The role of micropeptides in biology.

Dewitte M (2018) Computational protein discovery: can novel insights in the human transcriptome help us understand our genome? (eds) Ghent University. https://lib.ugent.be/fulltxt/RUG01/002/508/664/RUG01-002508664_2018_0001_AC.pdf

Kornienko AE, Dotter CP, Guenzl PM, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler FM, Barlow DP (2016) Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biol 17(1):14

pubmed: 26821746 pmcid: 4731934

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789. https://doi.org/10.1101/gr.132159.111

doi: 10.1101/gr.132159.111 pubmed: 22955988 pmcid: 3431493

Yin X, Hu J, Xu H (2018) Distribution of micropeptide-coding sORFs in transcripts. Chin Chem Lett 29(7):1029–1032

Chekulaeva M, Rajewsky N (2019) Roles of long noncoding RNAs and circular RNAs in translation. Cold Spring Harbor Perspect Biol 11(6):a032680

Waldron D (2015) Genomics: identification of sORFs. Nat Rev Genet 16(11):626

Olexiouk V, Crappé J, Verbruggen S, Verhegen K, Martens L, Menschaert G (2015) sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res 44(D1):D324–D329

pubmed: 26527729 pmcid: 4702841

Makarewich CA, Olson EN (2017) Mining for micropeptides. Trends Cell Biol 27(9):685–696

pubmed: 28528987 pmcid: 5565689

Sousa ME, Farkas MH (2018) Micropeptide. PLoS Genet 14(12):e1007764

pubmed: 30543625 pmcid: 6292567

Plaza S, Menschaert G, Payre F (2017) In search of lost small peptides. Annu Rev Cell Dev Biol 33:391–416

pubmed: 28759257

Drwiega J, Wang K, Shen T, Chaffin C, Youngblood P, Hardy R (2016) The significance of protein concentration on UPEP and UIFE analysis.: [51]. Ann Clin Lab Sci 46(3):331–332

Dumesic PA, Egan DF, Gut P, Tran MT, Parisi A, Chatterjee N, Jedrychowski M, Paschini M, Kazak L, Wilensky SE (2019) An evolutionarily conserved uORF regulates PGC1α and oxidative metabolism in mice, flies, and bluefin tsuna. Cell Metab 30:190–200

pubmed: 31105043 pmcid: 6620024

Mortz M, Dégletagne C, Romestaing C, Duchamp C (2020) Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA. Genomics 112(2):1120–1127

pubmed: 31247329

Anderson DM, Anderson KM, Chang C-L, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R (2015) A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160(4):595–606

pubmed: 25640239 pmcid: 4356254

Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang T, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A (2019) Regulation of the ER stress response by a mitochondrial microprotein. Nat Commun 10(1):4883. https://doi.org/10.1038/s41467-019-12816-z

doi: 10.1038/s41467-019-12816-z pubmed: 31653868 pmcid: 6814811

Cai B, Li Z, Ma M, Wang Z, Han P, Abdalla BA, Nie Q, Zhang X (2017) LncRNA-Six1 encodes a micropeptide to activate Six1 in Cis and is involved in cell proliferation and muscle growth. Front Physiol 8:230

pubmed: 28473774 pmcid: 5397475

Anderson DM, Makarewich CA, Anderson KM, Shelton JM, Bezprozvannaya S, Bassel-Duby R, Olson EN (2016) Widespread control of calcium signaling by a family of SERCA-inhibiting micropeptides. Sci Signal 9(457):ra119

pubmed: 27923914 pmcid: 5696797

Singh DR, Cho E, Dalton M, Pribadi M, Makarewich CA, Olson EN, Robia SL (2019) Oligomerization of micropeptides that regulate SERCA. Biophys J 116(3):30a–31a

Morozov SY, Ryazantsev DY, Tatiana NE (2019) Bioinformatics analysis of the novel conserved micropeptides encoded by the plants of family Brassicaceae. J Bioinform and Syst Biol 2:066–077

Olexiouk V, Menschaert G (2016) Identification of small novel coding sequences, a proteogenomics endeavor. In: Végvári Á. (eds) Proteogenomics. Advances in experimental medicine and biology, vol 926. Springer, Cham

Li Y, Chen X, Sun H, Wang H (2018) Long non-coding RNAs in the regulation of skeletal myogenesis and muscle diseases. Cancer Lett 417:58–64

pubmed: 29253523

Vogan K (2015) Micropeptide regulates muscle performance. Nat Genet 47(3):198

Clark N (2018) Small but important. Lab Anim 47(8):207–207

Makarewich CA, Munir AZ, Schiattarella GG, Bezprozvannaya S, Raguimova ON, Cho EE, Vidal AH, Robia SL, Bassel-Duby R, Olson EN (2018) The DWORF micropeptide enhances contractility and prevents heart failure in a mouse model of dilated cardiomyopathy. Elife 7:e38319

pubmed: 30299255 pmcid: 6202051

Lin Y-F, Xiao M-H, Chen H-X, Meng Y, Zhao N, Yang L, Tang H, Wang J-L, Liu X, Zhu Y (2019) A novel mitochondrial micropeptide MPM enhances mitochondrial respiratory activity and promotes myogenic differentiation. Cell Death Dis 10(7):1–11

Zhu M, Gribskov M (2019) MiPepid: MicroPeptide identification tool using machine learning. BMC Bioinform 20(1):559

Bi P, McAnally JR, Shelton JM, Sánchez-Ortiz E, Bassel-Duby R, Olson EN (2018) Fusogenic micropeptide Myomixer is essential for satellite cell fusion and muscle regeneration. Proc Natl Acad Sci 115(15):3864–3869

pubmed: 29581287

Niu L, Lou F, Sun Y, Sun L, Cai X, Liu Z, Zhou H, Wang H, Wang Z, Bai J, Yin Q, Zhang J, Chen L, Peng D, Xu Z, Gao Y, Tang S, Fan L, Wang H (2020) A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation. Sci Adv 6(21):eaaz2059. https://doi.org/10.1126/sciadv.aaz2059

doi: 10.1126/sciadv.aaz2059 pubmed: 32671205 pmcid: 7314557

Wu S, Zhang L, Deng J, Guo B, Li F, Wang Y, Wu R, Zhang S, Lu J, Zhou Y (2020) A novel micropeptide encoded by Y-linked LINC00278 links cigarette smoking and AR signaling in male esophageal squamous cell carcinoma. Cancer Res. https://doi.org/10.1158/0008-5472.can-19-3440

doi: 10.1158/0008-5472.can-19-3440 pubmed: 33323378 pmcid: 7899076

Li M, Li X, Zhang Y, Wu H, Zhou H, Ding X, Zhang X, Jin X, Wang Y, Yin X, Li C, Yang P, Xu H (2020) Micropeptide MIAC inhibits HNSCC progression by interacting with aquaporin 2. J Am Chem Soc 142(14):6708–6716. https://doi.org/10.1021/jacs.0c00706

doi: 10.1021/jacs.0c00706 pubmed: 32176498

Guo B, Wu S, Zhu X, Zhang L, Deng J, Li F, Wang Y, Zhang S, Wu R, Lu J, Zhou Y (2020) Micropeptide CIP2A-BP encoded by LINC00665 inhibits triple-negative breast cancer progression. EMBO J 39(1):e102190. https://doi.org/10.15252/embj.2019102190

doi: 10.15252/embj.2019102190 pubmed: 31755573

Bhatta A, Atianand M, Jiang Z, Crabtree J, Blin J, Fitzgerald KA (2020) A mitochondrial micropeptide is required for activation of the Nlrp3 inflammasome. J Immunol 204(2):428–437. https://doi.org/10.4049/jimmunol.1900791

doi: 10.4049/jimmunol.1900791 pubmed: 31836654

Ingolia NT, Hussmann JA, Weissman JS (2019) Ribosome profiling: global views of translation. Cold Spring Harbor Perspect Biol 11(5):a032698

Ingolia NT (2016) Ribosome footprint profiling of translation throughout the genome. Cell 165(1):22–33

pubmed: 27015305 pmcid: 4917602

McDermott B, McDonagh B, Clegg P, Tew S (2016) Ribosome profiling: Providing a snapshot of active protein translation by chondrocytic cells in response to interleukin-1β stimulation. Osteoarthritis Cartil 24:S42

Szavits-Nossan J, Ciandrini L (2019) Accurate measures of translation efficiency and traffic using ribosome profiling. BioRxiv 719302. https://doi.org/10.1101/719302

Chen BJ, Byrne FL, Takenaka K, Modesitt SC, Olzomer EM, Mills JD, Farrell R, Hoehn KL, Janitz M (2017) Transcriptome landscape of long intergenic non-coding RNAs in endometrial cancer. Gynecol Oncol 147(3):654–662

pubmed: 29050779

Smith JE, Alvarez-Dominguez JR, Kline N, Huynh NJ, Geisler S, Hu W, Coller J, Baker KE (2014) Translation of small open reading frames within unannotated RNA transcripts in Saccharomycescerevisiae. Cell Rep 7(6):1858–1866

pubmed: 24931603 pmcid: 4105149

Wyss L, Waser M, Gebetsberger J, Zywicki M, Polacek N (2018) mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii. Sci Rep 8(1):12502

pubmed: 30131517 pmcid: 6104027

Dominguez E, Zarnowski R, Sanchez H, Covelli A, Westler W, Azadi P, Nett J, Mitchell A, Andes D (2018) Conservation and divergence in the Candida species biofilm matrix mannan-glucan complex structure, function, and genetic control. mBio 9:e00451-18

pubmed: 29615504 pmcid: 5885036

Chew G-L, Pauli A, Schier AF (2016) Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 7:11663

pubmed: 27216465 pmcid: 4890304

Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC (2014) Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33(9):981–993

pubmed: 24705786 pmcid: 4193932

Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NG, Jansen H, Kanoni S, Nelson CP, Ferrario PG, König IR (2017) Systematic evaluation of pleiotropy identifies 6 further loci associated with coronary artery disease. J Am Coll Cardiol 69(7):823–836

pubmed: 28209224 pmcid: 5314135

Yang M, Lin X, Liu X, Zhang J, Ge F (2018) Genome annotation of a model diatom Phaeodactylumtricornutum using an integrated proteogenomic pipeline. Mol Plant 11(10):1292–1307

pubmed: 30176371

Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES (2013) Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell 154(1):240–251

pubmed: 23810193 pmcid: 3756563

Aspden JL, Eyre-Walker YC, Phillips RJ, Amin U, Mumtaz MAS, Brocard M, Couso J-P (2014) Extensive translation of small open reading frames revealed by Poly-Ribo-Seq. Elife 3:e03528

pubmed: 25144939 pmcid: 4359375

Pueyo JI, Magny EG, Couso JP (2016) New peptides under the s (ORF) ace of the genome. Trends Biochem Sci 41(8):665–678

pubmed: 27261332

Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G (2019) PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms. Mol Cell Proteom 18:S126–S140

Hasbrouck J, Tindal G (2017) An update to compiled ORF norms. Technical Report No. 1702. Online Submission

Olexiouk V, Menschaert G (2019) Using the sORFs. Org database. Org Database Curr Protoc Bioinform 65(1):e68

Wang H, Yang L, Wang Y, Chen L, Li H, Xie Z (2018) RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling. Nucleic Acids Res 47(D1):D230–D234

pmcid: 6324049

Yin X, Jing Y, Xu H (2019) Mining for missed sORF-encoded peptides. Expert Rev Proteom 16(3):257–266

Leney AC, Heck AJ (2017) Native mass spectrometry: what is in the name? J Am Soc Mass Spectrom 28(1):5–13

pubmed: 32020797

Guillarme D, Desfontaine V, Heinisch S, Veuthey J-L (2018) What are the current solutions for interfacing supercritical fluid chromatography and mass spectrometry? J Chromatogr B 1083:160–170

Smits AH, Vermeulen M (2016) Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. Trends Biotechnol 34(10):825–834

pubmed: 26996615

Rothnagel J, Menschaert G (2018) Short open reading frames and their encoded peptides. Proteomics 18(10):1700035

Yeasmin F, Yada T, Akimitsu N (2018) Micropeptides encoded in transcripts previously identified as long noncoding RNAs: a new chapter in transcriptomics and proteomics. Front Genet 9:144

pubmed: 29922328 pmcid: 5996887

Fouzia Yeasmin NITT, Kenzui T, Takeshi K, Tetsushi Y, Nobuyoshi A Identification and analysis of short Open Reading Frames (sORFs) on LINC00493 that is initially annotated as noncoding RNAs in human cell. J Biochem. https://doi.org/10.1093/jb/mvaa143

Matsumoto A, Clohessy JG, Pandolfi PP (2017) SPAR, a lncRNA encoded mTORC1 inhibitor. Cell Cycle 16(9):815

pubmed: 28319435 pmcid: 5444354

Volders P-J, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P (2014) An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res 43(D1):D174–D180

pubmed: 25378313 pmcid: 4383901

Verbruggen S (2015) Ribosome profiling, a useful tool in the search for micropeptides. https://lib.ugent.be/catalog/rug01:002216974

Verheggen K, Volders P-J, Mestdagh P, Menschaert G, Van Damme P, Gevaert K, Martens L, Vandesompele J (2017) Noncoding after all: biases in proteomics data do not explain observed absence of lncRNA translation products. J Proteome Res 16(7):2508–2515

pubmed: 28534634

Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik Y-K, Van Eyk JE, Liu S, Snyder M, Baker MS (2018) Progress on identifying and characterizing the human proteome: 2018 metrics from the HUPO human proteome project. J Proteome Res 17(12):4031–4041

pubmed: 30099871 pmcid: 6387656

Barbieri R, Guryev V, Brandsma CA, Suits F, Bischoff R, Horvatovich P (2016) Proteogenomics: ey driver for clinical discovery and personalized medicine. Adv Exp Med Bio 926:21–47

Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J (2016) Clinical implications of recent advances in proteogenomics. Expert Re Proteom 13(2):185–199

Huang T, Bamigbade AT, Xu S, Deng Y, Xie K, Ogunsade OO, Mirza AH, Wang J, Liu P, Zhang S (2020) Identification of a micropeptide on lipid droplet that mediates lipid storage and insulin sensitivity. bioRxiv. https://doi.org/10.1101/2020.04.10.036160

doi: 10.1101/2020.04.10.036160 pubmed: 33398272 pmcid: 7781300

Greninger AL, Knudsen GM, Roychoudhury P, Hanson DJ, Sedlak RH, Xie H, Guan J, Nguyen T, Peddu V, Boeckh M (2018) Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6. BMC Genom 19(1):204

Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J (2017) Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci 114(46):E10018–E10027

pubmed: 29087317

Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C (2017) An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res 27(12):2083–2095

pubmed: 29141959 pmcid: 5741054

Low TY, Mohtar MA, Ang MY, Jamal R (2019) Connecting proteomics to next-generation sequencing: proteogenomics and its current applications in biology. Proteomics 19(10):1800235

Hollerer I, Higdon A, Brar GA (2018) Strategies and challenges in identifying function for thousands of sORF-encoded peptides in meiosis. Proteomics 18(10):1700274

Budnik BA, Kellis M, Saghatelian A (2015) Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res 13(3):1757–1765

Miravet-Verde S, Ferrar T, Espadas-García G, Mazzolini R, Gharrab A, Sabido E, Serrano L, Lluch-Senar M (2019) Unraveling the hidden universe of small proteins in bacterial genomes. Mol Syst Biol 15(2):e8290

pubmed: 30796087 pmcid: 6385055

Kirk IK, Weinhold N, Brunak S, Belling K (2017) The impact of the protein interactome on the syntenic structure of mammalian genomes. PLoS ONE 12(9):e0179112

pubmed: 28910296 pmcid: 5598925

Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M (2015) Extensive identification and analysis of conserved small ORFs in animals. Genome Biol 16(1):179

pubmed: 26364619 pmcid: 4568590

Budamgunta H, Olexiouk V, Luyten W, Schildermans K, Maes E, Boonen K, Menschaert G, Baggerman G (2018) Comprehensive peptide analysis of mouse brain striatum identifies novel sORF-encoded polypeptides. Proteomics 18(10):1700218

Cabrera-Quio LE, Herberg S, Pauli A (2016) Decoding sORF translation–from small proteins to gene regulation. RNA Biol 13(11):1051–1059

pubmed: 27653973 pmcid: 5100344

Chu Q, Ma J, Saghatelian A (2015) Identification and characterization of sORF-encoded polypeptides. Crit Rev Biochem Mol Biol 50(2):134–141

pubmed: 25857697 pmcid: 4761265

Hazarika RR, De Coninck B, Yamamoto LR, Martin LR, Cammue BP, van Noort V (2017) ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsisthaliana. BMC Bioinform 18(1):37

Hazarika RR, De Coninck B, Yamamoto LR, Martin LR, Cammue BP, van Noort V (2017) ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. BMC Bioinform 18(1):37

Surendrarao A (2016) Identifying and understanding processes driving genomic drift of f-box gene families during plant evolution. University of California, Davis

D’Lima NG, Ma J, Winkler L, Chu Q, Loh KH, Corpuz EO, Budnik BA, Lykke-Andersen J, Saghatelian A, Slavoff SA (2017) A human microprotein that interacts with the mRNA decapping complex. Nat Chem Biol 13(2):174

pubmed: 27918561

Li L-J, Leng R-X, Fan Y-G, Pan H-F, Ye D-Q (2017) Translation of noncoding RNAs: focus on lncRNAs, pri-miRNAs, and circRNAs. Exp Cell Res 361(1):1–8

pubmed: 29031633

Vervliet T, Robinson EL, Roderick HL (2018) Lnc’ing Ca

pubmed: 29793762

Rion N, Rüegg MA (2017) LncRNA-encoded peptides: more than translational noise? Cell Res 27(5):604

pubmed: 28290465 pmcid: 5520851

Pauli A, Valen E, Schier AF (2015) Identifying (non-) coding RNAs and small peptides: challenges and opportunities. BioEssays 37(1):103–112

pubmed: 25345765

Pauli A, Norris ML, Valen E, Chew G-L, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D (2014) Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343(6172):1248636

pubmed: 24407481 pmcid: 4107353

Konina DO, Filatova AY, Skoblov MY (2019) LINC01420 RNA structure and influence on cell physiology. BMC Genom 20(3):298

Robicheau BM, Susko E, Harrigan AM, Snyder M (2017) Ribosomal RNA genes contribute to the formation of pseudogenes and junk DNA in the human genome. Genome Biol Evol 9(2):380–397

pubmed: 28204512 pmcid: 5381670

Saghatelian A, Couso JP (2015) Discovery and characterization of smORF-encoded bioactive polypeptides. Nat Chem Biol 11(12):909

pubmed: 26575237 pmcid: 4956473

Kaul R, Purushothaman P, Uppal T, Verma SC (2019) KSHV lytic proteins K-RTA and K8 bind to cellular and viral chromatin to modulate gene expression. PLoS ONE 14(4):e0215394

pubmed: 30998737 pmcid: 6472759

Tang S, Lomsadze A, Borodovsky M (2015) Identification of protein coding regions in RNA transcripts. Nucleic Acids Res 43(12):e78–e78

pubmed: 25870408 pmcid: 4499116

Pian C, Zhang G, Chen Z, Chen Y, Zhang J, Yang T, Zhang L (2016) LncRNApred: Classification of long non-coding RNAs and protein-coding transcripts by the ensemble algorithm with a new hybrid feature. PLoS Onse 11(5):e0154567

Combier J-P, Laures-sergues D, Becard G (2017) Use of micropeptides for promoting plant growth (ed). Google Patents

Combier J-P, Laures-sergues D, Becard G (2017) Use of micropeptides in order to stimulate mycorrhizal symbiosis (eds). Google Patents

Wen K, Yang L, Xiong T, Di C, Ma D, Wu M, Xue Z, Zhang X, Long L, Zhang W (2016) Critical roles of long noncoding RNAs in Drosophilaspermatogenesis. Genome Res 26(9):1233–1244

pubmed: 27516619 pmcid: 5052038

Zhu M, Hu X, Cao G, Xue R, Gong C (2018) Functions and impact of tal-like genes in animals with regard to applied aspects. Appl Microbiol Biotechnol 102(16):6841–6845

pubmed: 29909570

Li K, Tian Y, Yuan Y, Fan X, Yang M, He Z, Yang D (2019) Insights into the functions of LncRNAs in Drosophila. Int J Mol Sci 20(18):4646

pmcid: 6770079

Tharakan R, Kreimer S, Ubaida-Mohien C, Lavoie J, Olexiouk V, Menschaert G, Ingolia NT, Cole RN, Ishizuka K, Sawa A, Nucifora LG (2020) A methodology for discovering novel brain-relevant peptides: combination of ribosome profiling and peptidomics. Neurosci Res 151:31–37. https://doi.org/10.1016/j.neures.2019.02.006

doi: 10.1016/j.neures.2019.02.006 pubmed: 30862443

Kang S, Dahl R, Hsieh W, Shin A, Zsebo KM, Buettner C, Hajjar RJ, Lebeche D (2016) Small molecular allosteric activator of the sarco/endoplasmic reticulum Ca

pubmed: 26702054

Singh DR, Dalton MP, Cho EE, Pribadi MP, Zak TJ, Šeflová J, Makarewich CA, Olson EN, Robia SL (2019) Newly discovered micropeptide regulators of SERCA form oligomers but bind to the pump as monomers. J Mol Biol 431:4429–4443

pubmed: 31449798 pmcid: 6885550

Nelson BR, Makarewich CA, Reese AL, Winders BR, Anderson DM, McAnally JR, Kavalali ET, Bassel-Duby R, Olson EN (2015) DWORF: discovery and characterization of a cardiac micropeptide encoded in a putative long noncoding RNA. Circ Res 117(supp_1):A189–A189

Bi P, Ramirez-Martinez A, Li H, Cannavino J, McAnally JR, Shelton JM, Sánchez-Ortiz E, Bassel-Duby R, Olson EN (2017) Control of muscle formation by the fusogenic micropeptide myomixer. Science 356(6335):323–327

pubmed: 28386024 pmcid: 5502127

Slavoff SA, Heo J, Budnik BA, Hanakahi LA, Saghatelian A (2014) A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J Biol Chem 289(16):10950–10957

pubmed: 24610814 pmcid: 4036235

D’Alessandro G, di Fagagna FdA (2018) Long non-coding RNA in the control of genome stability and cancer phenotypes. Non-coding RNA Investig 2(3). https://doi.org/10.21037/ncri.2018.03.01

Hung PJ, Johnson B, Chen B-R, Byrum AK, Bredemeyer AL, Yewdell WT, Johnson TE, Lee BJ, Deivasigamani S, Hindi I (2018) MRI is a DNA damage response adaptor during classical non-homologous end joining. Mol Cell 71(2):332-342.e338

pubmed: 30017584 pmcid: 6083883

Xu Z-M, Huang F, Huang W-Q (2018) Angiogenic lncRNAs: a potential therapeutic target for ischaemic heart disease. Life Sci 211:157–171

pubmed: 30219334

Frieri M, Kumar K, Boutin A (2017) Antibiotic resistance. J Infect Public Health 10(4):369–378

pubmed: 27616769

Friedman ND, Temkin E, Carmeli Y (2016) The negative impact of antibiotic resistance. Clin Microbiol Infect 22(5):416–422

pubmed: 26706614

Wang J, Chou S, Yang Z, Yang Y, Wang Z, Song J, Dou X, Shan A (2018) Combating drug-resistant fungi with novel imperfectly amphipathic palindromic peptides. J Med Chem 61(9):3889–3907

pubmed: 29648811

Trepos R, Cervin G, Pile C, Pavia H, Hellio C, Svenson J (2015) Evaluation of cationic micropeptides derived from the innate immune system as inhibitors of marine biofouling. Biofouling 31(4):393–403

pubmed: 26057499

Starr CG, He J, Wimley WC (2016) Host cell interactions are a significant barrier to the clinical utility of peptide antibiotics. ACS Chem Biol 11(12):3391–3399

pubmed: 27797468 pmcid: 5521815

Sánchez-Gómez S, Ferrer-Espada R, Stewart PS, Pitts B, Lohner K, de Tejada GM (2015) Antimicrobial activity of synthetic cationic peptides and lipopeptides derived from human lactoferricin against Pseudomonasaeruginosa planktonic cultures and biofilms. BMC Microbiol 15(1):137

pubmed: 26149536 pmcid: 4491869

Tabish Rehman M, U Khan A (2015) Understanding the interaction between human serum albumin and anti-bacterial/anti-cancer compounds. Curr Pharm Des 21(14):1785–1799

Svendsen JSM, Grant TM, Rennison D, Brimble MA, Svenson J (2019) Very short and stable lactoferricin-derived antimicrobial peptides: design principles and potential uses. Acc Chem Res 52(3):749–759

pubmed: 30829472

Le L, Bokare A, Erogbogbo F (2018) Hand powered, cost effective, 3D printed nanoparticle synthesizer: effects of polymer end caps, drugs, and solvents on lipid polymer hybrid nanoparticles. Mater Res Express 6(2):025403

Lee J, Lee DG (2015) Antimicrobial peptides (AMPs) with dual mechanisms: membrane disruption and apoptosis. J Microbiol Biotechnol 25(6):759–764

pubmed: 25537721

Sim J-Y, Kim S, Lee J, Lim H, Kim HH, Park Z-Y, Kim JI (2019) A significantly enhanced antibacterial spectrum of D-enantiomeric lipopeptide bactenecin. Biochem Biophys Res Commun 514(2):497–502

pubmed: 31056261

Pang W, Lv J, Du S, Wang J, Wang J, Zeng Y (2017) Preparation of curcumin-piperazine coamorphous phase and fluorescence spectroscopic and density functional theory simulation studies on the interaction with bovine serum albumin. Mol Pharm 14(9):3013–3024

pubmed: 28703594

De Freitas GB, De Almeida DJ, Carraro E, Kerppers II, Martins GA, Mainardes RM, Khalil NM, Messias-Reason IJ (2018) Formulation, characterization, and in vitro/in vivo studies of capsaicin-loaded albumin nanoparticles. Mater Sci Eng C 93:70–79

Bolattin MB, Nandibewoor ST, Joshi SD, Dixit SR, Chimatadar SA (2016) Interaction between carisoprodol and bovine serum albumin and effect of β-cyclodextrin on binding: insights from molecular docking and spectroscopic techniques. RSC Adv 6(68):63463–63471

Tsai C-Y, Chen Y-J, Fu Y-S, Chang L-S (2015) Antibacterial and membrane-damaging activities of mannosylated bovine serum albumin. Arch Biochem Biophys 573:14–22

pubmed: 25752952

Iavarone F, Desiderio C, Vitali A, Messana I, Martelli C, Castagnola M, Cabras T (2018) Cryptides: latent peptides everywhere. Crit Rev Biochem Mol Biol 53(3):246–263

pubmed: 29564928

Li W, Cui T, Hu L, Wang Z, Li Z, He Z-G (2015) Cyclic diguanylate monophosphate directly binds to human siderocalin and inhibits its antibacterial activity. Nat Commun 6:8330

pubmed: 26390966 pmcid: 4595737

Rogoyski OM, Pueyo JI, Couso JP, Newbury SF (2017) Functions of long non-coding RNAs in human disease and their conservation in Drosophila development. Biochem Soc Trans 45(4):895–904

pubmed: 28673935

Haemmig S, Feinberg M (2018) Manipulation of long non-coding RNAs in cardiovascular disease using genome editing technology. In: Church G, Appasani K (ed) Genome editing and engineering: from TALENs, ZFNs and CRISPRs to molecular surgery. Cambridge University Press, Cambridge, pp 371–388. https://doi.org/10.1017/9781316756300.026

doi: 10.1017/9781316756300.026

Kato-Inui T, Takahashi G, Hsu S, Miyaoka Y (2018) Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair. Nucleic Acids Res 46(9):4677–4688

pubmed: 29672770 pmcid: 5961419

Goff LA, Rinn JL (2015) Linking RNA biology to lncRNAs. Genome Res 25(10):1456–1465

pubmed: 26430155 pmcid: 4579330

Olson E, Millay DP (2019) Compositions and methods relating to myomaker-induced muscle cell fusion (eds). Google Patents

Mallory AC, Shkumatava A (2015) LncRNAs in vertebrates: advances and challenges. Biochimie 117:3–14

pubmed: 25812751 pmcid: 5125525

Linse KD, Castro J What are micro peptides? https://blog-biosyn.com/2013/05/07/what-are-micro-peptides/

Ransohoff JD, Wei Y, Khavari PA (2018) The functions and unique features of long intergenic non-coding RNA. Nat Rev Mol Cell Biol 19(3):143

pubmed: 29138516

Pymm P, Illing PT, Ramarathinam SH, O’Connor GM, Hughes VA, Hitchen C, Price DA, Ho BK, McVicar DW, Brooks AG (2017) MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape. Nat Struct Mol Biol 24(4):387

pubmed: 28218747 pmcid: 7900914

Satpathy AT, Chang HY (2015) Long noncoding RNA in hematopoiesis and immunity. Immunity 42(5):792–804

pubmed: 25992856

Ray S, Rosenberg MI, Chanut-Delalande H, Decaras A, Schwertner B, Toubiana W, Auman T, Schnellhammer I, Teuscher M, Khila A (2018) Millepattes micropeptides are an ancient developmental switch required for embryonic patterning. BioRxiv 376111. https://doi.org/10.1101/376111

Zhan R, Li X, Guo W, Liu X, Liu Z, Xu K, Tang B (2019) An Aptamer-based near-infrared fluorescence nanoprobe for detecting and imaging of phospholamban micropeptide in cardiomyocytes. ACS Sens 4(3):733–739

pubmed: 30777430

Zhang J, Naik HS, Assefa T, Sarkar S, Reddy RC, Singh A, Ganapathysubramanian B, Singh AK (2017) Computer vision and machine learning for robust phenotyping in genome-wide studies. Sci Rep 7:44048

pubmed: 28272456 pmcid: 5358742

Sahu B, Pani S, Swalsingh G, Bal NC (2019) Epigenetic mechanisms in regulation of adaptive thermogenesis in skeletal muscle. Front Endocrinol 10:517

Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DY, Seydoux G, Mohr SE, Zuber J, Perrimon N (2017) Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. Nat Rev Genet 18(1):24

pubmed: 27795562

Gilmore C, Somasundaram V, Scheiblin D, Heinz W, Lockett S, Wink D (2019) Restricting diffusive exchange in vitro demonstrates inos modulates hypoxic gradients in the tumor microenvironment. Biophys J 116(3):284a

Niu Z, Zhang W, Yu C, Zhang J, Wen Y (2018) Recent advances in biological sample preparation methods coupled with chromatography, spectrometry and electrochemistry analysis techniques. TrAC Trends Anal Chem 102:123–146

Li L, Andrén PE, Sweedler JV (2018) Editorial and review: 29th ASMS sanibel conference on mass spectrometry—peptidomics: bridging the gap between proteomics and metabolomics by MS. J Am Soc Mass Spectrom 29(5):801–806

pubmed: 29623661

Fricker L (2018) Quantitative peptidomics: general considerations. Methods Mol Biol 1719:121–140. https://doi.org/10.1007/978-1-4939-7537-2_8

doi: 10.1007/978-1-4939-7537-2_8 pubmed: 29476508

Zhang H, Ji X, Li P, Liu C, Lou J, Wang Z, Wen W, Xiao Y, Zhang M, Zhu X (2020) Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci China Life Sci 63(7):953–985. https://doi.org/10.1007/s11427-020-1702-x

doi: 10.1007/s11427-020-1702-x pubmed: 32548680

Alberti S, Gladfelter A, Mittag T (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176(3):419–434. https://doi.org/10.1016/j.cell.2018.12.035

doi: 10.1016/j.cell.2018.12.035 pubmed: 30682370 pmcid: 6445271

Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, Baldwin AJ (2015) Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57(5):936–947. https://doi.org/10.1016/j.molcel.2015.01.013

doi: 10.1016/j.molcel.2015.01.013 pubmed: 25747659 pmcid: 4352761

Wang J, Choi J-M, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174(3):688-699.e616. https://doi.org/10.1016/j.cell.2018.06.006

doi: 10.1016/j.cell.2018.06.006 pubmed: 29961577 pmcid: 6063760

Dasgupta S, Yang C, Castro LM, Tashima AK, Ferro ES, Moir RD, Willis IM, Fricker LD (2016) Analysis of the yeast peptidome and comparison with the human peptidome. PLoS ONE 11(9):e0163312

pubmed: 27685651 pmcid: 5042401

Zelanis A, Silva DA, Kitano ES, Liberato T, Fukushima I, Serrano SM, Tashima AK (2019) A first step towards building spectral libraries as complementary tools for snake venom proteome/peptidome studies. Comp Biochem Physiol Part D Genom Proteom 31:100599

Liu T, Rodland KD, Smith RD (2018) Characterization of the ovarian tumor peptidome. Vitam Horm 107:515–531. https://doi.org/10.1016/bs.vh.2018.01.020

doi: 10.1016/bs.vh.2018.01.020 pubmed: 29544642 pmcid: 6233302

Piovesana S, Capriotti AL, Cavaliere C, La Barbera G, Samperi R, Chiozzi RZ, Laganà A (2015) Peptidome characterization and bioactivity analysis of donkey milk. J Proteom 119:21–29

Cao H, Shao F, Li M, Sweat M, Qian Q, Guo Y, Amendt B, Yang L (2019) Comprehensive identification of micropeptides encoded by long noncoding RNAs in human tissues. FASEB J 33(1_supplement):714.711-714.711

Skarshewski A, Stanton-Cook M, Huber T, Al Mansoori S, Smith R, Beatson SA, Rothnagel JA (2014) uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation. BMC Bioinform 15:36. https://doi.org/10.1186/1471-2105-15-36

doi: 10.1186/1471-2105-15-36

Lin MF, Jungreis I, Kellis M (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (Oxf Engl) 27(13):i275–i282. https://doi.org/10.1093/bioinformatics/btr209

doi: 10.1093/bioinformatics/btr209

Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH (2010) sORF finder: a program package to identify small open reading frames with high coding potential. Bioinformatics (Oxf Engl) 26(3):399–400. https://doi.org/10.1093/bioinformatics/btp688

doi: 10.1093/bioinformatics/btp688

Casimiro-Soriguer CS, Rigual MM, Brokate-Llanos AM, Muñoz MJ, Garzón A, Pérez-Pulido AJ, Jimenez J (2020) Using AnABlast for intergenic sORF prediction in the C.elegans genome. Bioinformatics (Oxf Engl). https://doi.org/10.1093/bioinformatics/btaa608

doi: 10.1093/bioinformatics/btaa608

Hu L, Xu Z, Hu B, Lu ZJ (2017) COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features. Nucleic Acids Res 45(1):e2–e2. https://doi.org/10.1093/nar/gkw798

doi: 10.1093/nar/gkw798 pubmed: 27608726

Crappé J, Van Criekinge W, Trooskens G, Hayakawa E, Luyten W, Baggerman G, Menschaert G (2013) Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genom 14(1):648. https://doi.org/10.1186/1471-2164-14-648

doi: 10.1186/1471-2164-14-648

Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4):789–802. https://doi.org/10.1016/j.cell.2011.10.002

doi: 10.1016/j.cell.2011.10.002 pubmed: 22056041 pmcid: 3225288

Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15(3):205–213. https://doi.org/10.1038/nrg3645

doi: 10.1038/nrg3645 pubmed: 24468696

Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS (2015) A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation. Mol Cell 60(5):816–827. https://doi.org/10.1016/j.molcel.2015.11.013

doi: 10.1016/j.molcel.2015.11.013 pubmed: 26638175 pmcid: 4720255

Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U (2016) Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 13(2):165–170. https://doi.org/10.1038/nmeth.3688

doi: 10.1038/nmeth.3688 pubmed: 26657557

The role of micropeptides in biology.

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Rui Vitorino (R)

Sofia Guedes (S)

Francisco Amado (F)

Manuel Santos (M)

Nobuyoshi Akimitsu (N)

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