DOCSLIB.ORG

Mouse Ythdf3 Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Ythdf3 Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Ythdf3 Knockout Project (CRISPR/Cas9) Objective: To create a Ythdf3 knockout Mouse model (C57BL/6N) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ythdf3 gene (NCBI Reference Sequence: NM_172677 ; Ensembl: ENSMUSG00000047213 ) is located on Mouse chromosome 3. 6 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 6 (Transcript: ENSMUST00000108346). Exon 3 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 3 starts from about 2.8% of the coding region. Exon 3 covers 4.81% of the coding region. The size of effective KO region: ~86 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 6 Legends Exon of mouse Ythdf3 Knockout region Page 2 of 8 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 3 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. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of Exon 3 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 8 https://www.alphaknockout.com Overview of the GC Content Distribution (up) Window size: 300 bp Sequence 12 Summary: Full Length(2000bp) | A(28.95% 579) | C(15.85% 317) | T(36.9% 738) | G(18.3% 366) Note: The 2000 bp section upstream of Exon 3 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(32.0% 640) | C(12.2% 244) | T(37.2% 744) | G(18.6% 372) Note: The 2000 bp section downstream of Exon 3 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 8 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% chr3 + 16187479 16189478 2000 browser details YourSeq 24 1538 1565 2000 92.9% chr2 + 28874005 28874032 28 Note: The 2000 bp section upstream of Exon 3 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% chr3 + 16189565 16191564 2000 browser details YourSeq 44 1484 1643 2000 90.8% chr12 - 70074423 70074582 160 browser details YourSeq 44 1489 1645 2000 90.8% chr18 + 60765739 60765921 183 browser details YourSeq 43 1474 1646 2000 90.4% chr11 + 97538307 97538492 186 browser details YourSeq 38 1577 1646 2000 80.7% chr9 + 110000911 110000981 71 browser details YourSeq 36 1595 1650 2000 87.8% chrX - 77006280 77006337 58 browser details YourSeq 35 1598 1645 2000 92.7% chr13 + 9364423 9364471 49 browser details YourSeq 32 1615 1652 2000 86.5% chr17 + 48053936 48053972 37 browser details YourSeq 28 851 891 2000 96.7% chr3 + 7669146 7669186 41 browser details YourSeq 28 1615 1648 2000 91.2% chr14 + 101850605 101850638 34 browser details YourSeq 27 1615 1645 2000 93.6% chr7 - 117678861 117678891 31 browser details YourSeq 27 1615 1643 2000 96.6% chr14 - 20800081 20800109 29 browser details YourSeq 27 1615 1645 2000 93.6% chr12 - 86670861 86670891 31 browser details YourSeq 27 1616 1648 2000 91.0% chr18 + 60798324 60798356 33 browser details YourSeq 27 1598 1631 2000 96.6% chr18 + 34082325 34082359 35 browser details YourSeq 27 1615 1645 2000 93.6% chr10 + 29336071 29336101 31 browser details YourSeq 27 1500 1536 2000 96.6% chr10 + 28079433 28079470 38 browser details YourSeq 26 1615 1646 2000 90.7% chr19 - 31157581 31157612 32 browser details YourSeq 26 1615 1646 2000 90.7% chr11 - 117403615 117403646 32 browser details YourSeq 26 1615 1646 2000 90.7% chr16 + 29852840 29852871 32 Note: The 2000 bp section downstream of Exon 3 is BLAT searched against the genome. No significant similarity is found. Page 5 of 8 https://www.alphaknockout.com Gene and protein information: Ythdf3 YTH N6-methyladenosine RNA binding protein 3 [ Mus musculus (house mouse) ] Gene ID: 229096, updated on 27-Aug-2019 Gene summary Official Symbol Ythdf3 provided by MGI Official Full Name YTH N6-methyladenosine RNA binding protein 3 provided by MGI Primary source MGI:MGI:1918850 See related Ensembl:ENSMUSG00000047213 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as 9130022A11Rik Expression Ubiquitous expression in CNS E11.5 (RPKM 17.9), limb E14.5 (RPKM 16.0) and 28 other tissues See more Orthologs human all Genomic context Location: 3; 3 A1 See Ythdf3 in Genome Data Viewer Exon count: 7 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (16183148..16217037) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (16083183..16117037) Chromosome 3 - NC_000069.6 Page 6 of 8 https://www.alphaknockout.com Transcript information: This gene has 4 transcripts Gene: Ythdf3 ENSMUSG00000047213 Description YTH N6-methyladenosine RNA binding protein 3 [Source:MGI Symbol;Acc:MGI:1918850] Gene Synonyms 9130022A11Rik Location Chromosome 3: 16,183,212-16,217,037 forward strand. GRCm38:CM000996.2 About this gene This gene has 4 transcripts (splice variants), 199 orthologues, 3 paralogues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Ythdf3-201 ENSMUST00000108345.8 5102 585aa ENSMUSP00000103982.2 Protein coding CCDS50869 Q8BYK6 TSL:1 GENCODE basic APPRIS P1 Ythdf3-202 ENSMUST00000108346.4 4929 596aa ENSMUSP00000103983.2 Protein coding CCDS38396 Q8BYK6 TSL:1 GENCODE basic Ythdf3-203 ENSMUST00000191774.5 3196 589aa ENSMUSP00000141610.1 Protein coding - Q8BYK6 TSL:1 GENCODE basic Ythdf3-204 ENSMUST00000193598.4 723 No protein - lncRNA - - TSL:5 53.83 kb Forward strand 16.18Mb 16.19Mb 16.20Mb 16.21Mb 16.22Mb Genes (Comprehensive set... Ythdf3-201 >protein coding Ythdf3-202 >protein coding Ythdf3-203 >protein coding Ythdf3-204 >lncRNA Contigs AC122053.3 > Regulatory Build 16.18Mb 16.19Mb 16.20Mb 16.21Mb 16.22Mb Reverse strand 53.83 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding merged Ensembl/Havana Ensembl protein coding Non-Protein Coding RNA gene Page 7 of 8 https://www.alphaknockout.com Transcript: ENSMUST00000108346 33.62 kb Forward strand Ythdf3-202 >protein coding ENSMUSP00000103... MobiDB lite Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF81995 Pfam YTH domain PROSITE profiles YTH domain PANTHER PTHR12357 PTHR12357:SF9 Gene3D 3.10.590.10 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 60 120 180 240 300 360 420 480 596 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 8 of 8.
Load more

Recommended publications
  • 'Next- Generation' Sequencing Data Analysis
    Novel Algorithm Development for ‘Next- Generation’ Sequencing Data Analysis Agne Antanaviciute Submitted in accordance with the requirements for the degree of Doctor of Philosophy University of Leeds School of Medicine Leeds Institute of Biomedical and Clinical Sciences 12/2017 ii The candidate confirms that the work submitted is her own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly given within the thesis where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement ©2017 The University of Leeds and Agne Antanaviciute The right of Agne Antanaviciute to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. Acknowledgements I would like to thank all the people who have contributed to this work. First and foremost, my supervisors Dr Ian Carr, Professor David Bonthron and Dr Christopher Watson, who have provided guidance, support and motivation. I could not have asked for a better supervisory team. I would also like to thank my collaborators Dr Belinda Baquero and Professor Adrian Whitehouse for opening new, interesting research avenues. A special thanks to Dr Belinda Baquero for all the hard wet lab work without which at least half of this thesis would not exist. Thanks to everyone at the NGS Facility – Carolina Lascelles, Catherine Daley, Sally Harrison, Ummey Hany and Laura Crinnion – for the generation of NGS data used in this work and creating a supportive and stimulating work environment.
    [Show full text]
  • 1 Supplemental Methods 4Su RNA Isolation Cells Were Incubated In
    Supplemental Methods 4sU RNA isolation Cells were incubated in 500uM 4-thiouridine for 2.5 mins before RNA extraction using Trizol. 15-20ug RNA was biotinylated in a volume of 250μl containing 10mM HEPES (pH7.5), 5ug MTSEA Biotin-XX (Iris Biotech, dissolved in dimethyl formamide). After incubation in the dark for 90 mins, biotinylated RNA was chloroform extracted, phenol chloroform extracted and ethanol precipitated. It was re-suspended in RPB (300mM NaCl, 10mM Tris pH7.5, 5mM EDTA) and incubated with 50ul streptavidin-coated magnetic beads (Miltenyi Biotech) for 15 mins. Beads were washed 5x in (100 mM Tris-HCl pH 7.4, 10 mM EDTA, 1 M NaCl, and 0.1% Tween-20) pre-heated to 60oC. RNA was eluted in 100μl of 0.1M DTT for 15 mins at 37oC before final phenol chloroform extraction and ethanol precipitation. Metaprofiling of effects of XRN2 vs CPSF73 depletion (Figure 2A) Single-end 50-base-pair (bp) reads were screened for sequencing quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc); adapter sequences were then removed using Trim Galore using the default settings (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). Trimmed reads passing QC steps were aligned to the GRCh38 (Ensembl) human genome using Hisat2 with default parameters, incorporating known splice sites (Kim et al. 2015). Unmapped, multi-mapped and reads with low mapping quality scores (MAPQ <20) were discarded using SAMtools (Li et al. 2009). For metagene analysis, expressed protein-coding genes (>50 reads per gene) were selected and a window extending 20 kb downstream from the transcription end site (TES) was applied.
    [Show full text]
  • Rna Methylation As a New Epigenetic Regulatory
    THE UNIVERSITY OF CHICAGO THE EXUBERANT VINE OF EPITRANSCRIPTOME: RNA METHYLATION AS A NEW EPIGENETIC REGULATORY MECHANISM A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE PHYSICAL SCIENCES IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF CHEMISTRY BY BOXUAN ZHAO CHICAGO, ILLINOIS AUGUST 2017 Table of Contents List of Figures ..................................................................................................................................v Acknowledgement ....................................................................................................................... viii Abstract .......................................................................................................................................... xi List of Publications ....................................................................................................................... xii Chapter 1 Introduction: RNA Modifications and Epitranscriptomics ................................. 1 1.1 Genetics and epigenetics: beyond the primary sequence .....................................................1 1.2 Epigenetic regulation of chromatin structure: histone and DNA modifications ..................2 1.3 Emergence of RNA epigenetics: chemical modifications on RNA .....................................4 1.4 N6-methyladenosine (m6A): the protagonist of epitranscriptomics ....................................7 1.5 Scope of this dissertation ...................................................................................................10
    [Show full text]
  • Comprehensive Analysis of YTH Domain Family in Lung Adenocarcinoma: Expression Profile, Association with Prognostic Value, and Immune Infiltration
    Hindawi Disease Markers Volume 2021, Article ID 2789481, 12 pages https://doi.org/10.1155/2021/2789481 Research Article Comprehensive Analysis of YTH Domain Family in Lung Adenocarcinoma: Expression Profile, Association with Prognostic Value, and Immune Infiltration Kuan Hu ,1 Lei Yao ,1 Yuanliang Yan ,2,3 Lei Zhou ,4 and Juanni Li 5 1Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China 2Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China 3National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China 4Department of Anesthesiology, Third Xiangya Hospital of Central South University, Changsha, 410008 Hunan, China 5Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China Correspondence should be addressed to Juanni Li; [email protected] Received 28 June 2021; Accepted 13 August 2021; Published 27 August 2021 Academic Editor: Cheng Zhan Copyright © 2021 Kuan Hu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. All YTH domain family members are m6A reader proteins accounting for the methylation modulation involved in the process of tumorgenesis and tumor progression. However, the expression profiles and roles of the YTH domain family in lung adenocarcinoma (LUAD) remain to be further illustrated. Methods. GEPIA2 and TNMplot databases were used to generate the expression profiles of the YTH family. Kaplan-Meier plotter database was employed to analysis the prognostic value of the YTH family. Coexpression profiles and genetic alterations analysis of the YTH family were undertaken using the cBioPortal database.
    [Show full text]
  • YTHDF3 Facilitates Translation and Decay of N6-Methyladenosine-Modified RNA
    Cell Research (2017) 27:315-328. © 2017 IBCB, SIBS, CAS All rights reserved 1001-0602/17 $ 32.00 ORIGINAL ARTICLE www.nature.com/cr YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA Hailing Shi1, 2, *, Xiao Wang1, 2, *, Zhike Lu1, 2, Boxuan S Zhao1, 2, Honghui Ma1, 2, Phillip J Hsu1, 2, 3, Chang Liu1, 2, Chuan He1, 2, 4 1Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; 2Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; 3Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA; 4Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in cell differentiation and tissue development. It regulates multiple steps throughout the RNA life cycle including RNA processing, translation, and decay, via the recognition by selective binding proteins. In the cytoplasm, m6A binding protein YTHDF1 facilitates translation of m6A-modified mRNAs, and YTHDF2 acceler- ates the decay of m6A-modified transcripts. The biological function of YTHDF3, another cytoplasmic m6A binder of the YTH (YT521-B homology) domain family, remains unknown. Here, we report that YTHDF3 promotes protein synthesis in synergy with YTHDF1, and affects methylated mRNA decay mediated through YTHDF2. Cells defi- cient in all three YTHDF proteins experience the most dramatic accumulation of m6A-modified transcripts. These results indicate that together with YTHDF1 and YTHDF2, YTHDF3 plays critical roles to accelerate metabolism of m6A-modified mRNAs in the cytoplasm.
    [Show full text]
  • 1 N 6-Methyladenosine of HIV-1 RNA Regulates Viral Infection And
    1 N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein 2 expression 3 4 Nagaraja Tirumuru1, #, Boxuan Simen Zhao2, 3, #, Wuxun Lu1, Zhike Lu2, 3, Chuan He2, 3, *, 5 Li Wu1, 4, 5, * 6 7 1 Center for Retrovirus Research, Department of Veterinary Biosciences, 4 Department of 8 Microbial Infection and Immunity, and 5 Comprehensive Cancer Center, The Ohio State 9 University, Columbus, Ohio 43210, USA. 10 11 2 Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for 12 Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA; 3 Howard 13 Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, USA. 14 15 # These authors contributed equally. 16 17 * Corresponding authors 18 LW: [email protected], Phone: (614)-292-5408 19 CH: [email protected], Phone: (773)-702-5061 20 21 Competing interests statement: The authors declare that no competing interests exist. 22 1 23 Abstract 24 25 The internal N6-methyladenosine (m6A) methylation of eukaryotic nuclear RNA controls 26 post-transcriptional gene expression, which is regulated by methyltransferases (writers), 27 demethylases (erasers), and m6A-binding proteins (readers) in cells. The YTH domain family 28 proteins (YTHDF1–3) bind to m6A-modified cellular RNAs and affect RNA metabolism and 29 processing. Here we show that YTHDF1–3 proteins recognize m6A-modified HIV-1 RNA and 30 inhibit HIV-1 infection in cell lines and primary CD4+ T-cells. We further mapped the 31 YTHDF1–3 binding sites in HIV-1 RNA from infected cells. We found that overexpression of 32 YTHDF proteins in cells inhibited HIV-1 infection mainly by decreasing HIV-1 reverse 33 transcription, while knockdown of YTHDF1–3 in cells had the opposite effects.
    [Show full text]
  • Evolution of Vertebrate Opioid Receptors
    Evolution of vertebrate opioid receptors Susanne Dreborg, Go¨ rel Sundstro¨ m, Tomas A. Larsson, and Dan Larhammar* Department of Neuroscience, Uppsala University, Box 593, SE-75124 Uppsala, Sweden Edited by Tomas Ho¨kfelt, Karolinska Institutet, Stockholm, Sweden, and approved August 15, 2008 (received for review June 9, 2008) The opioid peptides and receptors have prominent roles in pain Many vertebrate gene families have been found to have transmission and reward mechanisms in mammals. The evolution expanded in the early stages of vertebrate evolution, before the of the opioid receptors has so far been little studied, with only a radiation of jawed vertebrates. However, the high degree of few reports on species other than tetrapods. We have investigated sequence divergence over such large evolutionary distances species representing a broader range of vertebrates and found that often obscures orthology–paralogy relationships. Investigation the four opioid receptor types (delta, kappa, mu, and NOP) are of conserved synteny may facilitate identification of orthologs present in most of the species. The gene relationships were and gives important clues to the mechanisms by which the genes deduced by using both phylogenetic analyses and chromosomal were duplicated. We used this approach to investigate the location relative to 20 neighboring gene families in databases of evolution of a few other gene families, namely the neuropeptide assembled genomes. The combined results show that the verte- Y (NPY) family of peptides (27) and the large family of NPY brate opioid receptor gene family arose by quadruplication of a receptors (28). These families were found to have expanded as large chromosomal block containing at least 14 other gene fami- a result of extensive chromosome duplications, most likely lies.
    [Show full text]
  • Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
    Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein
    [Show full text]
  • C:\Users\Dweom\Desktop
    IMGC 2018 32nd International Mammalian Genome Conference 11-14 November 2018 Wyndham Grand Rio Mar Rio Grande, Puerto Rico Welcome to the 32nd International Mammalian Genome Conference Wyndham Grand Rio Mar Rio Grande, Puerto Rico November 11-14, 2018 We welcome you to the 32nd Annual Conference of the International Mammalian Genome Society and to the Wyndham Grand Rio Mar, Rio Grande, Puerto Rico. We are planning an exciting meeting with emphasis on cutting-edge research in the fields of mammalian genetics and genomics, with experts in a wide range of biology specialties participating. The meeting will begin with five Bioinformatics Workshops followed by a Student Satellite Symposium that offers the opportunity for budding scientists to compete for awards and presentation slots in the main meeting. The conference will once again include the popular mentoring lunch where those looking for career advice can interact with established scientists. The main conference will feature sessions on: • Technical Advances and Resources • Translational & Systems Genetics • Development, Epigenetics and Stem cells • Human disease models—cancer and environmental factors; infection and immunology; metabolic; neurobehavioral • Comparative Genomics, Computational Methods & Evolution Puerto Rico will captivate you with dynamic culture, rich heritage, local flavors, stunning beaches, and amazing adventures. Whether you're passionate about nature and love to explore, or you want to experience urban settings full of culture, activities and nightlife – there is something for you on this island. Enjoy the beach at the Wyndham Grand Rio Mar. Explore the Rainforest El Yunque or fall in love with Old San Juan as you become immersed in tropical colors, colonial architecture, epic fortresses, boutique and high-end shopping, and cultural events for the whole family.
    [Show full text]
  • Cytoplasmic M6a Reader YTHDF3 Promotes Mrna Translation Cell Research (2017) 27:444-447
    Cell Research (2017) 27:444-447. © 2017 IBCB, SIBS, CAS All rights reserved 1001-0602/17 $ 32.00 LETTER TO THE EDITOR www.nature.com/cr Cytoplasmic m6A reader YTHDF3 promotes mRNA translation Cell Research (2017) 27:444-447. doi:10.1038/cr.2017.10; published online 20 January 2017 Dear Editor, acted with both proteins (Figure 1A and Supplementary information, Figure S1A). We performed gene ontology N6-methyladenosine (m6A), as the most abundant in- (GO) analysis with DAVID bioinformatics database and ternal modification with ubiquitous feature in eukaryotic found that 68 proteins are enriched in functional path- mRNAs, has been connected with many fundamental ways related to translation (Figure 1B), including 23 aspects of RNA metabolism such as translation [1-3], proteins of 40S subunits and 35 proteins of 60S subunits splicing [4, 5], stability and decay [6]. m6A modifica- (Figure 1A), which is remarkable as total numbers of tion is reversible and can be regulated by three groups protein in eukaryotic 40S and 60S subunits are 33 and of molecules commonly referred to as writers, erasers 47, respectively. This result implies that YTHDF3 poten- and readers. m6A writers are the components of the tially plays a role in translation probably through ribo- multi-complex methyltransferase catalyzing the for- somal proteins. mation of m6A methylation, among which METTL3, To explore the effect of YTHDF1 and YTHDF3 on METTL14, WTAP and KIAA1429 are the key ones [7- each other’s RNA-binding affinity, we performed PAR- 11]. FTO and ALKBH5 (both belonging to AlkB family CLIP (photoactivatable ribonucleoside crosslinking and proteins) serve as the erasers of m6A modification [12, immunoprecipitation) combined with in vitro RNA-end 13].
    [Show full text]
  • Supplemental Material.Pdf
    Symmons et al. SUPPLEMENTARY INFORMATION Functional and topological characteristics of mammalian regulatory domains Orsolya Symmons 1, Veli Vural Uslu 1, Taro Tsujimura 1, Sandra Ruf 1, Sonya Nassari 1, Wibke Schwarzer 1, Laurence Ettwiller 2,# and François Spitz 1,* 1 Developmental Biology Unit – European Molecular Biology Laboratory - Meyerhofstrasse 1 - 69117 Heidelberg – Germany 2 Centre for Organismal Studies – University of Heidelberg – Germany # Present address : New England Biolabs - Ipswich – MA - United States Supplementary Figures 1-8 Supplementary Table 6 Supplementary Note - Methods 1 Symmons et al. Supplementary Figure 1 A Enrichment of insertions relative to heart EP300 sites B Enrichment of insertions relative to forebrain EP300 sites 9 9 8 8 7 7 6 6 5 5 4 4 Enrichment 3 3 Enrichment 2 2 1 1 0 0 0 200 400 600 800 1000 0 200 400 600 800 1000 distance to EP300 binding site (kb) distance to EP300 binding site (kb) C Enrichment of insertions relative to midbrain EP300 sites 12 limb 10 heartmidbrain 8 forebrain 6 midbrain negative Enrichment 4 2 0 0 200 400 600 800 1000 distance to EP300 binding site (kb) Enrichment of insertions in the proximity of EP300 sites bound in the same tissue. Enrichment of insertions with tissue-specific LacZ activity (compared to random insertions), at increasing distance (x-axis) from EP300 sites detected in heart (A), forebrain (B) and midbrain (C). Error bars represent one standard deviation from the mean. Colours indicate the tissue in which insertions were expressed (limb: green; heart: purple; forebrain: blue; midbrain: red; no LacZ activity: grey). EP300 data is taken from (Blow et al.
    [Show full text]
  • Determination of Molecular Markers for BRCA1 and BRCA2 Heterozygosity Using Gene Expression Profiling
    Published OnlineFirst January 22, 2013; DOI: 10.1158/1940-6207.CAPR-12-0105 Cancer Prevention Research Article Research Determination of Molecular Markers for BRCA1 and BRCA2 Heterozygosity Using Gene Expression Profiling Asher Y. Salmon4, Mali Salmon-Divon5, Tamar Zahavi1, Yulia Barash1, Rachel S. Levy-Drummer3, Jasmine Jacob-Hirsch2, and Tamar Peretz1 Abstract Approximately 5% of all breast cancers can be attributed to an inherited mutation in one of two cancer susceptibility genes, BRCA1 and BRCA2. We searched for genes that have the potential to distinguish healthy BRCA1 and BRCA2 mutation carriers from noncarriers based on differences in expression profiling. Using expression microarrays, we compared gene expression of irradiated lymphocytes from BRCA1 and BRCA2 mutation carriers versus control noncarriers. We identified 137 probe sets in BRCA1 carriers and 1,345 in BRCA2 carriers with differential gene expression. Gene Ontology analysis revealed that most of these genes relate to regulation pathways of DNA repair processes, cell-cycle regulation, and apoptosis. Real-time PCR was conducted on the 36 genes, which were most prominently differentially expressed in the microarray assay; 21 genes were shown to be significantly differentially expressed in BRCA1 and/or BRCA2 mutation carriers as compared with controls (P < 0.05). On the basis of a validation study with 40 mutation carriers and 17 noncarriers, a multiplex model that included six or more coincidental genes of 18 selected genes was constructed to predict the risk of carrying a mutation. The results using this model showed sensitivity 95% and specificity 88%. In summary, our study provides insight into the biologic effect of heterozygous mutations in BRCA1 and BRCA2 genes in response to ionizing irradiation-induced DNA damage.
    [Show full text]