Mouse Hars2 Knockout Project (CRISPR/Cas9)

Total Page:16

File Type:pdf, Size:1020Kb

Mouse Hars2 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Hars2 Knockout Project (CRISPR/Cas9) Objective: To create a Hars2 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Hars2 gene (NCBI Reference Sequence: NM_080636 ; Ensembl: ENSMUSG00000019143 ) is located on Mouse chromosome 18. 13 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 13 (Transcript: ENSMUST00000152954). Exon 2~13 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 6.8% of the coding region. Exon 2~13 covers 93.27% of the coding region. The size of effective KO region: ~5562 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 8 9 10 11 12 13 Legends Exon of mouse Hars2 Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. The gRNA site is selected outside of these tandem repeats. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 9 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(22.85% 457) | C(19.65% 393) | T(34.75% 695) | G(22.75% 455) Note: The 2000 bp section upstream of Exon 2 is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution (down) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(30.4% 608) | C(19.85% 397) | T(26.7% 534) | G(23.05% 461) Note: The 2000 bp section downstream of stop codon is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 4 of 9 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr18 + 36783566 36785565 2000 browser details YourSeq 223 1250 1765 2000 94.2% chr11 - 72555350 72555931 582 browser details YourSeq 221 1245 1768 2000 90.1% chr16 + 17231542 17231988 447 browser details YourSeq 208 1245 1750 2000 88.6% chr8 - 13970336 13970601 266 browser details YourSeq 198 1333 1768 2000 87.9% chr7 + 27630398 27630785 388 browser details YourSeq 197 1245 1750 2000 85.4% chr14 - 63518559 63518828 270 browser details YourSeq 195 1186 1751 2000 91.5% chr7 + 28397022 28397597 576 browser details YourSeq 191 1560 1767 2000 94.5% chr9 + 6237817 6238014 198 browser details YourSeq 187 1560 1750 2000 99.0% chr6 + 47857719 47857909 191 browser details YourSeq 186 1564 1765 2000 97.0% chr7 + 31493942 31494142 201 browser details YourSeq 184 1245 1750 2000 86.1% chr5 - 121563921 121564167 247 browser details YourSeq 183 1560 1750 2000 98.0% chr8 - 119180199 119180389 191 browser details YourSeq 183 1560 1750 2000 98.0% chr3 - 10432318 10432508 191 browser details YourSeq 183 1142 1728 2000 93.4% chr18 - 38606801 38607421 621 browser details YourSeq 183 1560 1750 2000 96.9% chr9 + 114502463 114502652 190 browser details YourSeq 183 1560 1750 2000 96.9% chr6 + 113175930 113176119 190 browser details YourSeq 183 1559 1750 2000 98.0% chr11 + 49810673 49810866 194 browser details YourSeq 182 1563 1750 2000 98.5% chr4 + 132798935 132799122 188 browser details YourSeq 182 1562 1750 2000 96.8% chr3 + 88154076 88154262 187 browser details YourSeq 182 1560 1750 2000 98.0% chr18 + 56582308 56582502 195 Note: The 2000 bp section upstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 2000 1 2000 2000 100.0% chr18 + 36791128 36793127 2000 browser details YourSeq 727 1 921 2000 89.9% chrX + 59197642 59198576 935 browser details YourSeq 79 707 908 2000 76.2% chr13 - 90953566 90953730 165 browser details YourSeq 71 742 867 2000 77.8% chr6 - 82299498 82299616 119 browser details YourSeq 64 745 908 2000 87.1% chr19 - 45195626 45195790 165 browser details YourSeq 60 708 1298 2000 65.8% chr19 + 58136336 58136518 183 browser details YourSeq 58 703 808 2000 86.3% chr1 - 178428123 178428584 462 browser details YourSeq 57 700 839 2000 80.5% chr6 - 38170533 38170671 139 browser details YourSeq 57 703 809 2000 78.7% chr19 - 8842446 8842550 105 browser details YourSeq 57 742 1756 2000 78.8% chr12 + 3632409 3875906 243498 browser details YourSeq 56 686 809 2000 93.8% chr5 + 144048282 144048406 125 browser details YourSeq 56 741 838 2000 87.0% chr15 + 94574163 94574259 97 browser details YourSeq 56 789 1240 2000 75.8% chr1 + 180627564 180627987 424 browser details YourSeq 55 703 843 2000 91.9% chr3 - 54594096 54594235 140 browser details YourSeq 53 700 851 2000 65.3% chr4 - 122906532 122906631 100 browser details YourSeq 53 704 806 2000 75.8% chr13 - 92687925 92688027 103 browser details YourSeq 53 1470 1767 2000 66.7% chr17 + 35689357 35689440 84 browser details YourSeq 53 700 809 2000 96.7% chr11 + 31812810 31812919 110 browser details YourSeq 52 605 841 2000 94.9% chr1 - 37793615 37794183 569 browser details YourSeq 52 734 808 2000 92.0% chr5 + 25718962 25719037 76 Note: The 2000 bp section downstream of stop codon is BLAT searched against the genome. No significant similarity is found. Page 5 of 9 https://www.alphaknockout.com Gene and protein information: Hars2 histidyl-tRNA synthetase 2 [ Mus musculus (house mouse) ] Gene ID: 70791, updated on 12-Aug-2019 Gene summary Official Symbol Hars2 provided by MGI Official Full Name histidyl-tRNA synthetase 2 provided by MGI Primary source MGI:MGI:1918041 See related Ensembl:ENSMUSG00000019143 Gene type protein coding RefSeq status REVIEWED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as HO3; HARSR; Harsl; 4631412B19Rik Summary This gene encodes a putative member of the class II family of aminoacyl-tRNA synthetases. These enzymes play a critical Expression role in protein biosynthesis by charging tRNAs with their cognate amino acids. This protein is encoded by the nuclear genome but is likely to be imported to the mitochondrion where it is thought to catalyze the ligation of histidine to tRNA molecules. Mutations in a similar gene in human have been associated with Perrault syndrome 2 (PRLTS2). [provided by RefSeq, Mar 2015] Orthologs Ubiquitous expression in CNS E11.5 (RPKM 11.8), CNS E14 (RPKM 10.4) and 28 other tissues See more human all Genomic context Location: 18; 18 B2 See Hars2 in Genome Data Viewer Exon count: 14 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (36783202..36792562) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 18 NC_000084.5 (36942934..36952216) Chromosome 18 - NC_000084.6 Page 6 of 9 https://www.alphaknockout.com Transcript information: This gene has 7 transcripts Gene: Hars2 ENSMUSG00000019143 Description histidyl-tRNA synthetase 2 [Source:MGI Symbol;Acc:MGI:1918041] Gene Synonyms 4631412B19Rik, HARSR, HO3, Harsl Location Chromosome 18: 36,783,008-36,792,562 forward strand. GRCm38:CM001011.2 About this gene This gene has 7 transcripts (splice variants), 225 orthologues, 1 paralogue and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Hars2-206 ENSMUST00000152954.7 3336 505aa ENSMUSP00000117231.1 Protein coding CCDS29165 Q99KK9 TSL:1 GENCODE basic APPRIS P1 Hars2-201 ENSMUST00000019287.8 2002 424aa ENSMUSP00000019287.8 Protein coding CCDS84376 G5E823 TSL:1 GENCODE basic Hars2-203 ENSMUST00000131952.1 819 No protein - Retained intron - - TSL:5 Hars2-205 ENSMUST00000145876.1 772 No protein - Retained intron - - TSL:2 Hars2-202 ENSMUST00000124204.1 769 No protein - Retained intron - - TSL:1 Hars2-207 ENSMUST00000155842.1 406 No protein - Retained intron - - TSL:5 Hars2-204 ENSMUST00000134122.7 896 No protein - lncRNA - - TSL:3 Page 7 of 9 https://www.alphaknockout.com 29.55 kb Forward strand 36.78Mb 36.79Mb 36.80Mb Genes Hars2-206 >protein coding Zmat2-201 >protein coding (Comprehensive set... Hars2-204 >lncRNA Zmat2-202 >retained intron Hars2-201 >protein coding Vaultrc5-201 >misc RNA Hars2-205 >retained intron Hars2-207 >retained intron Hars2-203 >retained intron Hars2-202 >retained intron Contigs AC027740.11 > Genes < Hars-201protein coding (Comprehensive set... < Hars-204retained intron < Hars-203nonsense mediated decay Regulatory Build 36.78Mb 36.79Mb 36.80Mb Reverse strand 29.55 kb Regulation Legend CTCF Open Chromatin Promoter Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding processed transcript RNA gene Page 8 of 9 https://www.alphaknockout.com Transcript: ENSMUST00000152954 9.55 kb Forward strand Hars2-206 >protein coding ENSMUSP00000117... Low complexity (Seg) Cleavage site (Sign..
Recommended publications
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • HARS2 Gene Histidyl-Trna Synthetase 2, Mitochondrial
    HARS2 gene histidyl-tRNA synthetase 2, mitochondrial Normal Function The HARS2 gene provides instructions for making an enzyme called mitochondrial histidyl-tRNA synthetase. This enzyme is important in the production (synthesis) of proteins in cellular structures called mitochondria, the energy-producing centers in cells. While most protein synthesis occurs in the fluid surrounding the nucleus (cytoplasm), some proteins are synthesized in the mitochondria. During protein synthesis, in either the mitochondria or the cytoplasm, a type of RNA called transfer RNA (tRNA) helps assemble protein building blocks (amino acids) into a chain that forms the protein. Each tRNA carries a specific amino acid to the growing chain. Enzymes called aminoacyl-tRNA synthetases, including mitochondrial histidyl- tRNA synthetase, attach a particular amino acid to a specific tRNA. Mitochondrial histidyl-tRNA synthetase attaches the amino acid histidine to the correct tRNA, which helps ensure that histidine is added at the proper place in the mitochondrial protein. Health Conditions Related to Genetic Changes Perrault syndrome At least two mutations in the HARS2 gene have been found to cause Perrault syndrome. This rare condition is characterized by hearing loss in males and females with the disorder and abnormalities of the ovaries in affected females. The HARS2 gene mutations involved in Perrault syndrome reduce the activity of mitochondrial histidyl- tRNA synthetase. A shortage of functional mitochondrial histidyl-tRNA synthetase prevents the normal assembly of new proteins within mitochondria. Researchers speculate that impaired protein assembly disrupts mitochondrial energy production. However, it is unclear exactly how HARS2 gene mutations lead to hearing problems and ovarian abnormalities in affected individuals.
    [Show full text]
  • Aminoacyl-Trna Synthetase Deficiencies in Search of Common Themes
    © American College of Medical Genetics and Genomics ARTICLE Aminoacyl-tRNA synthetase deficiencies in search of common themes Sabine A. Fuchs, MD, PhD1, Imre F. Schene, MD1, Gautam Kok, BSc1, Jurriaan M. Jansen, MSc1, Peter G. J. Nikkels, MD, PhD2, Koen L. I. van Gassen, PhD3, Suzanne W. J. Terheggen-Lagro, MD, PhD4, Saskia N. van der Crabben, MD, PhD5, Sanne E. Hoeks, MD6, Laetitia E. M. Niers, MD, PhD7, Nicole I. Wolf, MD, PhD8, Maaike C. de Vries, MD9, David A. Koolen, MD, PhD10, Roderick H. J. Houwen, MD, PhD11, Margot F. Mulder, MD, PhD12 and Peter M. van Hasselt, MD, PhD1 Purpose: Pathogenic variations in genes encoding aminoacyl- with unreported compound heterozygous pathogenic variations in tRNA synthetases (ARSs) are increasingly associated with human IARS, LARS, KARS, and QARS extended the common phenotype disease. Clinical features of autosomal recessive ARS deficiencies with lung disease, hypoalbuminemia, anemia, and renal tubulo- appear very diverse and without apparent logic. We searched for pathy. common clinical patterns to improve disease recognition, insight Conclusion: We propose a common clinical phenotype for recessive into pathophysiology, and clinical care. ARS deficiencies, resulting from insufficient aminoacylation activity Methods: Symptoms were analyzed in all patients with recessive to meet translational demand in specific organs or periods of life. ARS deficiencies reported in literature, supplemented with Assuming residual ARS activity, adequate protein/amino acid supply unreported patients evaluated in our hospital. seems essential instead of the traditional replacement of protein by Results: In literature, we identified 107 patients with AARS, glucose in patients with metabolic diseases. DARS, GARS, HARS, IARS, KARS, LARS, MARS, RARS, SARS, VARS, YARS, and QARS deficiencies.
    [Show full text]
  • AUCTSP: an Improved Biomarker Gene Pair Class Predictor Dimitri Kagaris1* , Alireza Khamesipour1 and Constantin T
    Kagaris et al. BMC Bioinformatics (2018) 19:244 https://doi.org/10.1186/s12859-018-2231-1 RESEARCH ARTICLE Open Access AUCTSP: an improved biomarker gene pair class predictor Dimitri Kagaris1* , Alireza Khamesipour1 and Constantin T. Yiannoutsos2 Abstract Background: The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule for classification and class prediction of gene expression profiles. The idea that differences in gene expression ranking are associated with presence or absence of disease is compelling and has strong biological plausibility. Nevertheless, the TSP formulation ignores significant available information which can improve classification accuracy and is vulnerable to selecting genes which do not have differential expression in the two conditions (“pivot" genes). Results: We introduce the AUCTSP classifier as an alternative rank-based estimator of the magnitude of the ranking reversals involved in the original TSP. The proposed estimator is based on the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) and as such, takes into account the separation of the entire distribution of gene expression levels in gene pairs under the conditions considered, as opposed to comparing gene rankings within individual subjects as in the original TSP formulation. Through extensive simulations and case studies involving classification in ovarian, leukemia, colon, breast and prostate cancers and diffuse large b-cell lymphoma, we show the superiority of the proposed approach in terms of improving classification accuracy, avoiding overfitting and being less prone to selecting non-informative (pivot) genes.
    [Show full text]
  • The Genetic Architecture of the Human Thalamus and Its Overlap with Ten
    ARTICLE https://doi.org/10.1038/s41467-021-23175-z OPEN The genetic architecture of the human thalamus and its overlap with ten common brain disorders ✉ Torbjørn Elvsåshagen 1,2,3 , Alexey Shadrin 1,3, Oleksandr Frei1,3,4, Dennis van der Meer1,5, Shahram Bahrami1,3, Vinod Jangir Kumar6, Olav Smeland 1,3, Lars T. Westlye 1,7,8, ✉ Ole A. Andreassen 1,3,8 & Tobias Kaufmann 1,3,9 The thalamus is a vital communication hub in the center of the brain and consists of distinct 1234567890():,; nuclei critical for consciousness and higher-order cortical functions. Structural and functional thalamic alterations are involved in the pathogenesis of common brain disorders, yet the genetic architecture of the thalamus remains largely unknown. Here, using brain scans and genotype data from 30,114 individuals, we identify 55 lead single nucleotide polymorphisms (SNPs) within 42 genetic loci and 391 genes associated with volumes of the thalamus and its nuclei. In an independent validation sample (n = 5173) 53 out of the 55 lead SNPs of the discovery sample show the same effect direction (sign test, P = 8.6e-14). We map the genetic relationship between thalamic nuclei and 180 cerebral cortical areas and find over- lapping genetic architectures consistent with thalamocortical connectivity. Pleiotropy ana- lyses between thalamic volumes and ten psychiatric and neurological disorders reveal shared variants for all disorders. Together, these analyses identify genetic loci linked to thalamic nuclei and substantiate the emerging view of the thalamus having central roles in cortical functioning and common brain disorders. 1 NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
    [Show full text]
  • Two Novel Likely Pathogenic Variants of HARS2 Identified in a Chinese
    Yu et al. Hereditas (2020) 157:47 https://doi.org/10.1186/s41065-020-00157-7 BRIEF REPORT Open Access Two novel likely pathogenic variants of HARS2 identified in a Chinese family with sensorineural hearing loss Jing Yu1†, Wei Jiang2,3†, Li Cao1, Xiaoxue Na2,3 and Jiyun Yang2,3* Abstract Mutations in HARS2 are one of the genetic causes of Perrault syndrome, characterized by sensorineural hearing loss (SNHL) and ovarian dysfunction. Here, we identified two novel putative pathogenic variants of HARS2 in a Chinese family with sensorineural hearing loss including two affected male siblings, c.349G > A (p.Asp117Asn) and c.908 T > C (p.Leu303Pro), through targeted next-generation sequencing methods. The two affected siblings (13 and 11 years old) presented with early-onset, rapidly progressive SNHL. The affected siblings did not have any inner ear malformations or delays in gross motor development. Combined with preexisting clinical reports, Perrault syndrome may be latent in some families with non-syndromic deafness associated with HARS2 mutations. The definitive diagnosis of Perrault syndrome based on clinical features alone is a challenge in sporadic males, and preadolescent females with no signs of POI. Our findings further expanded the existing spectrum of HARS2 variants and Perrault syndrome phenotypes, which will assist in molecular diagnosis and genetic counselling of patients with HARS2 mutations. Keywords: HARS2, Perrault syndrome, Next-generation sequencing Introduction of bilateral SNHL, a mild to profound degree of hearing The HARS2 gene is mapped to chromosome 5q31.3, loss, and ovarian dysgenesis in females. When the onset contains 13 exons and spans approximately 7.9 kb.
    [Show full text]
  • Network Mining Approach to Cancer Biomarker Discovery
    NETWORK MINING APPROACH TO CANCER BIOMARKER DISCOVERY THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Praneeth Uppalapati, B.E. Graduate Program in Computer Science and Engineering The Ohio State University 2010 Thesis Committee: Dr. Kun Huang, Advisor Dr. Raghu Machiraju Copyright by Praneeth Uppalapati 2010 ABSTRACT With the rapid development of high throughput gene expression profiling technology, molecule profiling has become a powerful tool to characterize disease subtypes and discover gene signatures. Most existing gene signature discovery methods apply statistical methods to select genes whose expression values can differentiate different subject groups. However, a drawback of these approaches is that the selected genes are not functionally related and hence cannot reveal biological mechanism behind the difference in the patient groups. Gene co-expression network analysis can be used to mine functionally related sets of genes that can be marked as potential biomarkers through survival analysis. We present an efficient heuristic algorithm EigenCut that exploits the properties of gene co- expression networks to mine functionally related and dense modules of genes. We apply this method to brain tumor (Glioblastoma Multiforme) study to obtain functionally related clusters. If functional groups of genes with predictive power on patient prognosis can be identified, insights on the mechanisms related to metastasis in GBM can be obtained and better therapeutical plan can be developed. We predicted potential biomarkers by dividing the patients into two groups based on their expression profiles over the genes in the clusters and comparing their survival outcome through survival analysis.
    [Show full text]
  • RNA Granules in the Mitochondria and Their Organization Under Mitochondrial Stresses
    International Journal of Molecular Sciences Review RNA Granules in the Mitochondria and Their Organization under Mitochondrial Stresses Vanessa Joanne Xavier and Jean-Claude Martinou * Department of Cell Biology, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland; [email protected] * Correspondence: [email protected] Abstract: The human mitochondrial genome (mtDNA) regulates its transcription products in spe- cialised and distinct ways as compared to nuclear transcription. Thanks to its mtDNA mitochondria possess their own set of tRNAs, rRNAs and mRNAs that encode a subset of the protein subunits of the electron transport chain complexes. The RNA regulation within mitochondria is organised within specialised, membraneless, compartments of RNA-protein complexes, called the Mitochon- drial RNA Granules (MRGs). MRGs were first identified to contain nascent mRNA, complexed with many proteins involved in RNA processing and maturation and ribosome assembly. Most recently, double-stranded RNA (dsRNA) species, a hybrid of the two complementary mRNA strands, were found to form granules in the matrix of mitochondria. These RNA granules are therefore components of the mitochondrial post-transcriptional pathway and as such play an essential role in mitochondrial gene expression. Mitochondrial dysfunctions in the form of, for example, RNA processing or RNA quality control defects, or inhibition of mitochondrial fission, can cause the loss or the aberrant accumulation of these RNA granules. These findings underline the important link between mitochondrial maintenance and the efficient expression of its genome. Citation: Xavier, V.J.; Martinou, J.-C. RNA Granules in the Mitochondria Keywords: mitochondrial RNA granules (MRGs); dsRNA; degradosome; nucleoids; mitochondrial and Their Organization under gene expression; RNA processing; RNA degradation; liquid–liquid phase separation (LLPS) Mitochondrial Stresses.
    [Show full text]
  • New Fusion Transcripts Identified in Normal Karyotype Acute Myeloid Leukemia
    University of Nebraska Medical Center DigitalCommons@UNMC Journal Articles: Genetics, Cell Biology & Anatomy Genetics, Cell Biology & Anatomy 12-2012 New fusion transcripts identified in normal karyotype acute myeloid leukemia Hongxiu Wen University of Nebraska Medical Center Yongjin Li University of Texas at Dallas Sami N. Malek University of Michigan - Ann Arbor Yeong C. Kim University of Nebraska Medical Center, [email protected] Jia Xu Shandong University FSeeollow next this page and for additional additional works authors at: https:/ /digitalcommons.unmc.edu/com_gcba_articles Part of the Medical Anatomy Commons, Medical Cell Biology Commons, and the Medical Genetics Commons Recommended Citation Wen, Hongxiu; Li, Yongjin; Malek, Sami N.; Kim, Yeong C.; Xu, Jia; Xian Chen, Pei; Xiao, Fengxia; Huang, Xin; Zhou, Xianzheng; Xuan, Zhenyu; Mankala, Shiva; Hou, Guihua; Rowley, Janet D.; Zhang, Michael Q.; and Ming Wang, San, "New fusion transcripts identified in normal karyotype acute myeloid leukemia" (2012). Journal Articles: Genetics, Cell Biology & Anatomy. 4. https://digitalcommons.unmc.edu/com_gcba_articles/4 This Article is brought to you for free and open access by the Genetics, Cell Biology & Anatomy at DigitalCommons@UNMC. It has been accepted for inclusion in Journal Articles: Genetics, Cell Biology & Anatomy by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. Authors Hongxiu Wen, Yongjin Li, Sami N. Malek, Yeong C. Kim, Jia Xu, Pei Xian Chen, Fengxia Xiao, Xin Huang, Xianzheng Zhou, Zhenyu Xuan, Shiva Mankala, Guihua Hou, Janet D. Rowley, Michael Q. Zhang, and San Ming Wang This article is available at DigitalCommons@UNMC: https://digitalcommons.unmc.edu/com_gcba_articles/4 New Fusion Transcripts Identified in Normal Karyotype Acute Myeloid Leukemia Hongxiu Wen1., Yongjin Li2., Sami N.
    [Show full text]
  • Intron Retention and Nuclear Loss of SFPQ Are Molecular Hallmarks of ALS
    ARTICLE DOI: 10.1038/s41467-018-04373-8 OPEN Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS Raphaelle Luisier1, Giulia E. Tyzack 1,2, Claire E. Hall2, Jamie S. Mitchell2, Helen Devine2,3, Doaa M. Taha2, Bilal Malik3, Ione Meyer3, Linda Greensmith3, Jia Newcombe4, Jernej Ule1,2, Nicholas M. Luscombe 1,5,6 & Rickie Patani1,2 Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate ubiquitously 1234567890():,; expressed regulators of RNA processing. To understand the molecular impact of ALS-causing mutations on neuronal development and disease, we analysed transcriptomes during in vitro differentiation of motor neurons (MNs) from human control and patient-specific VCP mutant induced-pluripotent stem cells (iPSCs). We identify increased intron retention (IR) as a dominant feature of the splicing programme during early neural differentiation. Importantly, IR occurs prematurely in VCP mutant cultures compared with control counterparts. These aberrant IR events are also seen in independent RNAseq data sets from SOD1- and FUS- mutant MNs. The most significant IR is seen in the SFPQ transcript. The SFPQ protein binds extensively to its retained intron, exhibits lower nuclear abundance in VCP mutant cultures and is lost from nuclei of MNs in mouse models and human sporadic ALS. Collectively, we demonstrate SFPQ IR and nuclear loss as molecular hallmarks of familial and sporadic ALS. 1 The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. 2 Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK. 3 Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
    [Show full text]
  • Broadening the Phenotype of the TWNK Gene Associated Perrault
    Fekete et al. BMC Medical Genetics (2019) 20:198 https://doi.org/10.1186/s12881-019-0934-4 CASE REPORT Open Access Broadening the phenotype of the TWNK gene associated Perrault syndrome Bálint Fekete1* , Klára Pentelényi1, Gabor Rudas2, Anikó Gál1, Zoltán Grosz1, Anett Illés1, Jimoh Idris1, Gabor Csukly3, Andor Domonkos4 and Maria Judit Molnar1 Abstract Background: Perrault syndrome is a genetically heterogenous, very rare disease, characterized clinically by sensorineural hearing loss, ovarian dysfunction and neurological symptoms. We present the case of a 33 years old female patient with TWNK-associated Perrault syndrome. The TWNK gene is coding the mitochondrial protein Twinkle and currently there are only two reports characterizing the phenotype of TWNK-associated Perrault syndrome. None of these publications reported about special brain MRI alterations and neuropathological changes in the muscle and peripheral nerves. Case presentation: Our patients with TWNK-dependent Perrault syndrome had severe bilateral hypoacusis, severe ataxia, polyneuropathy, lower limb spastic paraparesis with pyramidal signs, and gonadal dysgenesis. Psychiatric symptoms such as depression and paranoia were present as well. Brain MRI observed progressive cerebellar hyperintensive signs associated with cerebellar, medulla oblongata and cervical spinal cord atrophy. Light microscopy of the muscle biopsy detected severe neurogenic lesions. COX staining was centrally reduced in many muscle fibers. Both muscle and sural nerve electron microscopy detected slightly enlarged mitochondria with abnormal cristae surrounded by lipid vacuoles. In the sural nerve, dystrophic axons had focally uncompacted myelin lamellae present. Genetic investigation revealed multiple mtDNA deletion and compound heterozygous mutations of the TWNK gene (c.1196 A > G, c.1358 G > A).
    [Show full text]
  • HARS2 Antibody (N-Term) Blocking Peptide Synthetic Peptide Catalog # Bp7584a
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 HARS2 Antibody (N-term) Blocking Peptide Synthetic peptide Catalog # BP7584a Specification HARS2 Antibody (N-term) Blocking HARS2 Antibody (N-term) Blocking Peptide - Peptide - Background Product Information HARS2 is an enzyme belonging to the class II Primary Accession P49590 family of aminoacyl-tRNA synthetases. Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate HARS2 Antibody (N-term) Blocking Peptide - Additional Information amino acids. Functioning in the synthesis of histidyl-transfer RNA, this enzyme plays an accessory role in the regulation of protein Gene ID 23438 biosynthesis. Other Names HARS2 Antibody (N-term) Blocking Probable histidine--tRNA ligase, Peptide - References mitochondrial, Histidine--tRNA ligase-like, Histidyl-tRNA synthetase, HisRS, HARS2, Freist,W., Biol. Chem. 380 (6), 623-646 HARSL, HARSR, HO3 (1999)O'Hanlon,T.P., Biochem. Biophys. Res. Target/Specificity Commun. 210 (2), 556-566 The synthetic peptide sequence used to (1995)Tsui,H.W.,Gene 131 (2), 201-208 (1993) generate the antibody <a href=/products/AP7584a>AP7584a</a> was selected from the N-term region of human HARS2. A 10 to 100 fold molar excess to antibody is recommended. Precise conditions should be optimized for a particular assay. Format Peptides are lyophilized in a solid powder format. Peptides can be reconstituted in solution using the appropriate buffer as needed. Storage Maintain refrigerated at 2-8°C for up to 6 months. For long term storage store at -20°C. Precautions This product is for research use only.
    [Show full text]