spectrum of TCF3 gene rearrangements in children in Russian Federation. A cohort of 203 patients with BCP-ALL was selected based on FISH screening and was studied by karyotyping, FISH, RT-PCR and high throughput sequencing...
August 2023: International Journal of Laboratory Hematology
https://read.qxmd.com/read/37020021/mrna-recognition-and-packaging-by-the-human-transcription-export-complex
#34
JOURNAL ARTICLE
Belén Pacheco-Fiallos, Matthias K Vorländer, Daria Riabov-Bassat, Laura Fin, Francis J O'Reilly, Farja I Ayala, Ulla Schellhaas, Juri Rappsilber, Clemens Plaschka
Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export1,2 . However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood3 . Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes...
April 5, 2023: Nature
https://read.qxmd.com/read/36979701/nonsense-mediated-mrna-decay-factor-functions-in-human-health-and-disease
#35
REVIEW
Lingling Sun, Justine Mailliot, Christiane Schaffitzel
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance mechanism that degrades mRNAs with a premature stop codon, avoiding the synthesis of C-terminally truncated proteins. In addition to faulty mRNAs, NMD recognises ~10% of endogenous transcripts in human cells and downregulates their expression. The up-frameshift proteins are core NMD factors and are conserved from yeast to human in structure and function. In mammals, NMD diversified into different pathways that target different mRNAs employing additional NMD factors...
February 27, 2023: Biomedicines
https://read.qxmd.com/read/36902031/transcriptomic-analyses-of-brains-of-rbm8a-conditional-knockout-mice-at-different-developmental-stages-reveal-conserved-signaling-pathways-contributing-to-neurodevelopmental-diseases
#36
JOURNAL ARTICLE
Colleen McSweeney, Miranda Chen, Fengping Dong, Aswathy Sebastian, Derrick James Reynolds, Jennifer Mott, Zifei Pei, Jizhong Zou, Yongsheng Shi, Yingwei Mao
RNA-binding motif 8A (RBM8A) is a core component of the exon junction complex (EJC) that binds pre-mRNAs and regulates their splicing, transport, translation, and nonsense-mediated decay (NMD). Dysfunction in the core proteins has been linked to several detriments in brain development and neuropsychiatric diseases. To understand the functional role of Rbm8a in brain development, we have generated brain-specific Rbm8a knockout mice and used next-generation RNA-sequencing to identify differentially expressed genes (DEGs) in mice with heterozygous, conditional knockout (cKO) of Rbm8a in the brain at postnatal day 17 (P17) and at embryonic day 12...
February 27, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/36882295/exploring-the-targeting-spectrum-of-rocaglates-among-eif4a-homologs
#37
JOURNAL ARTICLE
Sai Kiran Naineni, Regina Cencic, Francis Robert, Lauren Brown, Minza Haque, Jordan Scott-Talib, Patrick Senechal, T Martin Schmeing, John Porco, Jerry Pelletier
Inhibition of eukaryotic translation initiation through unscheduled RNA clamping of the DEAD-box (DDX) RNA helicases eIF4A1 and eIF4A2 has been documented for pateamine A (Pat A) and rocaglates - two structurally different classes of compounds that share overlapping binding sites on eIF4A. Clamping of eIF4A to RNA causes steric blocks that interfere with ribosome binding and scanning, rationalizing the potency of these molecules since not all eIF4A molecules need to be engaged to elicit a biological effect...
March 7, 2023: RNA
https://read.qxmd.com/read/36881772/lncrna-hotairm1-functions-in-dna-double-strand-break-repair-via-its-association-with-dna-repair-and-mrna-surveillance-factors
#38
JOURNAL ARTICLE
Tzu-Wei Chuang, Chun-Hao Su, Pei-Yu Wu, Yao-Ming Chang, Woan-Yuh Tarn
The eukaryotic exon junction complex component Y14 participates in double-strand break (DSB) repair via its RNA-dependent interaction with the non-homologous end-joining (NHEJ) complex. Using immunoprecipitation-RNA-seq, we identified a set of Y14-associated long non-coding RNAs (lncRNAs). The lncRNA HOTAIRM1 serves as a strong candidate that mediates the interaction between Y14 and the NHEJ complex. HOTAIRM1 localized to near ultraviolet laser-induced DNA damage sites. Depletion of HOTAIRM1 delayed the recruitment of DNA damage response and repair factors to DNA lesions and compromised the efficiency of NHEJ-mediated DSB repair...
March 7, 2023: Nucleic Acids Research
https://read.qxmd.com/read/36755023/temporal-iclip-captures-co-transcriptional-rna-protein-interactions
#39
JOURNAL ARTICLE
Ross A Cordiner, Yuhui Dou, Rune Thomsen, Andrii Bugai, Sander Granneman, Torben Heick Jensen
Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC)...
February 8, 2023: Nature Communications
https://read.qxmd.com/read/36747106/prevalence-and-founder-effect-of-drc1-exon-1-4-deletion-in-korean-patients-with-primary-ciliary-dyskinesia
#40
JOURNAL ARTICLE
Man Jin Kim, Sheehyun Kim, Seung Won Chae, Seungbok Lee, Jihoon G Yoon, Boram Kim, Jee-Soo Lee, Jong Hee Chae, Moon-Woo Seong, Jangsup Moon
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder affecting ciliary structure and function. PCD exhibiting dynein regulatory complex subunit 1 (DRC1) exon 1-4 deletion has been reported in several Japanese PCD patients; however, no large scale studies have been performed. Here, we aimed to determine the prevalence and founder effect of this variant in the Korean population. Using an in-house copy number variation tool, we screened for DRC1 exon 1-4 deletion in 20 patients with PCD and exome data of 1435 patients in the Seoul National University Hospital repository...
February 7, 2023: Journal of Human Genetics
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