DOCSLIB.ORG

Mouse Krt31 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Krt31 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Krt31 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Krt31 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Krt31 gene (NCBI Reference Sequence: NM_010659 ; Ensembl: ENSMUSG00000048981 ) is located on Mouse chromosome 11. 7 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 7 (Transcript: ENSMUST00000007318). Exon 4~6 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Krt31 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-351F1 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 4 starts from about 47.2% of the coding region. The knockout of Exon 4~6 will result in frameshift of the gene. The size of intron 3 for 5'-loxP site insertion: 938 bp, and the size of intron 6 for 3'-loxP site insertion: 608 bp. The size of effective cKO region: ~1333 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Homology arm Exon of mouse Krt31 cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. Tandem repeats are found in the dot plot matrix. It may be difficult to construct this targeting vector. Overview of the GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(7833bp) | A(24.77% 1940) | C(23.4% 1833) | T(29.59% 2318) | G(22.24% 1742) Note: The sequence of homologous arms and cKO region 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 3 of 7 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr11 - 100048752 100051751 3000 browser details YourSeq 611 290 2287 3000 94.0% chr11 - 100014116 100270638 256523 browser details YourSeq 512 1256 2314 3000 93.6% chr11 - 100026435 100029839 3405 browser details YourSeq 432 1285 2305 3000 96.0% chr11 - 100039994 100041481 1488 browser details YourSeq 197 1407 2314 3000 89.9% chr11 - 100086348 100087954 1607 browser details YourSeq 167 1428 2317 3000 88.9% chr11 - 100104041 100135574 31534 browser details YourSeq 131 1432 1894 3000 89.3% chr11 - 100094846 100095901 1056 browser details YourSeq 125 1432 2254 3000 79.2% chr11 - 99387556 99542897 155342 browser details YourSeq 101 2695 2845 3000 91.8% chr12 - 43964523 43964669 147 browser details YourSeq 101 2695 2836 3000 96.4% chr13 + 108431365 108431637 273 browser details YourSeq 96 2705 2857 3000 89.2% chr12 - 46130688 46130820 133 browser details YourSeq 77 2702 2792 3000 94.4% chr2 - 18646884 18646978 95 browser details YourSeq 77 2703 2792 3000 89.3% chr1 + 67879754 67879838 85 browser details YourSeq 76 2705 2800 3000 87.1% chr12 + 11515879 11515968 90 browser details YourSeq 73 2696 2785 3000 91.1% chr11 + 63251233 63251322 90 browser details YourSeq 71 2694 2812 3000 96.2% chr3 + 34193712 34193887 176 browser details YourSeq 59 2753 2840 3000 81.9% chr8 - 94131361 94131432 72 browser details YourSeq 58 2196 2285 3000 82.3% chr11 - 100142079 100142168 90 browser details YourSeq 58 2694 2762 3000 94.0% chr12 + 20454415 20454503 89 browser details YourSeq 56 2652 2729 3000 98.4% chr15 - 23372414 23372717 304 Note: The 3000 bp section upstream of Exon 4 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 3000 1 3000 3000 100.0% chr11 - 100044419 100047418 3000 browser details YourSeq 75 1090 2450 3000 87.2% chr1 - 41961140 42038600 77461 browser details YourSeq 72 2281 2507 3000 79.4% chr6 + 115710121 115710317 197 browser details YourSeq 67 2397 2520 3000 82.6% chr11 - 117023612 117023736 125 browser details YourSeq 60 2402 2489 3000 84.1% chr14 + 31450281 31450368 88 browser details YourSeq 59 2412 2525 3000 85.6% chr11 - 116823087 116823202 116 browser details YourSeq 55 2410 2492 3000 83.2% chr14 + 118329975 118330057 83 browser details YourSeq 54 2394 2493 3000 80.8% chr12 + 3712580 3712677 98 browser details YourSeq 53 2413 2492 3000 87.4% chr11 + 62115088 62115171 84 browser details YourSeq 51 2307 2481 3000 78.7% chr14 + 99845439 99845691 253 browser details YourSeq 50 2403 2488 3000 79.1% chrX + 134319001 134319086 86 browser details YourSeq 50 2410 2471 3000 90.4% chr10 + 111903220 111903281 62 browser details YourSeq 49 2349 2487 3000 77.6% chr9 + 112517005 112517143 139 browser details YourSeq 49 2478 2816 3000 87.7% chr1 + 84906494 84911779 5286 browser details YourSeq 47 1080 1131 3000 98.1% chr11 - 113191251 113191309 59 browser details YourSeq 46 2410 2491 3000 85.8% chr1 - 72124964 72125043 80 browser details YourSeq 46 2390 2454 3000 86.0% chr5 + 143121641 143121706 66 browser details YourSeq 45 2401 2491 3000 74.8% chr12 - 84357206 84357296 91 browser details YourSeq 44 2769 2835 3000 92.5% chr7 - 45130440 45130508 69 browser details YourSeq 44 2406 2495 3000 74.5% chr6 - 112977208 112977297 90 Note: The 3000 bp section downstream of Exon 6 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Krt31 keratin 31 [ Mus musculus (house mouse) ] Gene ID: 16660, updated on 12-Aug-2019 Gene summary Official Symbol Krt31 provided by MGI Official Full Name keratin 31 provided by MGI Primary source MGI:MGI:1309993 See related Ensembl:ENSMUSG00000048981 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 Ha1; Kha1; Krt1-1; MKHA-1 Expression Low expression observed in reference dataset See more Genomic context Location: 11 D; 11 63.39 cM See Krt31 in Genome Data Viewer Exon count: 7 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (100046646..100050551, complement) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (99907960..99911865, complement) Chromosome 11 - NC_000077.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 1 transcript Gene: Krt31 ENSMUSG00000048981 Description keratin 31 [Source:MGI Symbol;Acc:MGI:1309993] Gene Synonyms Ha1, Kha1, Krt1-1, MKHA-1 Location Chromosome 11: 100,046,646-100,050,551 reverse strand. GRCm38:CM001004.2 About this gene This gene has 1 transcript (splice variant), 177 orthologues, 68 paralogues, is a member of 1 Ensembl protein family and is associated with 2 phenotypes. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Krt31-201 ENSMUST00000007318.1 1581 416aa ENSMUSP00000007318.1 Protein coding CCDS25405 Q61765 TSL:1 GENCODE basic APPRIS P1 23.91 kb Forward strand 100.04Mb 100.05Mb 100.06Mb Genes Gm11571-201 >lncRNA (Comprehensive set... Contigs AL592545.10 > Genes (Comprehensive set... < Krt34-201protein coding < Krt31-201protein coding Regulatory Build 100.04Mb 100.05Mb 100.06Mb Reverse strand 23.91 kb Regulation Legend CTCF Open Chromatin Promoter Flank Gene Legend Protein Coding merged Ensembl/Havana Non-Protein Coding RNA gene Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000007318 < Krt31-201protein coding Reverse strand 3.91 kb ENSMUSP00000007... Low complexity (Seg) Coiled-coils (Ncoils) Superfamily SSF64593 SSF46579 SMART Intermediate filament, rod domain Prints Keratin, type I Pfam Intermediate filament, rod domain PROSITE profiles Intermediate filament, rod domain PROSITE patterns Intermediate filament protein, conserved site PANTHER Keratin, type I PTHR23239:SF224 Gene3D 1.20.5.500 1.20.5.170 Intermediate filament, rod domain, coil 1B All sequence SNPs/i... Sequence variants (dbSNP and all other sources) Variant Legend missense variant synonymous variant Scale bar 0 40 80 120 160 200 240 280 320 360 416 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
Load more

Recommended publications
  • Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S
    www.nature.com/scientificreports OPEN Studies on the Proteome of Human Hair - Identifcation of Histones and Deamidated Keratins Received: 15 August 2017 Sunil S. Adav 1, Roopa S. Subbaiaih2, Swat Kim Kerk 2, Amelia Yilin Lee 2,3, Hui Ying Lai3,4, Accepted: 12 January 2018 Kee Woei Ng3,4,7, Siu Kwan Sze 1 & Artur Schmidtchen2,5,6 Published: xx xx xxxx Human hair is laminar-fbrous tissue and an evolutionarily old keratinization product of follicle trichocytes. Studies on the hair proteome can give new insights into hair function and lead to the development of novel biomarkers for hair in health and disease. Human hair proteins were extracted by detergent and detergent-free techniques. We adopted a shotgun proteomics approach, which demonstrated a large extractability and variety of hair proteins after detergent extraction. We found an enrichment of keratin, keratin-associated proteins (KAPs), and intermediate flament proteins, which were part of protein networks associated with response to stress, innate immunity, epidermis development, and the hair cycle. Our analysis also revealed a signifcant deamidation of keratin type I and II, and KAPs. The hair shafts were found to contain several types of histones, which are well known to exert antimicrobial activity. Analysis of the hair proteome, particularly its composition, protein abundances, deamidated hair proteins, and modifcation sites, may ofer a novel approach to explore potential biomarkers of hair health quality, hair diseases, and aging. Hair is an important and evolutionarily conserved structure. It originates from hair follicles deep within the der- mis and is mainly composed of hair keratins and KAPs, which form a complex network that contributes to the rigidity and mechanical properties.
    [Show full text]
  • Structural and Biochemical Changes Underlying a Keratoderma-Like Phenotype in Mice Lacking Suprabasal AP1 Transcription Factor Function
    Citation: Cell Death and Disease (2015) 6, e1647; doi:10.1038/cddis.2015.21 OPEN & 2015 Macmillan Publishers Limited All rights reserved 2041-4889/15 www.nature.com/cddis Structural and biochemical changes underlying a keratoderma-like phenotype in mice lacking suprabasal AP1 transcription factor function EA Rorke*,1, G Adhikary2, CA Young2, RH Rice3, PM Elias4, D Crumrine4, J Meyer4, M Blumenberg5 and RL Eckert2,6,7,8 Epidermal keratinocyte differentiation on the body surface is a carefully choreographed process that leads to assembly of a barrier that is essential for life. Perturbation of keratinocyte differentiation leads to disease. Activator protein 1 (AP1) transcription factors are key controllers of this process. We have shown that inhibiting AP1 transcription factor activity in the suprabasal murine epidermis, by expression of dominant-negative c-jun (TAM67), produces a phenotype type that resembles human keratoderma. However, little is understood regarding the structural and molecular changes that drive this phenotype. In the present study we show that TAM67-positive epidermis displays altered cornified envelope, filaggrin-type keratohyalin granule, keratin filament, desmosome formation and lamellar body secretion leading to reduced barrier integrity. To understand the molecular changes underlying this process, we performed proteomic and RNA array analysis. Proteomic study of the corneocyte cross-linked proteome reveals a reduction in incorporation of cutaneous keratins, filaggrin, filaggrin2, late cornified envelope precursor proteins, hair keratins and hair keratin-associated proteins. This is coupled with increased incorporation of desmosome linker, small proline-rich, S100, transglutaminase and inflammation-associated proteins. Incorporation of most cutaneous keratins (Krt1, Krt5 and Krt10) is reduced, but incorporation of hyperproliferation-associated epidermal keratins (Krt6a, Krt6b and Krt16) is increased.
    [Show full text]
  • The Correlation of Keratin Expression with In-Vitro Epithelial Cell Line Differentiation
    The correlation of keratin expression with in-vitro epithelial cell line differentiation Deeqo Aden Thesis submitted to the University of London for Degree of Master of Philosophy (MPhil) Supervisors: Professor Ian. C. Mackenzie Professor Farida Fortune Centre for Clinical and Diagnostic Oral Science Barts and The London School of Medicine and Dentistry Queen Mary, University of London 2009 Contents Content pages ……………………………………………………………………......2 Abstract………………………………………………………………………….........6 Acknowledgements and Declaration……………………………………………...…7 List of Figures…………………………………………………………………………8 List of Tables………………………………………………………………………...12 Abbreviations….………………………………………………………………..…...14 Chapter 1: Literature review 16 1.1 Structure and function of the Oral Mucosa……………..…………….…..............17 1.2 Maintenance of the oral cavity...……………………………………….................20 1.2.1 Environmental Factors which damage the Oral Mucosa………. ….…………..21 1.3 Structure and function of the Oral Mucosa ………………...….……….………...21 1.3.1 Skin Barrier Formation………………………………………………….……...22 1.4 Comparison of Oral Mucosa and Skin…………………………………….……...24 1.5 Developmental and Experimental Models used in Oral mucosa and Skin...……..28 1.6 Keratinocytes…………………………………………………….….....................29 1.6.1 Desmosomes…………………………………………….…...............................29 1.6.2 Hemidesmosomes……………………………………….…...............................30 1.6.3 Tight Junctions………………………….……………….…...............................32 1.6.4 Gap Junctions………………………….……………….….................................32
    [Show full text]
  • MALE Protein Name Accession Number Molecular Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean H Mean PDAC Mean T-Test PDAC Vs. H T-Test
    MALE t-test t-test Accession Molecular H PDAC PDAC vs. PDAC vs. Protein Name Number Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean Mean Mean H CP PDAC/H PDAC/CP - 22 kDa protein IPI00219910 22 kDa 7 5 4 8 1 0 6 6 1 0.1126 0.0456 0.1 0.1 - Cold agglutinin FS-1 L-chain (Fragment) IPI00827773 12 kDa 32 39 34 26 53 57 36 30 55 0.0309 0.0388 1.8 1.5 - HRV Fab 027-VL (Fragment) IPI00827643 12 kDa 4 6 0 0 0 0 5 0 0 - 0.0574 - 0.0 - REV25-2 (Fragment) IPI00816794 15 kDa 8 12 5 7 8 9 10 6 8 0.2225 0.3844 1.3 0.8 A1BG Alpha-1B-glycoprotein precursor IPI00022895 54 kDa 115 109 106 112 111 100 112 109 105 0.6497 0.4138 1.0 0.9 A2M Alpha-2-macroglobulin precursor IPI00478003 163 kDa 62 63 86 72 14 18 63 79 16 0.0120 0.0019 0.2 0.3 ABCB1 Multidrug resistance protein 1 IPI00027481 141 kDa 41 46 23 26 52 64 43 25 58 0.0355 0.1660 2.4 1.3 ABHD14B Isoform 1 of Abhydrolase domain-containing proteinIPI00063827 14B 22 kDa 19 15 19 17 15 9 17 18 12 0.2502 0.3306 0.7 0.7 ABP1 Isoform 1 of Amiloride-sensitive amine oxidase [copper-containing]IPI00020982 precursor85 kDa 1 5 8 8 0 0 3 8 0 0.0001 0.2445 0.0 0.0 ACAN aggrecan isoform 2 precursor IPI00027377 250 kDa 38 30 17 28 34 24 34 22 29 0.4877 0.5109 1.3 0.8 ACE Isoform Somatic-1 of Angiotensin-converting enzyme, somaticIPI00437751 isoform precursor150 kDa 48 34 67 56 28 38 41 61 33 0.0600 0.4301 0.5 0.8 ACE2 Isoform 1 of Angiotensin-converting enzyme 2 precursorIPI00465187 92 kDa 11 16 20 30 4 5 13 25 5 0.0557 0.0847 0.2 0.4 ACO1 Cytoplasmic aconitate hydratase IPI00008485 98 kDa 2 2 0 0 0 0 2 0 0 - 0.0081 - 0.0
    [Show full text]
  • Downloaded 18 July 2014 with a 1% False Discovery Rate (FDR)
    UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Chemical glycoproteomics for identification and discovery of glycoprotein alterations in human cancer Permalink https://escholarship.org/uc/item/0t47b9ws Author Spiciarich, David Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Chemical glycoproteomics for identification and discovery of glycoprotein alterations in human cancer by David Spiciarich A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemistry in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Carolyn R. Bertozzi, Co-Chair Professor David E. Wemmer, Co-Chair Professor Matthew B. Francis Professor Amy E. Herr Fall 2017 Chemical glycoproteomics for identification and discovery of glycoprotein alterations in human cancer © 2017 by David Spiciarich Abstract Chemical glycoproteomics for identification and discovery of glycoprotein alterations in human cancer by David Spiciarich Doctor of Philosophy in Chemistry University of California, Berkeley Professor Carolyn R. Bertozzi, Co-Chair Professor David E. Wemmer, Co-Chair Changes in glycosylation have long been appreciated to be part of the cancer phenotype; sialylated glycans are found at elevated levels on many types of cancer and have been implicated in disease progression. However, the specific glycoproteins that contribute to cell surface sialylation are not well characterized, specifically in bona fide human cancer. Metabolic and bioorthogonal labeling methods have previously enabled enrichment and identification of sialoglycoproteins from cultured cells and model organisms. The goal of this work was to develop technologies that can be used for detecting changes in glycoproteins in clinical models of human cancer.
    [Show full text]
  • Supplementary Material Contents
    Supplementary Material Contents Immune modulating proteins identified from exosomal samples.....................................................................2 Figure S1: Overlap between exosomal and soluble proteomes.................................................................................... 4 Bacterial strains:..............................................................................................................................................4 Figure S2: Variability between subjects of effects of exosomes on BL21-lux growth.................................................... 5 Figure S3: Early effects of exosomes on growth of BL21 E. coli .................................................................................... 5 Figure S4: Exosomal Lysis............................................................................................................................................ 6 Figure S5: Effect of pH on exosomal action.................................................................................................................. 7 Figure S6: Effect of exosomes on growth of UPEC (pH = 6.5) suspended in exosome-depleted urine supernatant ....... 8 Effective exosomal concentration....................................................................................................................8 Figure S7: Sample constitution for luminometry experiments..................................................................................... 8 Figure S8: Determining effective concentration .........................................................................................................
    [Show full text]
  • Transcriptome Profiling and Differential Gene Expression In
    G C A T T A C G G C A T genes Article Transcriptome Profiling and Differential Gene Expression in Canine Microdissected Anagen and Telogen Hair Follicles and Interfollicular Epidermis Dominique J. Wiener 1,* ,Kátia R. Groch 1 , Magdalena A.T. Brunner 2,3, Tosso Leeb 2,3 , Vidhya Jagannathan 2 and Monika M. Welle 3,4 1 Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Science, Texas A&M University, College Station, TX 77843, USA; [email protected] 2 Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; [email protected] (M.A.T.B.); [email protected] (T.L.); [email protected] (V.J.) 3 Dermfocus, Vetsuisse Faculty, University Hospital of Bern, 3010 Bern, Switzerland; [email protected] 4 Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland * Correspondence: [email protected]; Tel.: +1-979-862-1568 Received: 30 June 2020; Accepted: 3 August 2020; Published: 4 August 2020 Abstract: The transcriptome profile and differential gene expression in telogen and late anagen microdissected hair follicles and the interfollicular epidermis of healthy dogs was investigated by using RNAseq. The genes with the highest expression levels in each group were identified and genes known from studies in other species to be associated with structure and function of hair follicles and epidermis were evaluated. Transcriptome profiling revealed that late anagen follicles expressed mainly keratins and telogen follicles expressed GSN and KRT15. The interfollicular epidermis expressed predominately genes encoding for proteins associated with differentiation. All sample groups express genes encoding for proteins involved in cellular growth and signal transduction.
    [Show full text]
  • Damage of Hair Follicle Stem Cells and Alteration of Keratin Expression in External Radiation-Induced Acute Alopecia
    INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 30: 579-584, 2012 Damage of hair follicle stem cells and alteration of keratin expression in external radiation-induced acute alopecia NAOKI NANASHIMA, KOICHI ITO, TAKASHI ISHIKAWA, MANABU NAKANO and TOSHIYA NAKAMURA Department of Biomedical Sciences, Division of Medical Life Sciences, Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan Received April 4, 2012; Accepted May 28, 2012 DOI: 10.3892/ijmm.2012.1018 Abstract. Alopecia is known as a symptom of acute radia- disturbances and blood and bone marrow disorders are known tion, yet little is known concerning the mechanism of this to occur within several hours to several weeks after 1-6 Gy of phenomenon and the alteration of hair protein profiles. To radiation exposure (4,6). examine this, 6-week-old male C57/BL6 mice were exposed Hair loss is also an effect of ARS, but little is known to 6 Gy of X-ray irradiation, which caused acute alopecia. about the mechanism underlying radiation-induced hair loss. Their hair and skin were collected, and hair proteins were In humans, hair loss is caused by radiation of more than analyzed with liquid chromatography/electrospray-ionization 3 Gy, and almost complete hair loss occurs within weeks of mass spectrometry and immunohistochemistry. No change exposure to 6 Gy (4,6). Since blood stem cells are sensitive to was observed in the composition of major hair keratins, such radiation (7), hair loss is thought to be caused by irradiation- as Krt81, Krt83 and Krt86. However, cytokeratin Krt15 and induced stem cell damage, yet no studies have investigated CD34, which are known as hair follicle stem cell markers, this hypothesis.
    [Show full text]
  • Electronic Supplementary Material (ESI) for Chemcomm. This Journal Is © the Royal Society of Chemistry 2015
    Electronic Supplementary Material (ESI) for ChemComm. This journal is © The Royal Society of Chemistry 2015 tel26 Nuclear proteins identification ‐ Summary Accession Score Mass Matches tel26 Exp 1 Matches tel26 Exp 2 Protein(s) name* scr26 Exp1** scr26 Exp2** XRCC5_HUMAN 450 83222 39 49 X‐ray repair cross‐complementing protein 5 OS=Homo sapiens GN=XRCC5 PE=1 SV=3 yes yes XRCC6_HUMAN 444 70084 35 53 X‐ray repair cross‐complementing protein 6 OS=Homo sapiens GN=XRCC6 PE=1 SV=2 no no HMGB1_HUMAN 88 25049 9 25 High mobility group protein B1 OS=Homo sapiens GN=HMGB1 PE=1 SV=3 no no HMGB2_HUMAN 69 24190 4 17 High mobility group protein B2 OS=Homo sapiens GN=HMGB2 PE=1 SV=2 yes yes FUBP2_HUMAN 126 73355 9 9 Far upstream element‐binding protein 2 OS=Homo sapiens GN=KHSRP PE=1 SV=4 no no RFA1_HUMAN 67 68723 7 10 Replication protein A 70 kDa DNA‐binding subunit OS=Homo sapiens GN=RPA1 PE=1 SV=2 no no PPIA_HUMAN 95 18229 11 3 Peptidyl‐prolyl cis‐trans isomerase A OS=Homo sapiens GN=PPIA PE=1 SV=2 yes yes LMNB1_HUMAN 64 66653 6 8 Lamin‐B1 OS=Homo sapiens GN=LMNB1 PE=1 SV=2 no no ROAA_HUMAN 52 36316 3 10 Heterogeneous nuclear ribonucleoprotein A/B OS=Homo sapiens GN=HNRNPAB PE=1 SV=2 no no EHD4_HUMAN 70 61365 6 7 EH domain‐containing protein 4 OS=Homo sapiens GN=EHD4 PE=1 SV=1 no no FUBP1_HUMAN 49 67690 5 8 Far upstream element‐binding protein 1 OS=Homo sapiens GN=FUBP1 PE=1 SV=3 no yes MCM7_HUMAN 53 81884 5 7 DNA replication licensing factor MCM7 OS=Homo sapiens GN=MCM7 PE=1 SV=4 no no SEPT9_HUMAN 41 65646 3 9 Septin‐9 OS=Homo sapiens GN=SEPT9 PE=1
    [Show full text]
  • Types I and II Keratin Intermediate Filaments
    Downloaded from http://cshperspectives.cshlp.org/ on October 10, 2021 - Published by Cold Spring Harbor Laboratory Press Types I and II Keratin Intermediate Filaments Justin T. Jacob,1 Pierre A. Coulombe,1,2 Raymond Kwan,3 and M. Bishr Omary3,4 1Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205 2Departments of Biological Chemistry, Dermatology, and Oncology, School of Medicine, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland 21205 3Departments of Molecular & Integrative Physiologyand Medicine, Universityof Michigan, Ann Arbor, Michigan 48109 4VA Ann Arbor Health Care System, Ann Arbor, Michigan 48105 Correspondence: [email protected] SUMMARY Keratins—types I and II—are the intermediate-filament-forming proteins expressed in epithe- lial cells. They are encoded by 54 evolutionarily conserved genes (28 type I, 26 type II) and regulated in a pairwise and tissue type–, differentiation-, and context-dependent manner. Here, we review how keratins serve multiple homeostatic and stress-triggered mechanical and nonmechanical functions, including maintenance of cellular integrity, regulation of cell growth and migration, and protection from apoptosis. These functions are tightly regulated by posttranslational modifications and keratin-associated proteins. Genetically determined alterations in keratin-coding sequences underlie highly penetrant and rare disorders whose pathophysiology reflects cell fragility or altered
    [Show full text]
  • Keratin-Mediated Hair Growth
    Keratin is not only a Structural Protein in Hair: Keratin-mediated Hair Growth Seong Yeong An Kyung Hee University Eun Ji Choi Konkuk University So Yeon Kim Kyung Hee University Se Young Van Kyung Hee University Han Jun Kim Konkuk University Jae-Hyung Lee Kyung Hee University https://orcid.org/0000-0002-5085-6988 Song Wook Han KeraMedix Inc Il Keun Kwon Kyung Hee University Chul-Kyu Lee Chemon Inc. Sun Hee Do Konkuk University Yu-Shik Hwang ( [email protected] ) Kyung Hee University Article Keywords: Keratin , hair, intradermal injection, outer root sheath cells, Posted Date: November 18th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-101358/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/27 Abstract Keratin is known to be a major protein in hair, but the biological function of keratin in hair growth is unknown, which led us to conduct a pilot study to elucidate biological function of keratin in hair growth via cellular interactions with hair forming cells. Here, we show hair growth is stimulated by intradermal injection of keratin into mice, and show that outer root sheath cells undergo transforming growth factor- β2-induced apoptosis, resulting in keratin exposure. Keratin exposure appears to be critical for dermal papilla cell condensation and hair germ formation as immunodepletion and silencing keratin prevent dermal papilla cell condensation and hair germ formation. Furthermore, silencing keratin in mice resulted in a marked suppression of anagen follicle formation and hair growth. Our study imply a new nding of how to initiate hair regeneration and suggests the potent application of keratin biomaterial for the treatment of hair loss.
    [Show full text]
  • Transforming Growth Factor ß1-Mediated Functional Inhibition Of
    Myelodysplastic Syndromes SUPPLEMENTARY APPENDIX Transforming growth factor 1- mediated functional inhibition of mesenchymal stromal celβls in myelodysplastic syndromes and acute myeloid leukemia Stefanie Geyh, 1* Manuel Rodríguez-Paredes, 1,2 * Paul Jäger, 1 Annemarie Koch, 1 Felix Bormann, 2 Julian Gutekunst, 2 Christoph Zilkens, 3 Ulrich Germing, 1 Guido Kobbe, 1 Frank Lyko, 2 Rainer Haas 1 and Thomas Schroeder 1 1Department of Hematology, Oncology and Clinical Immunology, University of Duesseldorf, Medical Faculty; 2Division of Epigenetics, DKFZ- ZMBH Alliance, German Cancer Research Center, Heidelberg and 3Department of Orthopedic Surgery, University of Duesseldorf, Medical Faculty, Germany *SG and MR-P contributed equally to this work. ©2018 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2017.186734 Received: December 19, 2017. Accepted: May 14, 2018. Pre-published: May 17, 2018. Correspondence: [email protected] Figure S1 Downregulated genes Downregulated genes Upregulated Figure S1. Heatmaps showing the 50 most upregulated and downregulated genes between the 3 healthy MSC controls and the 9 RCMD-, RAEB- and AML-derived MSC samples. Color scale depicts the rlog-transformed FPKM values for each gene and every sample. Figure S2 Downregulated genes Downregulated genes Upregulated Figure S2. Heatmaps showing the 50 most upregulated and downregulated genes between the 3 healthy MSC controls and the 3 RCMD, RAEB and AML MSC samples, respectively. Color scales depict the rlog-transformed FPKM values for each gene and every sample. Figure S3 A. B. 0.0015 *** ** <-3 -2 0.0010 RCMD RAEB AML -1 0 1 0.0005 Log2FC LTF 2 CCL26/GAPDH INHBB >3 0.0000 TGFB2 y S h D ML M A ealt ll LTF H a EGF 0.003 *** ** INHBB TGFB2 0.002 INHBB IGFBP7 0.001 GDF11 LIF/GAPDH BMP1 0.000 y L th M TNFSF12 l A FGF13 ea ll MDS H a FGF13 0.0015 * TNFSF10 TNFSF10 0.0010 0.0005 SPP1/GAPDH 0.0000 y th l AML ea H all MDS Figure S3.
    [Show full text]